DOCSLIB.ORG

The Human Microbiome: Implications for Health and Disease, Including HIV Infection

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
The Human Microbiome: Implications for Health and Disease, Including HIV Infection HIV and the Microbiome Volume 26 Issue 3 September 2018 Perspective The Human Microbiome: Implications for Health and Disease, Including HIV Infection Our increased understanding of the human microbiome has brought insight The National Institutes of Health into the role it plays in health and disease, including HIV infection. Studies Human Microbiome Project has pro- have shown that the gut microbiome is less diverse in individuals with HIV duced a number of insights regarding infection than in noninfected control subjects. Efforts to modify the micro- the microbiome over the past 15 years, biome to bolster immune reconstitution in people with HIV infection have so beginning with the recognition that far been unsuccessful. The vaginal microbiome affects risk of HIV acquisition, each individual is not a single ecosys- with Lactobacillus dominance being protective compared with vaginosis tem but numerous ecosystems with characterized by larger populations of Gardnerella. The vaginal microbiome differences among body sites. Further, might also affect efficacy of topical tenofovir disoproxil fumarate preexposure whereas OTUs in the GI tract are very prophylaxis. This article summarizes a presentation by Robert T. Schooley, different from OTUs in the oral cavity MD, at the IAS–USA continuing education program held in San Francisco in a given individual, OTUs from these sites resemble each other across indi- in May 2018. viduals. In addition, in a given individ- Keywords: microbiome, HIV, gut, vaginal, Lactobacillus, Gardnerella ual, the microbial diversity at particular sites changes over time, although the difference in this regard is not as great The human microbiome is the collec- greater than 97% DNA sequence com- as the difference between individuals tion of organisms that lives in and on monality in the rRNA gene. This group- at a given site. us. They live on the skin, in the gas- ing may or may not reflect what has With regard to the gut microbiome trointestinal (GI) tract, and on virtually been traditionally considered a species in particular, we have identified a num- every other surface of the body. Each of microorganism. Diversity in microbial ber of key characteristics that affect human is composed of approximately communities is described by the metrics health and disease. (1) The microbi- 37 trillion cells and we carry some 100 of richness (number of OTUs), evenness ome is established in early life and dif- trillion microbiologic organisms. Our (relative abundance of different OTUs), fers between infants born by cesarean increasing knowledge of the microbi- dominance (emergence of a single OTU), delivery and by vaginal birth. (2) In ome has been made possible through and diversity index (calculated index of murine models, transfer of an “obese” use of metagenomics and the decreas- complexity based on richness and even- microbiome from obese adult animals 1 to a sterile infant mouse affects the ing costs of genetic sequencing, obviat- ness). Antibiotic treatment narrows the ing the need to grow microorganisms growth characteristics of the mouse for in culture for identification purposes. Table. Terms Describing Diversity in life. (3) The microbiome is drastically 1 The best handle we have on under- Microbial Communities. altered acutely by antibiotic adminis- standing the microbiome is 16s ribo- tration. (4) In farm animals (and mice), Term Definition somal RNA (rRNA). Every microbe has antibiotic exposure early in life pro- this region of RNA, including portions Richness Number of OTUs motes microbiota associated with high that are conserved across all of our caloric efficiency. (5) There is some evi- Evenness Relative abundance of OTUs microbiota, because it is the common dence that early exposure to antibiotics feature that allows organisms to trans- Dominance Emergence of single OTU affects humans the same way. (6) After late messenger RNA into protein. Am- cessation of antibiotics, the antibiotic Diversity Index Calculated index of complexity “footprint” remains—ie, the microbi- plification of variable regions permits based on richness and evenness identification of organisms by families ome reverts toward but does not reach Abbreviation: OTU is operational taxonomic pre-antibiotic richness and diversity for and phyla, for example, by evaluating units. relationships among sequences. a prolonged period. A number of concepts have evolved rich microbiome (rich diversity of OTUs) The 4 major phyla in the gut micro- to characterize microbial communities. in the human gut. Conditions such as biome are: firmicutes—Gram-positive One is the operational taxonomic unit obesity and inflammatory bowel dis- organisms (eg, Staphylococcus, Micro- (OTU), a group of organisms that share ease are characterized by low diversity, coccus, Streptococcus, and Lacto- whereas bacterial vaginosis is charac- bacillus), including sporulating Gram- Dr Schooley is Professor and Vice Chair of terized by an unhealthy high diversity positive rods; Bacteroidetes—3 large the Department of Medicine at University of in which lactobacilli that are dominant classes of Gram-negative, non-spore form- California San Diego. He is a member of the in the healthy vagina are replaced by ing, anaerobic or aerobic, rod-shaped Board of Directors of the IAS–USA. a wide variety of other organisms. bacteria (eg, Bacterioides); Actinobacteria 75 IAS–USA Topics in Antiviral Medicine ● No HIV infection