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Structural and functional bacterial biodiversity in a copper, zinc and nickel amended bioreactor:  shotgun metagenomic study

At lower concentrations copper (Cu), zinc (Zn) and nickel (Ni) are trace metals essential for some bacterial enzymes. At higher concentrations they might alter and inhibit microbial functioning in a bioreactor...

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Downregulation of Klebsiella pneumoniae RND efflux pump genes following indole signal produced by Escherichia coli

More than a century has passed since it was discovered that many bacteria produce indole, but research into the actual biological roles of this molecule is just now beginning. The influence of indole on bacter...

Alterations in the gut microbiota community are associated with childhood obesity and precocious puberty

To explore the distribution and differences in the intestinal microbiota in girls with obesity-related precocious puberty and the relationship between intestinal microbiota and obesity-related precocious puberty.

In vitro characterization of probiotic potential of Lactobacillus plantarum CM49 against selected cattle mastitogens

Bovine mastitis results in significant economic losses for the dairy industry globally due to milk production losses and decreased herd efficiency. This research aimed to isolate, select, and characterize indi...

Retrospective analysis of molecular characteristics, risk factors, and outcomes in carbapenem-resistant Klebsiella pneumoniae bloodstream infections

Klebsiella pneumoniae (KP) is the second most prevalent Gram-negative bacterium causing bloodstream infections (BSIs). In recent years, the management of BSIs caused by KP has become increasingly complex due to t...

Solid waste dumpsite leachate and contiguous surface water contain multidrug-resistant ESBL-producing Escherichia coli carrying Extended Spectrum β-Lactamase (ESBL) genes

Dumpsites generate leachates containing bacteria that may carry antibiotic resistance genes, such as extended spectrum β-lactamase (ESBL). However, the contribution of dumpsite leachates in the environmental s...

Vaginal colonization with virulent and methicillin resistant Staphylococcus aureus among Ugandan women in Labour

Staphylococcus aureus ( S. aureus ) often colonizes the human skin, upper respiratory and genital tracts. In the female genital tract, it can be passed on to the newborn during vaginal delivery leading to either or...

Diametral influence of deoxynivalenol (DON) and deepoxy-deoxynivalenol (DOM-1) on the growth of Campylobacter jejuni with consequences on the bacterial transcriptome

Deoxynivalenol (DON) is a type B trichothecene mycotoxin that is commonly found in cereals and grains worldwide. The presence of this fungal secondary-metabolite raises public-health concerns at both the agric...

Linking watershed formation with the phylogenetic distribution of a soil microscopic fungus in Yunnan Province, China

Phylogeographic studies have gained prominence in linking past geological events to the distribution patterns of biodiversity, primarily in mountainous regions. However, such studies often focus on plant taxa,...

Role of ectomycorrhizal colonization in enhancement of nutrients for survival of plants collected from mountainous cold stress areas

Ectomycorrhizal (ECM and ECM-like) structures associated with plant root systems are a challenge for scientists. The dispersion pattern of roots within the soil profile and the nutritional conditions are both ...

Antibiotic-resistant bacteria contaminating leafy vegetables in Saudi Arabia’s eastern region

Food-associated antibiotic-resistant bacteria can cause infections that may critically impact human health. The objectives of this study were to determine the microbial contamination level of green leafy veget...

Effective microorganism combinations improve the quality of compost-bedded pack products in heifer barns: exploring pack bacteria-fungi interaction mechanisms

Compost-bedded pack barns (CBP) are getting huge attention as an alternative housing system for dairy cows due to their beneficial impact on animal welfare. Effective microorganisms (EM) inoculums are believed...

Dynamic changes in and correlations between microbial communities and physicochemical properties during the composting of cattle manure with Penicillium oxalicum

Penicillium oxalicum is an important fungal agent in the composting of cattle manure, but the changes that occur in the microbial community, physicochemical factors, and potential functions of microorganisms at d...

Variations of soil metal content, soil enzyme activity and soil bacterial community in Rhododendron delavayi natural shrub forest at different elevations

Rhododendron delavayi is a natural shrub that is distributed at different elevations in the karst region of Bijie, China, and that has an important role in preventing land degradation in this region. In this stud...

The Velvet transcription factor PnVeA regulates necrotrophic effectors and secondary metabolism in the wheat pathogen Parastagonospora nodorum

The fungus Parastagonospora nodorum causes septoria nodorum blotch on wheat. The role of the fungal Velvet-family transcription factor VeA in P. nodorum development and virulence was investigated here. Deletion o...

Integrating multi-wet laboratory diagnostics to study staphylococci in animals in Uganda

Several diagnostic environments in Uganda lack real-time, robust and high-throughput technologies for comprehensive typing of microbes, which is a setback to infectious disease surveillance. This study combine...

Multi-omics analysis reveals genes and metabolites involved in Streptococcus suis biofilm formation

Streptococcus suis is an important zoonotic pathogen. Biofilm formation largely explains the difficulty in preventing and controlling S. suis . However, little is known about the molecular mechanism of S. suis bio...

Microbial life in preferential flow paths in subsurface clayey till revealed by metataxonomy and metagenomics

Subsurface microorganisms contribute to important ecosystem services, yet little is known about how the composition of these communities is affected by small scale heterogeneity such as in preferential flow pa...

Potential antivirulence and antibiofilm activities of sub-MIC of oxacillin against MDR S. aureus isolates: an in-vitro and in-vivo study

Multi-drug resistant Staphylococcus aureus is one of the most common causes of nosocomial and community-acquired infections, with high morbidity and mortality. Treatment of such infections is particularly problem...

Rhizosphere microbial community construction during the latitudinal spread of the invader Chromolaena odorata

The colonization of alien plants in new habitats is typically facilitated by microorganisms present in the soil environment. However, the diversity and structure of the archaeal, bacterial, and fungal communit...

Distribution and functional perspective analysis of epiphytic and endophytic bacterial communities associated with marine seaweeds, Alexandria shores, Egypt

There is an enormous diversity of life forms present in the extremely intricate marine environment. The growth and development of seaweeds in this particular environment are controlled by the bacteria that set...

Large-scale genetic correlation studies explore the causal relationship and potential mechanism between gut microbiota and COVID-19-associated risks

Recent observational studies suggest that gut microorganisms are involved in the onset and development of coronavirus disease 2019 (COVID-19), but the potential causal relationship behind them remains unclear....

Fungal endophytes of Taxus species and regulatory effect of two strains on taxol synthesis

Taxol, derived from Taxus trees, is a valuable natural resource for the development of anticancer drugs. Endophytic fungi from Taxus trees are a promising alternative source of Taxol. However, the impact of plant...

Low-dose zinc oxide nanoparticles trigger the growth and biofilm formation of Pseudomonas aeruginosa : a hormetic response

Hormesis describes an inverse dose-response relationship, whereby a high dose of a toxic compound is inhibitory, and a low dose is stimulatory. This study explores the hormetic response of low concentrations o...

The role of gut microbiota in chronic restraint stress-induced cognitive deficits in mice

Chronic stress induces cognitive deficits. There is a well-established connection between the enteric and central nervous systems through the microbiota-gut-brain (MGB) axis. However, the effects of the gut mi...

Microbial and transcriptional response of Acropora valida and Turbinaria peltata to Vibrio coralliilyticus challenge: insights into corals disease resistance

Coral diseases are significant drivers of global coral reef degradation, with pathogens dominated by Vibrio coralliilyticus playing a prominent role in the development of coral diseases. Coral phenotype, symbioti...

Effects of berberine hydrochloride on antioxidant response and gut microflora in the Charybdis japonica infected with Aeromonas hydrophila

This study used berberine hydrochloride to treat the Asian paddle crab, Charybdis japonica infected with the Gram-negative bacterium Aeromonas hydrophila at concentrations of 0, 100, 200 and 300 mg/L. The effect ...

Strain-dependent induction of primary bile acid 7-dehydroxylation by cholic acid

Bile acids (BAs) are steroid-derived molecules with important roles in digestion, the maintenance of host metabolism, and immunomodulation. Primary BAs are synthesized by the host, while secondary BAs are prod...

Microbial carbohydrate active enzyme (CAZyme) genes and diversity from Menagesha Suba natural forest soils of Ethiopia as revealed by shotgun metagenomic sequencing

The global over-reliance on non-renewable fossil fuels has led to the emission of greenhouse gases, creating a critical global environmental challenge. There is an urgent need for alternative solutions like bi...

Identification and antimicrobial susceptibility profiles of Staphylococcus species isolated from raw cow milk, and swabs in smallholder dairy farms in Meta district, Eastern Ethiopia

The safety of milk production in terms of foodborne infections is a worldwide issue, particularly in developing countries where production is often unhygienic. A cross-sectional study was conducted from Decemb...

Effects of antibiotic cocktail on the fecal microbiota and their potential correlation of local immune response

The guts of mammals are home to trillions of microbes, forming a complex and dynamic ecosystem. Gut microbiota is an important biological barrier for maintaining immune homeostasis. Recently, the use of antibi...

Unearthing Lactococcus lactis and Scheffersomyeces symbionts from edible wood-boring beetle larvae as a bio-resource for industrial applications

Gut microbiota have several advantages in influencing the host nutrition, metabolism, immunity and growth. However, the understanding of the gut microbiota in key edible wood-boring beetle larvae remain largel...

Vaginal microbiome differences between patients with adenomyosis with different menstrual cycles and healthy controls

Adenomyosis is a commonly observed benign gynecological disease that affects the quality of life and social psychology of women of childbearing age. However, because of the unknown etiology and incidence of ad...

Investigation of cross-opsonic effect leads to the discovery of PPIase-domain containing protein vaccine candidate to prevent infections by Gram-positive ESKAPE pathogens

Enterococcus faecium and Staphylococcus aureus are the Gram-positive pathogens of the ESKAPE group, known to represent a great threat to human health due to their high virulence and multiple resistances to antibi...

The transcriptional regulator Fur modulates the expression of uge , a gene essential for the core lipopolysaccharide biosynthesis in Klebsiella pneumoniae

Klebsiella pneumoniae is a Gram-negative pathogen that has become a threat to public health worldwide due to the emergence of hypervirulent and multidrug-resistant strains. Cell-surface components, such as polysa...

Emergence of heteroresistance to carbapenems in Gram-negative clinical isolates from two Egyptian hospitals

Antimicrobial resistance is a global concern, linking bacterial genotype and phenotype. However, variability in antibiotic susceptibility within bacterial populations can lead to misclassification. Heteroresis...

Silver nanoparticle with potential antimicrobial and antibiofilm efficiency against multiple drug resistant, extensive drug resistant Pseudomonas aeruginosa clinical isolates

The study aims to investigate the effect of combining silver nanoparticles (AGNPs) with different antibiotics on multi-drug resistant (MDR) and extensively drug resistant (XDR) isolates of Pseudomonas aeruginosa ...

Potentially pathogenic culturable bacteria in hemodialysis waters

Hemodialysis patients are at risk of acquiring healthcare-related infections due to using non-sterile water to prepare hemodialysis fluid. Therefore, microbiological control and monitoring of used water are of...

Low salinity stress increases the risk of Vibrio parahaemolyticus infection and gut microbiota dysbiosis in Pacific white shrimp

Extreme precipitation events often cause sudden drops in salinity, leading to disease outbreaks in shrimp aquaculture. Evidence suggests that environmental stress increases animal host susceptibility to pathog...

Sustained gut dysbiosis and intestinal inflammation show correlation with weight gain in person with chronic HIV infection on antiretroviral therapy

Person with human immunodeficiency virus type-1 (PWH) are prone to chronic inflammation due to residual viral production, even with antiretroviral therapy (ART), which increases the risk of age-related disease...