inflammation. The recently reported 200 ● HIV infection Promaltia study, performed by Serrano- Villar and colleagues, evaluated whether 150 the gut microbiome could be altered in ● ● ● HIV infection to improve immune re- ● 3 ● constitution. In the placebo-controlled 100 ● ● ● ● ● ● study, patients with advanced HIV ● ● ● infection were randomly assigned to ● ● ● 50 receive treatment with a placebo (skim ● ● ● milk) or an immunonutrition mixture Number of Observed Species of prebiotics, probiotics, oligonutrients, ● 0 ● 0 100 200 300 400 500 600 700 800 900 1000 docosahexaenoic acid, eicosapentaenoic Number of Sequences acid, gamma linolenic acid, and amino acids for 48 weeks, each in combination with initial antiretroviral therapy. The Figure 1. Reduced richness of the gut microbiome with HIV infection compared with no HIV infection. Adapted from Mutlu et al.2 mixture represented a collation of sub- stances used in prior studies aimed at —primarily Gram-positive bacteria (in- Some of these differences may be producing changes in the microbiome. cluding those that are acid fast; eg, due to changes in the innate and adap- At 48 weeks, there were no significant Mycobacteria and Gardnerella); and pro- tive immune response at the level of differences in microbiome diversity teobacteria—primarily Gram-negative the gut, one of the first organs attacked between the treatment and placebo rods (eg, Escherichia coli, Salmonella). during acute HIV infection. Some dif- groups. Some enrichment of unclassi- The firmicutes, in particular, are highly ferences may reflect use of antibiotics fied bacteria from the Lachnospiraceae adept at metabolizing food to help us in individuals with HIV infection. Stud- and Victivallaceae families and deple- better absorb calories. ies that have attempted to evaluate tion of Blautia species were observed in the change in microbiome over time as the treatment group compared with the HIV infection progresses suggest that placebo group. No differences in inflam- Gut Microbiome in HIV Infection some of the organisms found more fre- matory markers were found between quently in HIV-infected microbiomes treatment and placebo groups, with An initial study investigating the gut are more associated with inflamma- no significant differences in changes microbiome in HIV infection performed tion and become enriched as immune in CD4+ or CD8+ cell counts being by Mutlu and colleagues demonstrated response declines. observed between groups over time. differences between individuals with The microbiome is important from Thus, the test of whether or not HIV and without HIV infection. The study the standpoint of maintenance of the immune reconstitution can be achieved involved 56 samples from individu- gut barrier. A considerable amount of by changing the microbiome has not als with HIV infection (mean CD4+ work has been done over the past really been documented, since the cell count of 425/µL; plasma HIV-1 RNA decade to ascertain whether trans- treatment in this study did not change level <75 copies/mL in 17 of 21 par- location of gut bacterial components the microbiome. There is more work to ticipants) and 65 samples from 22 across the GI tract have an impact on be done in this area. age- and sex-matched noninfected control participants undergoing elec- HIV infection No HIV infection tive colonoscopy (primarily for cancer 20 20 screening).2 The microbiome was found to be markedly less diverse in 15 15 individuals with HIV infection (Figure 1). In addition, the microbiomes of individuals with HIV infection and non- 10 10 infected control participants contained different bacterial species, with nonin- 5 5 fected control participants harboring Number of Participants significantly more Bacteroides (P = .0002) and Clostridiales-unclassified 0 0 (P = .002), and participants with HIV 0 1 2 3 0 1 2 3 infection harboring more Enterobac- Species Diversity (using the Shannon Diversity Index) teriaceae-unclassified (P = .0002) and Campylobacter (P = .0034), as well as Figure 2. Increased risk of HIV infection with greater vaginal bacterial diversity. Adapted from more fusobacteria
Load more

Recommended publications
  • Human Microbiome: Your Body Is an Ecosystem
    Human Microbiome: Your Body Is an Ecosystem This StepRead is based on an article provided by the American Museum of Natural History. What Is an Ecosystem? An ecosystem is a community of living things. The living things in an ecosystem interact with each other and with the non-living things around them. One example of an ecosystem is a forest. Every forest has a mix of living things, like plants and animals, and non-living things, like air, sunlight, rocks, and water. The mix of living and non-living things in each forest is unique. It is different from the mix of living and non-living things in any other ecosystem. You Are an Ecosystem The human body is also an ecosystem. There are trillions tiny organisms living in and on it. These organisms are known as microbes and include bacteria, viruses, and fungi. There are more of them living on just your skin right now than there are people on Earth. And there are a thousand times more than that in your gut! All the microbes in and on the human body form communities. The human body is an ecosystem. It is home to trillions of microbes. These communities are part of the ecosystem of the human Photo Credit: Gaby D’Alessandro/AMNH body. Together, all of these communities are known as the human microbiome. No two human microbiomes are the same. Because of this, you are a unique ecosystem. There is no other ecosystem like your body. Humans & Microbes Microbes have been around for more than 3.5 billion years.