Antibiotic feeding changes the bacterial community of Chilo suppressalis and thereby affects its pesticide tolerance

Owing to the widespread use of chemical pesticides to control agricultural pests, pesticide tolerance has become a serious problem. In recent years, it has been found that symbiotic bacteria are related to pes...

Gut microbiota in preterm infants with late-onset sepsis and pneumonia: a pilot case-control study

Late-onset sepsis (LOS) and pneumonia are common infectious diseases, with high morbidity and mortality in neonates. This study aimed to investigate the differences in the gut microbiota among preterm infants ...

Optimization of fermentation parameters to improve the biosynthesis of selenium nanoparticles by Bacillus licheniformis F1 and its comprehensive application

Selenium nanoparticles (SeNPs) are increasingly gaining attention due to its characteristics of low toxicity, high activity, and stability. Additionally, Bacillus licheniformis , as a probiotic, has achieved remar...

Cutibacterium acnes biofilm formation is influenced by bone microenvironment, implant surfaces and bacterial internalization

The bacterial persistence, responsible for therapeutic failures, can arise from the biofilm formation, which possesses a high tolerance to antibiotics. This threat often occurs when a bone and joint infection ...

Chitinase-functionalized UiO-66 framework nanoparticles active against multidrug-resistant Candida Auris

Candida auris ( C. auris ) is a yeast that has caused several outbreaks in the last decade. Cell wall chitin plays a primary role in the antifungal resistance of C. auris . Herein, we investigated the potential of c...

Adolescent gut microbiome imbalance and its association with immune response in inflammatory bowel diseases and obesity

Recently, there has been an increase in the number of studies focusing on the association between the gut microbiome and obesity or inflammatory diseases, especially in adults. However, there is a lack of stud...

A single viral amino acid shapes the root system architecture of a plant host upon virus infection

Grapevine fanleaf virus (GFLV) is one of the most detrimental viral pathogens of grapevines worldwide but no information is available on its effect on the root system architecture (RSA) of plant hosts. We used...

Legionella pneumophila cell surface RtxA release by LapD/LapG and its role in virulence

Legionella pneumophila is a Gram-negative intracellular bacillus and is the causative agent of a severe form of pneumonia called Legionnaires’ disease which accounts for 2-9% of cases of community acquired pneumo...

Investigation of gyrA and parC mutations and the prevalence of plasmid-mediated quinolone resistance genes in Klebsiella pneumoniae clinical isolates

The emergence of fluoroquinolone resistance in clinical isolates of Klebsiella pneumoniae is a growing concern. To investigate the mechanisms behind this resistance, we studied a total of 215 K. pneumoniae isolat...

Coagulase-negative staphylococci from bovine milk: Antibiogram profiles and virulent gene detection

Coagulase-negative Staphylococcus species are an emerging cause of intramammary infection, posing a significant economic and public health threat. The aim of this study was to assess the occurrence of coagulase-n...

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Citation Impact 2023 Journal Impact Factor: 4.0 5-year Journal Impact Factor: 4.6 Source Normalized Impact per Paper (SNIP): 1.081 SCImago Journal Rank (SJR): 0.999 Speed 2023 Submission to first editorial decision (median days): 15 Submission to acceptance (median days): 135 Usage 2023 Downloads: 2,970,572 Altmetric mentions: 1,619

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BMC Microbiology

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Microbiology

Regenerating Deep-Sea Worms Harness Live-In Algae as They Split into Three

Gutless, solar-powered worms genetically control their resident algae

Rohini Subrahmanyam

See What Gives Sourdough Its Distinctive Taste and Smell

You can thank yeast and bacteria cultivated over generations for the distinctive taste and smell of the oldest leavened bread in history

Daniel Veghte, The Conversation US

Viral Genetics Confirms What On-the-Ground Activists Knew Early in the Mpox Outbreak

Molecular biology could have changed the mpox epidemic—and could stop future outbreaks

Joseph Osmundson

Cannibal Cells Inspire Cancer Treatment Improvement

Giving cells an appetite for cancer could enhance treatments

Kate Graham-Shaw

Is Raw-Milk Cheese Safe to Eat?

Recent bacterial outbreaks from consuming cheese made from unpasteurized milk, or “raw milk,” raise questions about the safety of eating these artisanal products

Riis Williams

Many Pregnancy Losses Are Caused by Errors in Cell Division

Odd cell divisions could help explain why even young, healthy couples might struggle to get pregnant

Gina Jiménez

'Microbiome of Death' Uncovered on Decomposing Corpses Could Aid Forensics

Microbes that lurk in decomposing human corpses could help forensic detectives establish a person's time of death

Christoph Schwaiger, LiveScience

Weird ‘Obelisks’ Found in Human Gut May be Virus-Like Entities

Rod-shaped fragments of RNA called “obelisks” were discovered in gut and mouth bacteria for the first time

Joanna Thompson

Semen Has Its Own Microbiome—And It Might Influence Fertility

Recent research found a species of bacteria living in semen that’s associated with infertility and has links to the vaginal microbiome

Andrew Chapman

Bacteria Make Decisions Based on Generational Memories

Bacteria choose to swarm based on what happened to their great-grandparents

Allison Parshall

Your Body Has Its Own Built-In Ozempic

Popular weight-loss and diabetes drugs, such as Ozempic and Wegovy, target metabolic pathways that gut microbes and food molecules already play a key role in regulating

Christopher Damman, The Conversation US

See Your Body’s Cells in Size and Number

The larger a cell type is, the rarer it is in the body—and vice versa—a new study shows

Clara Moskowitz, Jen Christiansen, Ni-ka Ford

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Advancements in immunology and microbiology research: a comprehensive exploration of key areas.

1. Introduction

2. unveiling the potential of bacterial proteins as antibody reagents and engineering chimeric proteins, 3. illuminating pathways in vaccine development and clinical studies, 3.1. an hiv experimental vaccine, 3.2. african swine fever virus vaccine update, 3.3. vaccine development faces challenges in inducing strong immune responses, 3.4. new developments in hiv vaccines and challenges, 3.5. tuberculosis vaccines, 3.6. messenger rna (mrna) vaccines, 4. microbiological insights and antimicrobial resistance surveillance, 4.1. extended-spectrum beta-lactamases (esbls): a global public health challenge, 4.2. types of esbl and mechanisms of resistance, 4.3. detection of esbls in medical institutions, 4.4. methicillin-resistant staphylococcus aureus (mrsa) in the caribbean and globally, 4.5. mechanisms of bacterial resistance, 5. evolution of immunological techniques and advancements in blood banking, 6. immunological techniques’ impact on global health and the support of quantitative data, 7. navigating clinical immunology: from bench to bedside management, 7.1. severe combined immunodeficiency disorders, 7.2. transient hypogammaglobulinemia of infancy, 7.3. chronic granulomatous disease (cgd), 7.4. neuropsychiatric systemic lupus erythematosus (npsle), 7.5. viral infections in children with scid, 8. advancements in cancer research: insights and innovations, 9. conclusions, author contributions, institutional review board statement, informed consent statement, data availability statement, acknowledgments, conflicts of interest.

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Justiz-Vaillant, A.; Gopaul, D.; Soodeen, S.; Unakal, C.; Thompson, R.; Pooransingh, S.; Arozarena-Fundora, R.; Asin-Milan, O.; Akpaka, P.E. Advancements in Immunology and Microbiology Research: A Comprehensive Exploration of Key Areas. Microorganisms 2024 , 12 , 1672. https://doi.org/10.3390/microorganisms12081672

Justiz-Vaillant A, Gopaul D, Soodeen S, Unakal C, Thompson R, Pooransingh S, Arozarena-Fundora R, Asin-Milan O, Akpaka PE. Advancements in Immunology and Microbiology Research: A Comprehensive Exploration of Key Areas. Microorganisms . 2024; 12(8):1672. https://doi.org/10.3390/microorganisms12081672

Justiz-Vaillant, Angel, Darren Gopaul, Sachin Soodeen, Chandrashekhar Unakal, Reinand Thompson, Shalini Pooransingh, Rodolfo Arozarena-Fundora, Odalis Asin-Milan, and Patrick Eberechi Akpaka. 2024. "Advancements in Immunology and Microbiology Research: A Comprehensive Exploration of Key Areas" Microorganisms 12, no. 8: 1672. https://doi.org/10.3390/microorganisms12081672

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Aims and scope

Aims and scope Current Microbiology serves as a pivotal platform for scientists to share their discoveries, exchange ideas, and contribute to the progress of microbiological knowledge. The journal prioritizes articles of broad interest, with significant novelty in any of the fields of Microbiology.  Current Microbiology publishes significant and original contributions in various domains of basic microbiology research, encompassing original research articles, short communications, reviews, and letters to the editor. The sections include:

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Editorial Policies: Manuscripts submitted to Current Microbiology must adhere to rigorous scientific standards, ensuring originality, clarity, and ethical conduct. The journal advocates for open science, encouraging data and resource sharing to foster collaboration and transparency in microbiological research. Topical review articles are welcomed , provided authors demonstrate sufficient expertise in the field . Authors are advised to discuss the content with the Editors before submission, outlining how the manuscript differs from recent review articles in the field. In its origins, Current Microbiology was a reference journal for microbial taxonomists. Recently the journal has expanded its scope and is considering technically sound science in any sub-discipline of Microbiology. However, it keeps strict for microbe identification . Microbial isolates must be accurately identified and characterized using molecular methods . A mandatory 16S rRNA gene sequence comparison (more than 1000 nt) is required between prokaryotic isolates and validly named type strains of species. The journal does not consider for publication:  

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Turning microbiome research into a force for health

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The microbiome comprises trillions of microorganisms living on and inside each of us. Historically, researchers have only guessed at its role in human health, but in the last decade or so, genetic sequencing techniques have illuminated this galaxy of microorganisms enough to study in detail.

As researchers unravel the complex interplay between our bodies and microbiomes, they are beginning to appreciate the full scope of the field’s potential for treating disease and promoting health.

For instance, the growing list of conditions that correspond with changes in the microbes of our gut includes type 2 diabetes, inflammatory bowel disease, Alzheimer’s disease, and a variety of cancers.

“In almost every disease context that’s been investigated, we’ve found different types of microbial communities, divergent between healthy and sick patients,” says professor of biological engineering Eric Alm. “The promise [of these findings] is that some of those differences are going to be causal, and intervening to change the microbiome is going to help treat some of these diseases.”

Alm’s lab, in conjunction with collaborators at the Broad Institute of MIT and Harvard, did some of the early work characterizing the gut microbiome and showing its relationship to human health. Since then, microbiome research has exploded, pulling in researchers from far-flung fields and setting new discoveries in motion. Startups are now working to develop microbiome-based therapies, and nonprofit organizations have also sprouted up to ensure these basic scientific advances turn into treatments that benefit the maximum number of people.

 “The first chapter in this field, and our history, has been validating this modality,” says Mark Smith PhD ’14, a co-founder of OpenBiome, which processes stool donations for hospitals to conduct stool transplants for patients battling gut infection. Smith is also currently CEO of the startup Finch Therapeutics, which is developing microbiome-based treatments. “Until now, it’s been about the promise of the microbiome. Now I feel like we’ve delivered on the first promise. The next step is figuring out how big this gets.”

An interdisciplinary foundation

MIT’s prominent role in microbiome research came, in part, through its leadership in a field that may at first seem unrelated. For decades, MIT has made important contributions to microbial ecology, led by work in the Parsons Laboratory in the Department of Civil and Environmental Engineering and by scientists including Institute Professor Penny Chisholm.

Ecologists who use complex statistical techniques to study the relationships between organisms in different ecosystems are well-equipped to study the behavior of different bacterial strains in the microbiome.

Not that ecologists — or anyone else — initially had much to study involving the human microbiome, which was essentially a black box to researchers well into the 2000s. But the Human Genome Project led to faster, cheaper ways to sequence genes at scale, and a group of researchers including Alm and visiting professor Martin Polz began using those techniques to decode the genomes of environmental bacteria around 2008.

Those techniques were first pointed at the bacteria in the gut microbiome as part of the Human Microbiome Project, which began in 2007 and involved research groups from MIT and the Broad Institute.

Alm first got pulled into microbiome research by the late biological engineering professor David Schauer as part of a research project with Boston Children’s Hospital. It didn’t take much to get up to speed: Alm says the number of papers explicitly referencing the microbiome at the time could be read in an afternoon.

The collaboration, which included Ramnik Xavier, a core institute member of the Broad Institute, led to the first large-scale genome sequencing of the gut microbiome to diagnose inflammatory bowel disease. The research was funded, in part, by the Neil and Anna Rasmussen Family Foundation.

The study offered a glimpse into the microbiome’s diagnostic potential. It also underscored the need to bring together researchers from diverse fields to dig deeper.

Taking an interdisciplinary approach is important because, after next-generation sequencing techniques are applied to the microbiome, a large amount of computational biology and statistical methods are still needed to interpret the resulting data — the microbiome, after all, contains more genes than the human genome. One catalyst for early microbiome collaboration was the Microbiology Graduate PhD Program, which recruited microbiology students to MIT and introduced them to research groups across the Institute.

As microbiology collaborations increased among researchers from different department and labs, Neil Rasmussen, a longtime member of the MIT Corporation and a member of the visiting committees for a number of departments, realized there was still one more component needed to turn microbiome research into a force for human health.

“Neil had the idea to find all the clinical researchers in the [Boston] area studying diseases associated with the microbiome and pair them up with people like [biological engineers, mathematicians, and ecologists] at MIT who might not know anything about inflammatory bowel disease or microbiomes but had the expertise necessary to solve big problems in the field,” Alm says.

In 2014, that insight led the Rasmussen Foundation to support the creation of the Center for Microbiome Informatics and Therapeutics (CMIT), one of the first university-based microbiome research centers in the country. CMIT is based at the MIT Institute for Medical Engineering and Science (IMES).

Tami Lieberman, the Hermann L. F. von Helmholtz Career Development Professor at MIT, whose background is in ecology, says CMIT was a big reason she joined MIT’s faculty in 2018. Lieberman has developed new genomic approaches to study how bacteria mutate in healthy and sick individuals, with a particular focus on the skin microbiome.

Laura Kiessling, a chemist who has been recognized for contributions to our understanding of cell surface interactions, was also quick to join CMIT. Kiessling, the Novartis Professor of Chemistry, has made discoveries relating to microbial mechanisms that influence immune function. Both Lieberman and Kiessling are also members of the Broad Institute.

Today, CMIT, co-directed by Alm and Xavier, facilitates collaborations between researchers and clinicians from hospitals around the country in addition to supporting research groups in the area. That work has led to hundreds of ongoing clinical trials that promise to further elucidate the microbiome’s connection to a broad range of diseases.

Fulfilling the promise of the microbiome

Researchers don’t yet know what specific strains of bacteria can improve the health of people with microbiome-associated diseases. But they do know that fecal matter transplants, which carry the full spectrum of gut bacteria from a healthy donor, can help patients suffering from certain diseases.

The nonprofit organization OpenBiome, founded by a group from MIT including Smith and Alm, launched in 2012 to help expand access to fecal matter transplants by screening donors for stool collection then processing, storing, and shipping samples to hospitals. Today OpenBiome works with more than 1,000 hospitals, and its success in the early days of the field shows that basic microbiome research, when paired with clinical trials like those happening at CMIT, can quickly lead to new treatments.

“You start with a disease, and if there’s a microbiome association, you can start a small trial to see if fecal transplants can help patients right away,” Alm explains. “If that becomes an effective treatment, while you’re rolling it out you can be doing the genomics to figure out how to make it better. So you can translate therapeutics into patients more quickly than when you’re developing small-molecule drugs.”

Another nonprofit project launched out of MIT, the Global Microbiome Conservancy, is collecting stool samples from people living nonindustrialized lifestyles around the world, whose guts have much different bacterial makeups and thus hold potential for advancing our understanding of host-microbiome interactions.

A number of private companies founded by MIT alumni are also trying to harness individual microbes to create new treatments, including, among others, Finch Therapeutics founded by Mark Smith; Concerto Biosciences, co-founded by Jared Kehe PhD ’20 and Bernardo Cervantes PhD ’20; BiomX, founded by Associate Professor Tim Lu; and Synlogic, founded by Lu and Jim Collins, the Termeer Professor of Medical Engineering and Science at MIT.

“There’s an opportunity to more precisely change a microbiome,” explains CMIT’s Lieberman. “But there’s a lot of basic science to do to figure out how to tweak the microbiome in a targeted way. Once we figure out how to do that, the therapeutic potential of the microbiome is quite limitless.”

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Microbiology in the 21st Century: Where Are We and Where Are We Going?

• Copyright and Permissions
• The impact of microbes on the health of the planet and its inhabitants;
• The fundamental significance of microbiology to the study of all life forms;
• Research challenges faced by microbiologists and the barriers to meeting those challenges;
• The need to integrate microbiology into school and university curricula; and
• Public microbial literacy.

This is an exciting time for microbiology. We are becoming increasingly aware that microbes are the basis of the biosphere. They are the ancestors of all living things and the support system for all other forms of life. Paradoxically, certain microbes pose a threat to human health and to the health of plants and animals. As the foundation of the biosphere and major determinants of human health, microbes claim a primary, fundamental role in life on earth. Hence, the study of microbes is pivotal to the study of all living things, and microbiology is essential for the study and understanding of all life on this planet.

Microbiology research is changing rapidly. The field has been impacted by events that shape public perceptions of microbes, such as the emergence of globally significant diseases, threats of bioterrorism, increasing failure of formerly effective antibiotics and therapies to treat microbial diseases, and events that contaminate food on a large scale. Microbial research is taking advantage of the technological advancements that have opened new fields of inquiry, particularly in genomics. Basic areas of biological complexity, such as infectious diseases and the engineering of designer microbes for the benefit of society, are especially ripe areas for significant advancement. Overall, emphasis has increased in recent years on the evolution and ecology of microorganisms. Studies are focusing on the linkages between microbes and their phylogenetic origins and between microbes and their habitats. Increasingly, researchers are striving to join together the results of their work, moving to an integration of biological phenomena at all levels.

While many areas of the microbiological sciences are ripe for exploration, microbiology must overcome a number of technological hurdles before it can fully accomplish its potential. We are at a unique time when the confluence of technological advances and the explosion of knowledge of microbial diversity will enable significant advances in microbiology, and in biology in general, over the next decade. To make the best progress, microbiology must reach across traditional departmental boundaries and integrate the expertise of scientists in other disciplines. Microbiologists are becoming increasingly aware of the need to harness the vast computing power available and apply it to better advantage in research. Current methods for curating research materials and data should be rethought and revamped. Finally, new facilities should be developed to house powerful research equipment and make it available, on a regional basis, to scientists who might otherwise lack access to the expensive tools of modern biology.

It is not enough to accomplish cutting-edge research. We must also educate the children and college students of today, as they will be the researchers of tomorrow. Since microbiology provides exceptional teaching tools and is of pivotal importance to understanding biology, science education in schools should be refocused to include microbiology lessons and lab exercises. At the undergraduate level, a thorough knowledge of microbiology should be made a part of the core curriculum for life science majors.

Since issues that deal with microbes have a direct bearing on the human condition, it is critical that the public-at-large become better grounded in the basics of microbiology. Public literacy campaigns must identify the issues to be conveyed and the best avenues for communicating those messages. Decision-makers at federal, state, local, and community levels should be made more aware of the ways that microbiology impacts human life and the ways school curricula could be improved to include valuable lessons in microbial science.

• Front Matter

The American Academy of Microbiology is the honorific leadership group of the American Society for Microbiology. The mission of the American Academy of Microbiology is to recognize scientific excellence and foster knowledge and understanding in the microbiological sciences.

The opinions expressed in this report are those solely of the colloquium participants and may not necessarily reflect the official position of the American Society for Microbiology.

Board of Governors, American Academy of Microbiology

Eugene W. Nester, Ph.D. (Chair) University of Washington

Kenneth I. Berns, M.D., Ph.D. University of Florida Genetics Institute

James E. Dahlberg, Ph.D. University of Wisconsin, Madison

Arnold L. Demain, Ph.D. Drew University

E. Peter Greenberg, Ph.D. University of Iowa

J. Michael Miller, Ph.D. Centers for Disease Control and Prevention

Stephen A. Morse, Ph.D. Centers for Disease Control and Prevention

Harriet L. Robinson, Ph.D. Emory University

Abraham L. Sonenshein, Ph.D. Tufts University Medical Center

David A. Stahl, Ph.D. University of Washington

Judy D. Wall, Ph.D. University of Missouri

Colloquium Steering Committee

Roberto G. Kolter, Ph.D. Harvard Medical School (Co-Chair)

Moselio Schaechter, Ph.D. San Diego State University (Co-Chair)

Stanley R. Maloy, Ph.D. San Diego State University

David A. Relman, M.D. Stanford University School of Medicine

Margaret A. Riley, Ph.D. Yale University

Carol A. Colgan, Director American Academy of Microbiology

Colloquium Participants

Victor de Lorenzo, Ph.D. Centro Nacional de Biotecnologia, Madrid, Spain

William E. Goldman, Ph.D. Washington University of Medicine, St. Louis

Peter M. Hecht, Ph.D. Microbia, Inc., Cambridge, Massachusetts

Laura A. Katz, Ph.D. Smith College

Roberto G. Kolter, Ph.D. Harvard Medical School

Mary E. Lidstrom, Ph.D. University of Washington

William W. Metcalf, Ph.D. University of Illinois

Eugene W. Nester, Ph.D. University of Washington

Gary J. Olsen, Ph.D. University of Illinois

Moselio Schaechter, Ph.D. San Diego State University

Gisela Storz, Ph.D. National Institutes of Health

Saeed Tavazoie, Ph.D. Princeton University

Jennifer J. Wernegreen, Ph.D. Marine Biology Laboratory, Woods Hole, Massachusetts

Merry Buckley, Ph.D. Freelance Science Writer, Ithaca, New York

• Executive Summary
• Introduction

Microbiology has never been more exciting or important than it is today. Powerful new technologies, including novel imaging techniques, genomics, proteomics, nanotechnology, rapid DNA sequencing, and massive computational capabilities have converged to make it possible for scientists to delve into inquiries that many thought would never be approachable. As a result, hardly a day goes by without another discovery that points to the central importance microbial life has in carrying out the cycles of gases and nutrients that sustain all life and affect conditions on this planet. The increasing human population, combined with increases in global travel, has apparently created a sharp rise in the emergence and re-emergence of infectious diseases, alarming the public and frustrating public health officials.

Issues of microbial contamination are also more pressing now than ever. The microbial quality of our food and water in a crowded, complex world must be vigorously addressed to maintain health and a high quality of life for the all citizens of the world. Finally, a bioterrorism event involving spores of Bacillis anthracis occurred in the United States in 2001, and continuing investigations worldwide reveal that bioterrorism is a genuine threat from ill-intentioned groups and individuals using other microbes and toxins.

As microbiology is faced with this tumult of advancements, opportunities, problems, and threats, the science stands at the threshold of a new era. But in what direction is microbial science going? What is really important and what is merely distraction? What will best improve people's lives and the health of our shared planet? In short, what new directions should microbiology take in the 21 st century?

Microbiologists want to know how microbial science is changing in the wake of advancements in technology and growing human pressures on the world's resources. They want to know what topics deserve exploration and where the obstacles to exploring those areas lie. As we stand at the convergence of genomics, public concerns about bioterrorism, global outbreaks of infectious diseases, unprecedented computational power, and the possibility of large-scale ecological disasters, where do the greatest opportunities lie in microbiology and what obstacles must be overcome for these opportunities to be realized?

It is clear to microbiologists that microbes are the basis of the biosphere; they are the support system for life on earth and the wellspring from which all other life has arisen through billions of years of evolution. Since microbes are fundamental to life and microbial science is in the headlines now more than ever before, it follows that educating young people in microbial science is critical. But where does microbiology fit into existing school curricula? How can college biology coursework be updated to reflect more accurately the pivotal place of microbial science in understanding our world? How can the public-at-large be made aware of microbes, the role of microbes in sustaining life, and the danger posed by modern infectious diseases? And how should public outreach campaigns be conducted? What are the important messages to deliver? How can the importance of microbes and microbiology be conveyed to people in power, the decision-makers?

To answer such questions, the American Academy of Microbiology convened a colloquium in Charleston, South Carolina on September 5–7, 2003. Experts in the fields of bacteriology, virology, eukaryotic microbiology, medicine, biotechnology, molecular biology, and education met to discuss the central role of microbes in maintaining life on earth, the current research challenges that face the field, the pivotal role of microbiology education to training in all life sciences, and methods for encouraging public literacy of microbial science.

• The Central Role of Microbes and Microbiology

Microbes affect all life and the physical and chemical make-up of our planet. They have done so since the origin of life. No other group of organisms can make such a claim. Life without all other creatures is possible, but life without microbes is not. Consequently, we believe that one cannot carry out in-depth studies of any branch of biology or geology without taking into account the activities of microbes. Microbes are the masters of the biosphere, and ours indeed is a planet of the microbes.

Microorganisms are also determinants of human health and the source of critical materials for medical and industrial use. Microbiology, therefore, is as central to the study of life as biochemistry, genetics, evolution, or molecular biology. The informed biologist must treat microbiology as core and not as a particular branch of biology.

Microbes As the Basis of Life

The root of the tree of life.

Microbes were the progenitors of all the complex and varied biological forms that now exist on Earth. Plants and animals emerged within a microbial world and have retained intimate connections with, and dependency upon, microorganisms. As the root of the tree of life, microbes were the original templates from which all life was formed and to which all life has an intimate familiarity. In order to understand the evolution of organisms we see today at the tips of the branches of the tree of life, it is necessary to study how they are related to their ancestors and what those ancestors were like.

By studying the microorganisms living today that echo the properties of the first life forms, microbiologists seek to understand the forces and processes that created our global ecosystem. Moreover, microorganisms are the preeminent systems to use in experimental evolution, as they offer the researcher fast generation times, genetic flexibility, unequaled experimental scale, and manageable study systems. Studies using microbes have led to groundbreaking insights into the evolution of all species. For example, investigations of the interrelatedness of microbes first brought to light the current model of the evolutionary relatedness of all life on earth, the tree of life (See Box 1 – the Tree of Life).

The Tree of Life Before and After Molecular Microbiology.

MAINTAINING LIFE ON EARTH

Life not only began with microorganisms, the continued existence of life on earth totally relies on the inconspicuous microbe. It has been estimated that a staggering 5×10 31 (50,000,000,000,000,000,000,000,000,000,000—weighing more than 50 quadrillion metric tons) microbial cells exist on this planet, and it is difficult to overstate their importance to the biosphere. Microbes are responsible for cycling the critical elements for life, including carbon, nitrogen, sulfur, hydrogen, and oxygen. By cycling these elements in soils, microbes regulate the availability of plant nutrients, thereby governing soil fertility and enabling the efficient plant growth that sustains human and animal life. Microbes also play a big role in cycling atmospheric gases, including the compounds responsible for the “greenhouse effect,” which, paradoxically, sustains life on our planet, but through global warming, poses a threat to all living things. More photosynthesis is carried out by microbes than by green plants. It turns out that, excluding cellulose, microbes constitute approximately 90% of the biomass of the whole biosphere (more than 60% if cellulose is considered).

Since microbes can take up nutrients and other elements that larger organisms often cannot exploit, microorganisms are positioned at the base of many food chains, where they siphon previously inert, inorganic materials into the biosphere. Microbes are also master recycling experts; they degrade biological wastes and release the critical elements for use by other organisms.

Scientists have only begun to understand the ways that microorganisms are tuned into their environments, how they respond to changes, and how they communicate with other members of microbial communities to carry out the functions that sustain the biosphere. Understanding these phenomena will lead to a more complete knowledge of our global ecosystem and may allow scientists to correct human damage to ecosystems, large and small. Humans are latecomers to this planet, and a great deal may be learned from microbes about the maintenance of essential planetary processes.

VITAL BUT DANGEROUS TO HUMAN HEALTH

Humans have an intimate relationship with microorganisms. Despite their overwhelmingly beneficial impact on the environment, a small notorious set of bacteria, fungi, parasites, and viruses may cause disease. In the struggle against disease, our bodies attempt to establish a delicate balance between the microorganisms and viruses that are beneficial to our health and those that exploit the human host to the body's detriment. More than 90% of the cells in our bodies are microorganisms; bacteria and fungi populate our skin, mouth, and other orifices. Microbes enable efficient digestion in our guts, synthesize essential nutrients, and maintain benign or even beneficial relationships with the body's organs. The presence of these organisms influences our physical and mental health. In experiments, it has been found that sterile animals are markedly less healthy than animals that have been naturally colonized by microorganisms.

How do microorganisms cause disease? Pathogenic microorganisms and viruses have an individual ecological strategy that determines where they strike and what impacts they have on the host. One root of the problem is that pathogens colonize areas within the human body that our immune system sees as “privileged.” In the process of gaining access to these locations or in maintaining their colonies, microorganisms and viruses may cause damage to human tissues, creating signs and symptoms of disease. Disease may also begin when the immune system detects a microbial cell or virus. The body's immune system responds with an attack on the foreign organism that may cause harm to the body itself. In some cases, the damage caused by pathogens in human tissues or the immune response to them can promote the transmission of the pathogen to a new host. Hence, causing disease is just another ecological strategy for certain microorganisms—one in which the human body is used as a habitat for multiplication, persistence, and transmission.

Disease emergence—the situation where a new disease-causing microbe or virus is identified or an old one causes a new disease—is a hot-button topic today. From the E. coli strain O157 to SARS, new diseases and new pathogens are identified every year, frightening the public and confounding public health officials responsible for stemming the tide of outbreaks. Many circumstances likely play a role in the increased rate of disease emergence, including a variety of host, environmental, and social factors.

USEFUL TO INDUSTRY AND MEDICINE

Industry and medicine are increasingly reliant on microorganisms to generate chemicals, antibiotics, and enzymes that improve our world and save lives. Microbes are being domesticated with the tools of molecular biology for production of biodegradable plastics and all types of new materials. Biotechnology, which will soon be a pillar of the industrial base in the U.S., employs microorganisms and viruses in a number of ways, including such divergent applications as the genetic engineering of crops and gene therapy. Microbiology research has enabled these successful technologies, and future advancements in using microbes in industry and medicine rely on conducting effective research today.

• Microbiology as the Foundation of Biology

In light of the critical functions microbes carry out to the benefit and detriment of life on earth, the study of microbiology must be treated as a core subject. Moreover, microbes are ideal experimental systems for investigating many of the otherwise confounding key questions in biology.

Microbiology directly provides important tools for experimental science. Because of their relative simplicity, microbes are ideal systems for sorting out basic questions about the origin of sex, speciation, adaptation, cellular function, genetics, biochemistry, and physical properties of all other living organisms. Of particular significance is the ability, using single-celled microorganisms, to match a gene with a characteristic of the organism, otherwise known as linking genotype with phenotype. Microbial cells in culture are not the only available microbial tools. Microbial communities can be put to good use in exploring ecological principles and identifying the metabolic properties, interactions, and communications at work in a relatively simple ecosystem.

The “virtual microbial cell” (a complete computer simulation of the minimal set of genes and functions at work in one live bacterium or yeast) also may be highly instructive, allowing researchers to build models of complete metabolic pathways, cell circuits, and other phenomena to create a virtual network that describes a cell. Such a virtual status may, in fact, soon turn into a physical reality, as the emerging field of Synthetic Biology (building up bacteria from scratch endowed with desired properties) develops and comes to fruition.

Current Issues and Research Challenges

• “Calm urged over mystery virus; a flu-like illness has downed at least 50 staff in two days at the Prince of Wales Hospital,” South China Morning Post (Hong Kong), March 13, 2003.
• “Probe Begins Trip to Mars In Quest for Water, and Life,” The New York Times, June 11, 2003.
• “3rd Death in Hepatitis Outbreak; Pa. probe focuses on handling of produce,” Newsday, November 15, 2003.
• “Engineered corn found to kill butterflies,” Milwaukee Journal Sentinel, August 22, 2000.
• “Infections eyed as cause of cancer, heart disease,” The Boston Herald, April 18, 1999.

Today, microbiology is in the headlines more than ever before, and research behind the headlines, and behind other critical issues of which the public is largely unaware, is changing rapidly.

HOW THE IMPORTANCE OF MICROBIOLOGY TO SOCIETY HAS CHANGED IN THE LAST TEN YEARS

The public is now more aware of microorganisms and viruses than at any other time in history. Unfortunately, that public awareness is usually laced with anxiety and dread. Events of the last ten years and the tone of the media coverage of those events have served to feed the public's fear and create the perception of an increased risk from the microbial world. Such “microbiophobia” has resulted in surges in the popularity of disinfectants, antimicrobial soaps, and other products that purport to keep disease at bay. Bioterrorism and the distinct possibility that anthrax or another infectious microbe could be used as a weapon against innocent civilians, crops, or livestock have frightened people across the globe. An apparent increase in the emergence of novel infectious diseases, including SARS, West Nile disease, and others, has also brought microbes into the public eye. Recently, conventional health therapies to combat certain infectious diseases, including AIDS and tuberculosis, have failed due to the ongoing evolution of these pathogens, heightening public doubts about the ability of scientists and physicians to protect the public even from familiar diseases. A few chronic diseases that were once thought to be due to factors like genetic susceptibility or chance have instead been shown to be the work of bacteria or viruses. And in the U.S. and other developed nations, large-scale food contamination events are on the rise, often sickening tens or hundreds of people before public health officials can identify the sources of infection and restrict the public's exposure.

Advancements in microbiology over the last ten years are frequently overlooked in the wake of public concerns about biowarfare, infectious disease, and foodborne illness. Yet, the progress of the last decade is undeniable. Pharmaceutical research now relies heavily on microbes and microbiology for drug discovery and production. Green chemistry, in which microorganisms are employed to carry out industrial processes, is an increasingly effective strategy for tackling issues of safety and sustainability in chemical-related industries. Biotechnology, too, relies on microbial technologies and microbial genes for carrying out modifications that improve crops, breeds of livestock, and synthetic feed-stocks. In agriculture, microbes and microbial products are now used in probiotic therapies, antibiotics, and pest control measures. Advancements in food microbiology have improved the safety of the food we buy in our supermarkets and restaurants, doubtlessly saving lives every single day. At hazardous waste sites, microbes have been put to work digesting noxious chemicals—metabolizing them into harmless materials, thereby preventing further contamination of soil and water. Bioterrorism and disease are frightening, but progress in microbiology and advancements in applying microbes to solve seemingly intractable human problems should be kept in mind.

How Research Is Changing

Not only has the public's perception of microbiology changed in the last decade, the practice of microbiology research has been altered as well. The past ten years of microbiology have been dynamic and exciting, and new discoveries have been built upon the remarkable work of the past.

MORE SYNTHESIS, LESS REDUCTIONISM

Microbiology once focused almost solely on individual microorganisms grown in isolation under artificial conditions, attempting to extrapolate an understanding of disease or the environment from minute observations recorded in the laboratory. Today, however, much of the science is moving away from reductionist approaches and into the realm of synthesis—weaving together a fabric of measurements and observations of the microorganism, its environment, and the influence of other organisms at many scales to create an integrative picture of microbial activities. Once unfamiliar, the concept that cells consist of a network of interacting proteins now permeates the science. A greater emphasis is now being placed on systems-level research, in which microbes in their habitats are being treated as a series of interrelated compartments, processes, and feedbacks. Placing a synthetic or systems lens on microbiology can be highly instructive and has several advantages over strict reductionism. It is hoped that in the future, integrative approaches will enable microbiologists to predict microbiological outcomes, allowing them to pinpoint the consequences of a perturbation of human health or of a given ecosystem.

INCREASED EMPHASIS ON EVOLUTION AND ECOLOGY

In the past ten years, microbiologists have increasingly recognized the importance of ecology and evolution. Studies in experimental ecology and evolution have provided evidence on the principles that apply not only to microbes, but possibly to larger organisms as well. Ecological thinking has become dominant, and microbiology is no longer the test tube science of the past. An example is the realization that the way microbes cause disease is, in fact, an ecological problem requiring understanding of both the microbe and its environment—the host in the case of disease.

A change has also taken place in the investigative style of research in microbiology. Previously, many lines of inquiry were closed due to technological limitations or a lack of expertise in fields tangential to microbiology, like soil science, geology, or medicine. In these cases, the problem under investigation was often re-defined to suit the techniques at hand and the academic experience of the principal investigator. Today, these lines of inquiry are often explored head-on by applying the technology advancements of the last ten years and, more importantly, recruiting expertise and resources from other disciplines, often through collaborations.

TECHNOLOGICAL ADVANCEMENTS

Technological progress has reformed the landscape of microbiology research, making long-standing questions about microbes finally amenable to study. Chief among the significant advancements of the last ten years is the development of technologies that make genomics possible, including increased computational power, more rapid DNA sequencing, and other laboratory techniques. Genomics employs all or part of the genome, the full genetic complement of a cell, to answer questions about an organism. Although genomics has impacted most of the life sciences and enabled new insights into the functions and processes of all life forms, its most significant impact has been on microbiology, a development that has opened new insights into the ecology and evolution of microorganisms. Other large-scale research, such as proteomics or transcriptomics (the pattern of gene expression), has also had a great impact on the practice of microbiology research. Improvements in information technology have increased interactions between researchers of all fields, enabling a continuing dialogue on the commonalties between microbiology and other disciplines. Nanotechnology and related approaches should allow researchers to experiment with single cells, answering long-standing questions about microbial physiology. Finally, high-end imaging techniques such as nuclear magnetic resonance imaging (NMR), ESR, and others have allowed detailed analyses of microbial cell structure and the structure of microbial communities.

With the advent of molecular microbiology, traditional approaches for defining microbial causation of disease, such as Koch's postulates, have been found insufficient, as they oftentimes lead to “false negative” conclusions. Researchers have struggled with creating robust standards for identifying microbial causation that go beyond Koch's postulates and make use of technological advancements to identify causative links even for microbes that cannot be cultivated in the lab.

• Hot Research Topics

A number of areas of microbiology research are particularly topical in the wake of technological advancements and discoveries that have brought to light previously unexplored aspects of microbial life. Topics including genomics, biocomplexity, infectious disease, the origins of life, and the application of microbes to improve quality of life are at the forefront of the list of previously unattainable research areas that are being actively pursued today.

ENVIRONMENTAL GENOMICS AND ENVIRONMENTAL METAGENOMICS

Bacteria and archaea tend to have smaller genomes than eukarytic cells, which makes them more amenable to sequencing. The study of genomics has had a huge impact on microbiology. Lines of inquiry related to the factors that govern microbial genome organization, dynamics, and stability are highly approachable using these genomic techniques. But, despite the vast tracts of sequence data that are available, more rapid and accurate methods of annotation attributing a function to a gene are sorely needed. Scientists can now explore questions related to the extents of diversity within naturally occurring microbial communities and to the functional significance of that diversity. Metagenomic technologies are being used to examine the DNA of nonculturable bacteria and microbial consortia without any sub-culturing, thereby allowing us to understand the interplay of genes and functions in an ecosystem, regardless of the specific microbial hosts. We can now ask how the genes of all members of a community relate to the functions carried out by that particular community.

Many other critical questions about microbial life may now be addressed using genomics. Interested readers are referred to the American Academy of Microbiology's colloquia reports “The Global Genome Question: Microbes as the Key to Understanding Evolution and Ecology” and “Microbial Ecology and Genomics: A Crossroads of Opportunity” (see http://www.asm.org ).

BIOCOMPLEXITY

In addition to genomics-related topics, questions related to biocomplexity are at the forefront of microbiology research. Biocomplexity in microbiology encompasses the interactions among microbes and between microbes and their environment. The emphasis in biocomplexity research is on the whole ecosystem, rather than its parts, seeking to identify the emergent properties that cannot be found in studies of individual components. Interdisciplinary collaboration is inherent in this kind of research since it often calls for the expertise of environmental engineers, biologists who study larger organisms, soil scientists, hydrologists, marine biologists, and other related professionals. Research in biocomplexity should progress rapidly in the coming years. Questions on the shape of microbial biocomplexity, its temporal and spatial variability, will doubtless be investigated. Other questions related to microbial biocomplexity are the definition of a microbial “species,” how species are created, and at what rate.

INFECTIOUS DISEASE

Grappling with topics related to infectious disease is certainly not new for microbiologists, but the discoveries and advancements of the past ten years have revealed new horizons in the field, presenting exciting opportunities to improve the quality of human life. The ability to predict the emergence of disease is a particularly critical topic. Research into the environmental factors that trigger the emergence of pathogens, the factors that drive disease migration, and seasonal patterns in disease frequency may shed light on the factors that affect how new and old diseases emerge and persist in populations. These observations will enable us to design better therapeutic strategies for new and existing pathogens.

Recent discoveries that have linked human diseases (e.g., stomach ulcers and cervical cancer) to bacterial or viral causes highlight the possibility that other chronic illnesses with mysterious etiologies may also be microbially mediated. Candidates include inflammatory bowel disease, diabetes, rheumatoid arthritis, sarcoidosis, systemic lupus erythematosus, and coronary artery disease. Research into the causes of these diseases and others will shed more light on these diseases and their diagnosis, prevention, and treatment.

THE ORIGINS AND HISTORY OF LIFE

Science now has better tools at its disposal to explore the origins of life, and microbes are well suited to experimental approaches for understanding these first organisms. The evolutionary origins of sex may also be explored using microbial systems. Analysis of the distribution of sex (here referring to the fusion of gametes) on the emerging tree of life indicates that this process arose very early in the evolution of eukaryotic cells. Research will also focus on assembling the complete tree of life, a comprehensive phylogenetic framework that includes all life forms on earth.

ENGINEERING MICROBES TO IMPROVE THE QUALITY OF LIFE

To an ever-greater extent, microbes can be put to use to improve the human condition. Methods of detecting and identifying novel microbial products are likely to be scrutinized and improved upon, expanding the ability to exploit the metabolic versatility of microbes in providing powerful antibiotics, therapeutics, and other materials. It is also likely that microbes can be put to work in energy recovery and utilization. In this respect, microbial production of H 2 is bound to be one of the keys for addressing the unavoidable shortage of energy in the future and for mitigating the greenhouse effect of fuel combustion.

Other Hot Topics in Microbiology.

• Meeting Future Research Challenges

The future is bright for microbiology. Advancements in the study of infectious disease, microbial ecology, plant and animal pathology, and biotechnology promise to improve human life and the well being of the environment, and new opportunities have come about through social and scientific changes. Progress on these synthetic activities will be hastened through improvements in technology and through changes in education and training.

Technological Hurdles

Several technological hurdles stand before today's microbiology researchers. To make progress, science should not accept the limitations placed on discovery by traditional methods, conventional approaches, or existing infrastructure. Particular attention should be focused on the technologies that enable genomics, single-cell analyses, microbial cultivation, and establishment and maintenance of microbiological databases.

Although progress in microbial genomics is being made at a fantastic rate, availability of appropriate tools still places limits on research. It would be ideal to have the complete genomes of many thousands of species and strains of microbes, but this is currently not possible, given the limits on the speed of sequencing and computational capacity for data manipulation, which both translate into limitations in funds available for such an endeavor. Accelerated and inexpensive sequencing capabilities are needed to conduct sequencing on this scale. In order to interpret microbial genome sequence data in a meaningful way, more tools and approaches beyond those that solely rely on gene homology for inferring gene function are sorely needed. Annotation of genomes is currently a major hurdle for the field, and standards and methods are needed that can accelerate the process and provide consistent high quality results.

STUDYING SINGLE CELLS

The ability to analyze single cells has eluded microbiologists in the past. In order to better understand the activities of microbes in their natural settings, technologies and assays that would allow the monitoring of single cells in a variety of conditions, including in situ , are necessary. Specific capabilities should include genome sequencing, gene expression analysis, and the ability to measure intracellular pools of small molecules. Ideally, these analyses should be amenable to high-throughput approaches.

CULTIVATION

Improved technologies for cultivating diverse microbes are badly needed. It is never far from a microbiologist's mind that more than 99% of microbes have never been cultivated in the laboratory. The fact that the vast majority of microbial life cannot be scrutinized with respect to growth, metabolism, and reproduction comprises a massive gap in our understanding of the microbial world.

Currently, a need exists for quantitative digital formatting of microbiological data in a portable and standardized fashion. To better integrate microbiological data from multiple studies and from multiple laboratories, an effort should be made to standardize data collection and annotation.

Scientific Needs

• Researchers must integrate their work with that of scientists in related fields.
• Computational scientists should become more familiar with and integral to microbiology.
• Microbiology materials and data must be more carefully curated.
• Powerful, but expensive, modern equipment should be housed in community facilities, open to researchers who might not otherwise have access to these technologies.

INTEGRATING DISCIPLINES

The issues surrounding microbiology touch on so many other disciplines that meeting the grand challenges in microbiology requires integrating the expertise of professionals in many fields. The response to public concerns about bioterrorism, for example, presents a formidable task that requires the contributions of micro-biologists, physicians, pathologists, forensic scientists, and others.

In light of the opportunities and challenges in microbiology today, a number of fields of expertise are especially ripe for integration. Pathogenic microbiologists should see themselves as microbial ecologists who should study both the microbe and the host with analogous intensity. Enhancing the linkages between organic chemistry and microbiology would prove helpful to a number of areas of inquiry, including bioremediation and green chemistry. Microbiology should borrow expertise from systems engineering in efforts to create networks of metabolic pathways. Other interdisciplinary opportunities include collaborations with professionals in imaging sciences, statistics, nanotechnology, biosystematics, mathematics, biochemistry, ecology, and structural chemistry. Moreover, some relatively neglected fields within microbiology should be revived and facilitated by integrating with these related disciplines, including microbial physiology and the biology of eukaryotic microbes (fungi, protists). Collaborations between micro-biologists who work with prokaryotic or eukaryotic microbes and virologists should also be encouraged.

Some successful integrations have already taken place. The fields of geology and microbiology have already been joined on a number of levels to cope with questions surrounding the significance of microorganisms in global geological processes, and molecular biology has met up with information science to provide bioinformatics, which is used to manage genetic and protein sequence data.

A number of routes could be developed to foster these integrations. Visiting fellowships could be established to bring professionals with expertise in statistics, biochemistry, or ecology, for example, into microbiology labs and vice versa, placing microbiologists into statistics, biochemistry, or ecology labs. Microbiologists and professionals in related disciplines could also assemble into working communities across departmental boundaries to cooperate on subjects best addressed through multidisciplinary collaborations. Other integrations could be encouraged by funding agencies.

COMPUTATIONAL SCIENCE

There is a need to bring computational science into closer contact with the daily work of microbiology. The basic skills involved in computer science, including programming, for instance, should be acquired, or at least be highly familiar, to the average microbiologist.

CURATION OF MATERIALS AND DATA

A great need exists to improve the current modes of curation, entry, storage, and distribution of materials and data related to microbiology. The procedures surrounding culture collections, in particular, need to be revamped. Distribution of cultures has to be conducted in a way that both respects the need for national security and recognizes the ability of these materials, in the hands of researchers, to further the science that directly benefits society. If the international microbiological community does not confront the need for thoughtful review of potentially problematic materials and data, then mechanisms governing release and distribution of data will be imposed by others.

Progress in microbiology has always been enabled by the technology available, a fact that is still true today. However, many researchers are stymied by a lack of access to the expensive instruments that would enable them to make the greatest strides. Facilities for housing and making these technologies available to microbiology researchers would allow investigators in moderately funded and underfunded labs to achieve their full potential. In these technology centers, investigators could come to conduct work, using techniques like NMR, spectroscopy, and other imaging methods, under the guidance of trained staff. Regional centers could even promote technology development and could play a part in advancing training, education, and out-reach among participating educational institutions.

• Key Opportunities for Microbial Biologists

There are more opportunities available for microbiologists today than at any time in the history of the field. Although the microbiological advancements of the last two centuries have been profound, a great deal of biology remains to be discovered and described through study of the microbial world. Microbiology can be used to push back the frontiers of biology, opening up new ways to harness the power of biology to improve human health and the environment. Microbiologists must participate in this effort.

CAREER OPPORTUNITIES

Career opportunities for microbiologists abound in the wake of new technologies that have changed the face of biology. Biotechnology, in particular, is intimately connected with microbiology and calls for the skills of microbiologists to execute the work that holds the potential to improve the quality of human life. Without a profound grasp of microbiology, much of biotechnology is not possible. As a future pillar of the industrial base in the United States, biotechnology offers many chances for microbiologists to contribute in substantive ways to the future of the world.

Antibiotic discovery is also closely tied to the skills of microbiologists. The importance of this field cannot be overstated, since most individuals in developed countries have experienced first-hand the life-saving power of antibiotic therapies. However, the threat of microbial resistance to antibiotics looms large.

Scientific discoveries can be put into action more rapidly through greater collaborations between academia and industry. By cooperating to develop concepts and inquiries, microbiologists and industrial decision-makers can bring technologies to market or apply microbial solutions to persistent manufacturing problems. Efforts should be made to overcome regulatory and cultural obstacles that stand in the way of such collaborations.

Finally, increased emphasis on systems-level and quantitative research in microbiology has opened new doors for microbiologists working in interdisciplinary research teams or who have backgrounds in other disciplines. Individuals with experience in physics, mathematics, engineering, or computer sciences are in high demand in microbiology today, and this will likely continue for the foreseeable future.

INDUSTRIAL SUSTAINABILITY

As planet resources become more scarce, and environmental awareness is translated into a widespread social demand, industry is bound to reformulate many of its traditional chemically-catalyzed processes into more environmentally-friendly alternatives and products. Every prospective study (for instance the OECD reports “Biotechnology for a Clean Environment” and “The Application of Biotechnology to Industrial Sustainability”) predicts the booming of a new multi-billion dollar market around processes and goods originating in biocatalysis, both for biosynthesis of added-value molecules or for biodegradation and pollutant removal.

The emerging interfaces between chemical engineering and microbial genetics/metabolism will create countless job opportunities for those who seize the right training early enough in the process. The fields of large-scale mining and metallurgy, so far limited to hard-core engineering, will soon benefit from ongoing advances in geomicrobiology, and experts in this field soon will be in great demand. The relatively new field of green chemistry will, thus, offer employment perspectives for microbiologists and present a chance for scientists to work at the forefront of developing sustainable technologies.

NATIONAL DEFENSE

Growing concern about biological security promises to create a number of employment and research opportunities for microbiologists. Bioterrorism has defined a need, in this country and elsewhere, for new and improved infrastructures to address issues related to national security. Microbial science is key to proper execution of these new security measures. The opportunities are diverse; establishment of research centers related to bioterrorism, development of secure culture collections, vaccine development, database development, and other activities will all require the contributions of microbiologists. It is important to note that, with respect to biological security, global preparation requires global knowledge. It is critical for science to protect the freedom to exchange information on the biological agents of disease.

• Training to Meet the Needs and Challenges of the Future

The training of tomorrow's microbiologists is taking place in fourth grade classrooms, in high school biology labs, and in the lecture halls of universities all over the world. Although the educational systems of past and present have produced the great minds of microbiology, improvements need to be made if microbiology is to fulfill its potential in the new century.

Given the central importance of microbial science to biology in general, teaching of microbiology should be thoroughly integrated into school curricula. At the undergraduate level, emphasis needs to be placed on textbook revision and on integrating microbial sciences into the basic coursework for biology.

Microbiology Education in Schools

As both the root of the tree of life and the matrix that supports the biosphere, microbes should take center stage in science curricula at the elementary, middle, and high school levels. If we are to achieve a well-educated public, versed in the fundamentals of biology and capable of tackling the demands of the new century, the importance of microbiology must be acknowledged by teachers and policy-makers and translated into meaningful school lessons. In practice, this means that microbiology should be integrated into all phases of biology education, not segregated as separate coursework or, as is often the case, as a few sessions at the beginning of a biology course. Achieving integration of microbiology in school curricula will require that educational decision-makers understand and acknowledge the magnitude of microbial contributions to life on earth.

Reorienting school curricula begins with changes in biology textbooks. General biology texts should be organized around a microbiology core. In this way, studying micro-biology can enrich the study of plants, insects, and animals. For example, explaining the importance of microbial gut flora to termites would lend depth and greater applicability to the simple lesson that “termites eat wood.” The food chain in the ocean does not start out by small fish being eaten by big fish, but by microbial populations providing the bulk of the organic material required to set the chain in motion. The oxygen we breathe is not made just by plant photosynthesis, but, to an even greater extent, by the activities of microbes.

More specialized books can also be developed to address the “Grand Challenge” questions, those issues that continue to inspire and confound biologists. Such texts can serve to illustrate the latest discoveries, technologies, and the future of inquiry in microbiology.

Changing the textbooks that schools use has, in the past, proven to be an arduous, protracted process. But, educating the public, beginning with young people, about the importance of microbiology in day-to-day life and in the future of industry is more than a worthy goal—it is an imperative.

Games could also be used for injecting microbiology into curricula. Through creative games or video games based on microbial themes like natural selection, teachers can bring the lessons and fascination of microbiology to students in a friendly, hands-on way. Biology education can be made more engaging with microbial demonstrations and hands-on microbiology lab exercises, which are inexpensive and accessible to a wide range of classroom budgets. Centering lab experiments around simple illustrations of microbial phenomena like decomposition or growth would circumvent both the tedium associated with rote memorization of science lessons and the “gross-out factor” involved, e.g., with frog dissection. Placing a microscope and a sleeve of Petri dishes in every classroom would go a long way toward engaging students in microbiology and in the scientific exploration of the world around them. Some of these activities have already been developed, and more should be created.

Better visual aids are also needed in science classrooms; children would find micrographs of elegant and grotesque microbes appealing, for example. One successful demonstration of the power of microbial illustrations in education can be found on the website for the Marine Biological Laboratory at http://microscope.mbl.edu . A powerful resource for teachers is http://microbeworld.org , sponsored, in part, by the American Society for Microbiology.

In high school biology, in particular, microbiology needs to be taught in an appealing, captivating manner. Many current teachers need to be retrained in the technology and theory associated with the modern microbial science.

Training at the Undergraduate Level

At the undergraduate level, microbiology education takes on two different aspects: training future microbiologists and training biologists in other fields. With respect to training the microbiologists of tomorrow, efforts need to be directed toward revising textbooks to reflect new knowledge on the global importance of microbes and toward overcoming the emphasis on memorization that may still plague some microbiology coursework.

It is clear that all life scientists should receive microbiology training as part of their core curriculum. The topics of microbial physiology, evolution, biochemistry, and genetics should all be worked into the curriculum of undergraduate life sciences students. Luckily, there are many opportunities to introduce appropriate microbiology coursework into the curricula of other disciplines. Organic chemistry courses, for example, which are required for almost all biology students, would benefit from examples taken from microbiology and green chemistry to demonstrate the synthesis of complex compounds from simple precursors. Even students in fields outside of the life sciences would benefit from lessons in microbiology, perhaps presented in biology exploration courses for non-majors as a “microbes and you” segment.

In addition to changes in curricula, improvements are needed at the departmental and college levels as well. In many universities, microbiology is treated strictly as a field of specialization, not as a core subject. Given the fundamental significance of microbial sciences, there should be recognition of the importance of a having a critical mass of microbial sciences faculty. Such faculty need not necessarily be housed in microbiology departments. Appointments of microbiologists are highly desirable in departments of geology, chemistry, clinical medicine, engineering, and even history. These faculty can cross traditional departmental barriers to interact across many fields, effectively educating and training the next generation of scientists.

Promoting Microbial Literacy

Review the facts: microbes were the first life forms, they are important determinants of human health, and they carry out the processes that ensure clean drinking water and fertile soil. They are the most genetically and biochemically diverse forms of life and are the most rapidly evolving organisms on the planet. Microbes govern environmental cycling of the world's nutrients and the substances necessary for life. In every crevice and on every surface, from the deep earth's crust to steaming sulfurous plumes, to the gut of every insect on the planet, microbes are there. They are a key component of all biological systems. In light of these truths, it is readily apparent that microbiologists must make an effort to educate both the public and policy-makers. However, it is less obvious which messages should be conveyed and how best to communicate these facts.

Public Literacy

There is a serious gulf between the excitement experienced by those working in microbiology and the level of awareness in the general public. However, there is evidence to indicate that increased levels of support for public literacy on major public health issues like HIV-AIDS, West Nile disease, and SARS, influences college student choices of majors and research projects. In other words, increased public literacy may help guide students into fields where their energies are most needed. Moreover, public opinion can be guided by an increased awareness of the unsolved problems in microbiology and thus influence leaders to dedicate resources to areas of need. Hence, training programs that are designed to address the grand problems of microbiology should include outreach programs that foster public and governmental awareness.

What is the best way to educate the public about micro-biology? Mechanisms for informing the public about successes in microbiology and about pressing public health issues are sorely needed.

COMMUNICATING THE ISSUES

In conveying information about microbiology to the public, it is critical first to define the target audiences and the type of information that is appropriate to convey to each audience. Potential target audiences for microbio-logical outreach comprise a long list, including business leaders, students and teachers at all levels, public officials, health professionals (who may not be sufficiently familiar with microbiology), farmers, restaurant personnel, decision-makers at federal agencies, and others.

In order to achieve the most effective outreach programs, the process of educating the public should have well-defined goals. Specific outreach programs should be conceived with specific educational goals in mind that can be implemented over a designated time period. This approach would allow targeted assessments to determine whether outreach programs were effective in communicating microbiology to the public. For example, it could be the goal of one program to educate the public on a particular microbiology topic within five to ten years, and surveys or other metrics could be used to measure the level of knowledge of the target audience.

• The intimate connections between microbial ecology and evolution, infectious disease, and the failure of standard antimicrobial therapies.
• Microbial diversity as one of the last uncharted frontiers with tremendous potential for fundamental new discoveries.
• Microbes as the foundation of the biosphere.
• The concept that the human body is nine parts microbe and one part human—for every nine microbial cells there is just one human cell.
• The tree of life and the relative placements of plants, animals, and microbes.
• The development and use of microbes as factories.

AVENUES OF COMMUNICATION

What are the best ways to convey science information to non-scientists? A number of avenues are open for outreach. For example, it may be possible to launch a campaign to present science information to the people who use public transportation: buses, trains, taxis, or in airports. The publication of popular books based on microbiological themes would also reach a significance audience. Science museums are a powerful outlet for educating young people, and interactive microbial exhibits could stimulate the minds of many future scientists in an engaging way. The mass media may also be employed. Some of these programs are already in place. For example, radio programs, like the American Society for Microbiology's “Microbe World” are well received and are proving to be highly effective.

It may be instructive to study in a systematic manner the quality of material related to microbiology that is currently being used for communication to the public. It is possible that the current lack of public savvy is due to the poor quality of information available, rather than to low availability.

Improving delivery of knowledge to the public requires engaging and informing communication professionals. Microbiological organizations should place a priority on reaching out to communication professionals and should aid in training of science writers.

Communicating with Decision-Makers

With respect to advancing the goals outlined in this report, the term “decision-makers” includes federal agencies, such as the National Science Foundation, National Institutes of Health, Environmental Protection Agency, Department of Energy, the Centers for Disease Control and Prevention, and the Department of Agriculture. Others include local and state boards of education, the Department of Homeland Security, the Food and Drug Administration, private foundations, and others.

Informed individuals who are affected by advancements in microbial science, but are not microbiologists themselves, may be among the best advocates for microbiology. Examples include representatives of biotechnology companies and their clients, business leaders who rely on the skills of highly-trained microbiologists, members of communities where property was remediated using microbes, and the beneficiaries of microbially-based therapies, including bacterially-derived antibiotics and other drugs.

The communications goals outlined in this report would be pursued most effectively by a consortium of professional societies, possibly including the American Society for Microbiology, the Society for Industrial Microbiology, the Infectious Diseases Society of America, and others.

Recommendations

Failure to acknowledge and weigh the pervasive effects of the microbial world deprives us of a powerful tool to assess the functioning of our planet and make decisions on its future as a live whole. In light of what is now known about the contributions of microorganisms to sustaining life and creating the physical and chemical properties of this planet, detailed studies in any branch of biology or geology must fully recognize the activities of microbes.

Since microbes are of fundamental importance to life and their activities must be taken into account in biology research, all biologists must have a firm background in microbial science. Coursework in micro-biology should be integrated into the core curriculum for all students in the life and earth sciences.

Building an understanding of microbes in young students will ultimately improve public awareness of the importance of microbes to the everyday health of the individual and of the planet. School science curricula in the elementary, middle, and high school levels must be amended to include lessons and lab exercises in microbiology.

The public is profoundly impacted by microbes and microbiology through disease-related matters, biotechnology, bioterrorism, and food safety. In order to improve the ability of individuals to manage their health and make informed judgments with respect to microbial science, microbiology-related professional societies should support programs that foster public microbial literacy.

• Suggested reading
• Beja, O., L. Aravind, E. V. Koonin, M. T. Suzuki, A. Hadd, L. P. Nguyen, S. B. Jovanovich, C. M. Gates, R. A. Feldman, J. L. Spudich, E. N. Spudich, and E. F. DeLong. 2000. Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science 289:1902–1906. http://www ​.ncbi.nlm.nih ​.gov/entrez/query ​.fcgi?cmd=Retrieve&db ​=PubMed&list_uids ​=10988064&dopt ​=Abstract . [ PubMed : 10988064 ]
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• Cite this Page Microbiology in the 21st Century: Where Are We and Where Are We Going? This report is based on a colloquium sponsored by the American Academy of Microbiology held September 5–7, 2003, in Charleston, South Carolina. Washington (DC): American Society for Microbiology; 2004. doi: 10.1128/AAMCol.5Sept.2003
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Researchers Find E-Cigarette Use Disrupts Nasal Microbiome

August 23, 2024

By Kendall Daniels

The nose plays more roles that just allowing us to smell and shaping our facial profiles. It also acts as a gatekeeper for the respiratory tract, capable of preventing bacteria and other pathogens from leaving the nasal passage and taking residence in the lungs.  

Similar to the microbiome in the gastrointestinal tract and the skin, the precious balance between beneficial bacterial, fungal, and viral colonies in the nose can be disrupted. This imbalance, termed dysbiosis, can lead to an overgrowth of harmful bacteria and predispose people to respiratory diseases, such as chronic obstructive pulmonary disease and asthma.  

Elise Hickman, PhD, a former student in the lab of inhalation toxicologist Ilona Jaspers, PhD , director of the UNC Center for Environmental Medicine, Asthma, and Lung Biology at the UNC School of Medicine, discovered that e-cigarette and cigarette use can cause an imbalance in the nasal microbiome. Their research, published in Nicotine & Tobacco Research , could be important in understanding the immunological implications of vaping and smoking.  

“We found that the composition of the nasal microbiome varies depending on sex, e-cigarette versus cigarette use, and how much of a nicotine biomarker is found in the blood,” said Hickman, who is now a postdoctoral researcher at the Department of E nvironmental Sciences and Engineering at the UNC Gillings School of Public Health . “Our findings warrant further investigation into why and how e-cigarette use dysregulates the immune system in the nasal microbiome and causes imbalance in the respiratory microbiome.”  

The Jaspers lab’s previous research showed that e-cigarette use can affect the daily operations of the immune system in the nose and make one more susceptible to viral infections like influenza. Knowing that the respiratory microbiome supports respiratory immune defense, Hickman and Jaspers wanted to know if dysbiosis in the nasal microbiome, which is often related to lower airway disease, could be caused by e-cigarette or cigarette use.  

Teaming up with Matt Wolfgang, PhD , and Cristian Roca from the Marsico Lung Institute/UNC Cystic Fibrosis Center , Hickman and Jaspers collected and analyzed nasal epithelial lining fluid samples from 20 non-smokers, 28 e-cigarette users, and 19 smokers. They then used genetic sequencing to identify the type and quantity of bacteria in the nasal microbiome.  

Researchers identified different bacteria, some harmful and some protective, depending on whether people used e-cigarettes, smoked regular cigarettes, or neither. Staphylococcus aureus , a bacterium that can cause pneumonia and other life-threatening infections, was found in greater number in both e-cigarette users and smokers compared to non-smokers. Lactobacillus iners – a beneficial bacterium that can protect against respiratory disease – was found more often in smokers than non-smokers.  

Surprisingly, researchers found that there were differences in the microbiomes of male and female e-cigarette users. Hickman and Jaspers also found that there were differences in nasal bacteria between people who had high and low levels of cotinine, a metabolite and indicator of nicotine exposure.  

“Taken together, our data identified unique, sex-dependent host immune dysfunction associated with e-cigarette use in the nasal mucosa,” said Jaspers, who is also a UNC Lineberger Comprehensive Cancer Center member researching inhaled toxicants and their effects on the respiratory mucosa.  

This research adds to the increasing number of studies demonstrating respiratory health effects associated with e-cigarette use. Considering that there is a growing body of research showing that changes in the nasal microbiome can be related to lung disease and health, dysbiosis in the balance of harmful and protective bacteria in the nose of e-cigarette users should be of concern.   

Media contact:  Kendall Daniels , Communications Specialist, UNC Health | UNC School of Medicine  

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Collection  10 March 2022

Top 100 in Microbiology

This collection highlights our most downloaded* microbiology papers published in 2021. Featuring authors from around the world, these papers showcase valuable research from an international community.

*Data obtained from SN Inights, which is based on Digital Science's Dimensions.

The in-vitro effect of famotidine on SARS-CoV-2 proteases and virus replication

• Madeline Loffredo
• Hector Lucero
• Ali H. Munawar

In vitro efficacy of artemisinin-based treatments against SARS-CoV-2

• Yuyong Zhou
• Kerry Gilmore
• Peter H. Seeberger

Identification of CRF89_BF, a new member of an HIV-1 circulating BF intersubtype recombinant form family widely spread in South America

• Elena Delgado
• Aurora Fernández-García
• Michael M. Thomson

The effectiveness of various gargle formulations and salt water against SARS-CoV-2

• Vunjia Tiong
• Pouya Hassandarvish
• Ilina Isahak

The serotonin reuptake inhibitor Fluoxetine inhibits SARS-CoV-2 in human lung tissue

• Melissa Zimniak
• Luisa Kirschner
• Jochen Bodem

Probenecid inhibits SARS-CoV-2 replication in vivo and in vitro

• Jackelyn Murray
• Robert J. Hogan
• Ralph A. Tripp

UV-C irradiation is highly effective in inactivating SARS-CoV-2 replication

• Mara Biasin
• Andrea Bianco
• Mario Clerici

Diagnostic performance of rapid antigen tests (RATs) for SARS-CoV-2 and their efficacy in monitoring the infectiousness of COVID-19 patients

• John G. Routsias
• Maria Mavrouli
• Athanasios Tsakris

Epidemiology and outcomes of COVID-19 in HIV-infected individuals: a systematic review and meta-analysis

• Paddy Ssentongo
• Emily S. Heilbrunn

Temporal dynamics of viral load and false negative rate influence the levels of testing necessary to combat COVID-19 spread

• Katherine F. Jarvis
• Joshua B. Kelley

Nasopharyngeal SARS-CoV-2 viral loads in young children do not differ significantly from those in older children and adults

• Sharline Madera
• Emily Crawford
• Joseph L. DeRisi

Morphometry of SARS-CoV and SARS-CoV-2 particles in ultrathin plastic sections of infected Vero cell cultures

• Michael Laue
• Anne Kauter
• Andreas Nitsche

Glycan reactive anti-HIV-1 antibodies bind the SARS-CoV-2 spike protein but do not block viral entry

• Dhiraj Mannar
• Karoline Leopold
• Sriram Subramaniam

The Spanish gut microbiome reveals links between microorganisms and Mediterranean diet

• Adriel Latorre-Pérez
• Marta Hernández
• Luis Collado

In vitro inactivation of SARS-CoV-2 by commonly used disinfection products and methods

Methylene Blue has a potent antiviral activity against SARS-CoV-2 and H1N1 influenza virus in the absence of UV-activation in vitro

• Valeria Cagno
• Chiara Medaglia
• Caroline Tapparel

A novel highly quantitative and reproducible assay for the detection of anti-SARS-CoV-2 IgG and IgM antibodies

• Kouki Matsuda
• Akinobu Hamada

Colorimetric RT-LAMP SARS-CoV-2 diagnostic sensitivity relies on color interpretation and viral load

• Mateus Nóbrega Aoki
• Bruna de Oliveira Coelho
• Lucas Blanes

Field-deployable, rapid diagnostic testing of saliva for SARS-CoV-2

• Hemant Suryawanshi
• Zev Williams

No evidence for basigin/CD147 as a direct SARS-CoV-2 spike binding receptor

• Jarrod Shilts
• Thomas W. M. Crozier
• Gavin J. Wright

Carvacrol exhibits rapid bactericidal activity against Streptococcus pyogenes through cell membrane damage

• Niluni M. Wijesundara
• Song F. Lee
• H. P. Vasantha Rupasinghe

In silico analysis of epitope-based vaccine candidate against tuberculosis using reverse vaccinology

• Shaheen Bibi
• Inayat Ullah
• Shiquan Niu

Antiviral activity of lambda-carrageenan against influenza viruses and severe acute respiratory syndrome coronavirus 2

• Heegwon Shin
• Meehyein Kim

Nicotinamide mononucleotide production by fructophilic lactic acid bacteria

• Kazane Sugiyama
• Kana Iijima
• Nobuyuki Yoshida

Molecular features similarities between SARS-CoV-2, SARS, MERS and key human genes could favour the viral infections and trigger collateral effects

• Lucas L. Maldonado
• Andrea Mendoza Bertelli
• Laura Kamenetzky

Silicon nitride: a potent solid-state bioceramic inactivator of ssRNA viruses

• Giuseppe Pezzotti
• Francesco Boschetto

The meta-gut: community coalescence of animal gut and environmental microbiomes

• Christopher L. Dutton
• Amanda L. Subalusky
• David M. Post

Ingestion of probiotic ( Lactobacillus helveticus and Bifidobacterium longum ) alters intestinal microbial structure and behavioral expression following social defeat stress

• Katherine A. Partrick
• Anna M. Rosenhauer
• Kim L. Huhman

Direct diagnostic testing of SARS-CoV-2 without the need for prior RNA extraction

• Esther Kohl

Solar UV-B/A radiation is highly effective in inactivating SARS-CoV-2

• Fabrizio Nicastro
• Giorgia Sironi

High prevalence of antibiotic resistance in commensal Escherichia coli from healthy human sources in community settings

• Emmanuel Nji
• Joseph Kazibwe
• La Thi Quynh Lien

Pupal cannibalism by worker honey bees contributes to the spread of deformed wing virus

• Francisco Posada-Florez
• Zachary S. Lamas
• Eugene V. Ryabov

Network analysis of Down syndrome and SARS-CoV-2 identifies risk and protective factors for COVID-19

• Ilario De Toma
• Mara Dierssen

MRC5 cells engineered to express ACE2 serve as a model system for the discovery of antivirals targeting SARS-CoV-2

• Kentaro Uemura
• Michihito Sasaki
• Akihiko Sato

A descriptive analysis of antimicrobial resistance patterns of WHO priority pathogens isolated in children from a tertiary care hospital in India

• Vijayalaxmi V. Mogasale
• Prakash Saldanha
• Vittal Mogasale

Metagenomic identification of a new sarbecovirus from horseshoe bats in Europe

• Jack M. Crook
• Ivana Murphy

Comprehensive study of antimicrobial susceptibility pattern and extended spectrum beta-lactamase (ESBL) prevalence in bacteria isolated from urine samples

• Mohammad Javad Gharavi
• Javad Zarei
• Niloufar Rashidi

A PCR amplicon-based SARS-CoV-2 replicon for antiviral evaluation

• Tomohiro Kotaki
• Masanori Kameoka

An inter-laboratory study to investigate the impact of the bioinformatics component on microbiome analysis using mock communities

• Denise M. O’Sullivan
• Ronan M. Doyle
• Jim F. Huggett

Microplastics accumulate fungal pathogens in terrestrial ecosystems

• Gerasimos Gkoutselis
• Stephan Rohrbach
• Gerhard Rambold

The lower respiratory tract microbiome of critically ill patients with COVID-19

• Paolo Gaibani
• Elisa Viciani
• Simone Ambretti

Functional profiling of COVID-19 respiratory tract microbiomes

• Niina Haiminen
• Filippo Utro
• Laxmi Parida

The rhizosphere microbiome plays a role in the resistance to soil-borne pathogens and nutrient uptake of strawberry cultivars under field conditions

• Cristina Lazcano
• Kelly Ivors

Comparative evaluation of 19 reverse transcription loop-mediated isothermal amplification assays for detection of SARS-CoV-2

• Yajuan Dong
• Chiyu Zhang

Respiratory viral co-infections among SARS-CoV-2 cases confirmed by virome capture sequencing

• Ki Wook Kim
• Ira W. Deveson
• William D. Rawlinson

UVC disinfects SARS-CoV-2 by induction of viral genome damage without apparent effects on viral morphology and proteins

• Chieh-Wen Lo
• Ryosuke Matsuura

Co-infection of SARS-CoV-2 and influenza virus causes more severe and prolonged pneumonia in hamsters

• Takaaki Kinoshita
• Kenichi Watanabe
• Jiro Yasuda

Identification of ebselen and its analogues as potent covalent inhibitors of papain-like protease from SARS-CoV-2

• Ewelina Weglarz-Tomczak
• Jakub M. Tomczak
• Stanley Brul

Neurotropic influenza A virus infection causes prion protein misfolding into infectious prions in neuroblastoma cells

• Hideyuki Hara
• Junji Chida
• Suehiro Sakaguchi

The Edible Plant Microbiome represents a diverse genetic reservoir with functional potential in the human host

• Maria J. Soto-Giron
• Gerardo Toledo

Blockade of SARS-CoV-2 spike protein-mediated cell–cell fusion using COVID-19 convalescent plasma

Dynamics of SARS-CoV-2 mutations reveals regional-specificity and similar trends of N501 and high-frequency mutation N501Y in different levels of control measures

• Santiago Justo Arevalo
• Daniela Zapata Sifuentes
• Roberto Pineda Chavarría

Lactobacillus reuteri AN417 cell-free culture supernatant as a novel antibacterial agent targeting oral pathogenic bacteria

• Kyung Mi Yang
• Kwang-Hak Bae

CRISPR-based transcriptional activation tool for silent genes in filamentous fungi

• László Mózsik
• Mirthe Hoekzema
• Arnold J. M. Driessen

An immortalized porcine macrophage cell line competent for the isolation of African swine fever virus

• Kentaro Masujin
• Tomoya Kitamura
• Takehiro Kokuho

The potential of COVID-19 patients’ sera to cause antibody-dependent enhancement of infection and IL-6 production

• Jun Shimizu
• Tadahiro Sasaki
• Tatsuo Shioda

Digital PCR for high sensitivity viral detection in false-negative SARS-CoV-2 patients

• Paolo Poggio
• Paola Songia
• Maurizio Pesce

Natural variants in SARS-CoV-2 Spike protein pinpoint structural and functional hotspots with implications for prophylaxis and therapeutic strategies

• Suman Pokhrel
• Benjamin R. Kraemer
• Daria Mochly-Rosen

Asymptomatic COVID-19 Adult Outpatients identified as Significant Viable SARS-CoV-2 Shedders

• Marie Glenet
• Anne-Laure Lebreil
• Laurent Andreoletti

Bacterial associations in the healthy human gut microbiome across populations

• Mark Loftus
• Sayf Al-Deen Hassouneh
• Shibu Yooseph

Analysis and forecasting of global real time RT-PCR primers and probes for SARS-CoV-2

• Gowri Nayar
• Edward E. Seabolt
• James H. Kaufman

Antibiotic-resistant bacteria and gut microbiome communities associated with wild-caught shrimp from the United States versus imported farm-raised retail shrimp

• Laxmi Sharma
• Ravinder Nagpal
• Prashant Singh

Emergence of novel SARS-CoV-2 variants in the Netherlands

• Aysun Urhan
• Thomas Abeel

Induction of interferon response by high viral loads at early stage infection may protect against severe outcomes in COVID-19 patients

• Eric C. Rouchka
• Julia H. Chariker
• Donghoon Chung

Early life dietary intervention in dairy calves results in a long-term reduction in methane emissions

• S. J. Meale
• D. P. Morgavi

The relationships between microbiota and the amino acids and organic acids in commercial vegetable pickle fermented in rice-bran beds

• Kazunori Sawada
• Hitoshi Koyano
• Takuji Yamada

Response of bacterial and fungal communities to high petroleum pollution in different soils

• Polina Galitskaya
• Liliya Biktasheva
• Svetlana Selivanovskaya

A streamlined clinical metagenomic sequencing protocol for rapid pathogen identification

• Xiaofang Jia
• Xiaonan Zhang

Sensitive detection and quantification of SARS-CoV-2 in saliva

• Mustafa Fatih Abasiyanik
• Blake Flood
• Evgeny Izumchenko

Whole genome sequencing of clinical samples reveals extensively drug resistant tuberculosis (XDR TB) strains from the Beijing lineage in Nigeria, West Africa

• Idowu B. Olawoye
• Jessica N. Uwanibe
• Christian T. Happi

The SARS-CoV-2 viral load in COVID-19 patients is lower on face mask filters than on nasopharyngeal swabs

• Agnieszka Smolinska
• David S. Jessop
• Marc P. van der Schee

Metagenomics analysis of bacteriophages and antimicrobial resistance from global urban sewage

• Josephine E. S. Strange
• Pimlapas Leekitcharoenphon
• Frank M. Aarestrup

Limited intestinal inflammation despite diarrhea, fecal viral RNA and SARS-CoV-2-specific IgA in patients with acute COVID-19

• Graham J. Britton
• Alice Chen-Liaw
• Jeremiah J. Faith

Genomic evolution of antimicrobial resistance in Escherichia coli

• Markus Hans Kristofer Johansson

Outer membrane vesicles containing OmpA induce mitochondrial fragmentation to promote pathogenesis of Acinetobacter baumannii

• Varnesh Tiku
• Eric M. Kofoed
• Man-Wah Tan

Meta-analysis of host transcriptional responses to SARS-CoV-2 infection reveals their manifestation in human tumors

• Fengju Chen
• Yiqun Zhang
• Chad J. Creighton

Detection of extended spectrum beta-lactamase genes in Pseudomonas aeruginosa isolated from patients in rural Eastern Cape Province, South Africa

• Mojisola C. Hosu
• Sandeep D. Vasaikar
• Teke Apalata

Production of bacterial cellulose using Gluconacetobacter kombuchae immobilized on Luffa aegyptiaca support

• Sameeha Syed Abdul Rahman
• T. Vaishnavi
• Sugumaran Karuppiah

An efficient direct screening system for microorganisms that activate plant immune responses based on plant–microbe interactions using cultured plant cells

• Mari Kurokawa
• Masataka Nakano
• Toshiki Furuya

Glucose confers protection to Escherichia coli against contact killing by Vibrio cholerae

• Cristian V. Crisan
• Holly L. Nichols
• Brian K. Hammer

Neutral evolution test of the spike protein of SARS-CoV-2 and its implications in the binding to ACE2

• Georgina I. López-Cortés
• Miryam Palacios-Pérez
• Marco V. José

Bispecific repurposed medicines targeting the viral and immunological arms of COVID-19

• Martin A. Redhead
• C. David Owen
• Martin A. Walsh

Assessing the efficacy of eDNA metabarcoding for measuring microbial biodiversity within forest ecosystems

• Zachary S. Ladin
• Barbra Ferrell
• K. Eric Wommack

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Current Research in Microbiology and Biotechnology (ISSN: 2320-2246)

Publisher AIZEON Publishers

ISSN-L 2320-2246

ISSN 2320-2246

IF(Impact Factor) 2024 Evaluation Pending

Website http://crmb.aizeonpublishers.net/

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Last modified: 2013-03-20 15:20:07

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