    [Show full text]
  • Downloaded from 3
    Philips et al. BMC Genomics (2020) 21:402 https://doi.org/10.1186/s12864-020-06810-9 RESEARCH ARTICLE Open Access Analysis of oral microbiome from fossil human remains revealed the significant differences in virulence factors of modern and ancient Tannerella forsythia Anna Philips1, Ireneusz Stolarek1, Luiza Handschuh1, Katarzyna Nowis1, Anna Juras2, Dawid Trzciński2, Wioletta Nowaczewska3, Anna Wrzesińska4, Jan Potempa5,6 and Marek Figlerowicz1,7* Abstract Background: Recent advances in the next-generation sequencing (NGS) allowed the metagenomic analyses of DNA from many different environments and sources, including thousands of years old skeletal remains. It has been shown that most of the DNA extracted from ancient samples is microbial. There are several reports demonstrating that the considerable fraction of extracted DNA belonged to the bacteria accompanying the studied individuals before their death. Results: In this study we scanned 344 microbiomes from 1000- and 2000- year-old human teeth. The datasets originated from our previous studies on human ancient DNA (aDNA) and on microbial DNA accompanying human remains. We previously noticed that in many samples infection-related species have been identified, among them Tannerella forsythia, one of the most prevalent oral human pathogens. Samples containing sufficient amount of T. forsythia aDNA for a complete genome assembly were selected for thorough analyses. We confirmed that the T. forsythia-containing samples have higher amounts of the periodontitis-associated species than the control samples. Despites, other pathogens-derived aDNA was found in the tested samples it was too fragmented and damaged to allow any reasonable reconstruction of these bacteria genomes. The anthropological examination of ancient skulls from which the T.
    [Show full text]
  • The Human Gut Microbiota: a Dynamic Interplay with the Host from Birth to Senescence Settled During Childhood
    Review nature publishing group The human gut microbiota: a dynamic interplay with the host from birth to senescence settled during childhood Lorenza Putignani1, Federica Del Chierico2, Andrea Petrucca2,3, Pamela Vernocchi2,4 and Bruno Dallapiccola5 The microbiota “organ” is the central bioreactor of the gastroin- producing immunological memory (2). Indeed, the intestinal testinal tract, populated by a total of 1014 bacteria and charac- epithelium at the interface between microbiota and lymphoid terized by a genomic content (microbiome), which represents tissue plays a crucial role in the mucosa immune response more than 100 times the human genome. The microbiota (2). The IS ability to coevolve with the microbiota during the plays an important role in child health by acting as a barrier perinatal life allows the host and the microbiota to coexist in a against pathogens and their invasion with a highly dynamic relationship of mutual benefit, which consists in dispensing, in modality, exerting metabolic multistep functions and stimu- a highly coordinated way, specific immune responses toward lating the development of the host immune system, through the biomass of foreign antigens, and in discriminating false well-­organized programming, which influences all of the alarms triggered by benign antigens (2). The failure to obtain growth and aging processes. The advent of “omics” technolo- or maintain this complex homeostasis has a negative impact gies (genomics, proteomics, metabolomics), characterized by on the intestinal and systemic health (2). Once the balance complex technological platforms and advanced analytical and fails, the “disturbance” causes the disease, triggering an abnor- computational procedures, has opened new avenues to the mal inflammatory response as it happens, for example, for the knowledge of the gut microbiota ecosystem, clarifying some inflammatory bowel diseases in newborns (2).
    [Show full text]
  • Alteration of Salivary Microbiome in Periodontitis with Or Without Type-2 Diabetes Mellitus and Metformin Treatment
    www.nature.com/scientificreports OPEN Alteration of salivary microbiome in periodontitis with or without type‑2 diabetes mellitus and metformin treatment Xiaoyu Sun1,2,3, Meihui Li1,2, Li Xia4, Zhaohui Fang5, Shenjun Yu3, Jike Gao3, Qiang Feng1,2* & Pishan Yang1,6* We aimed to explore the efects of type‑2 diabetes mellitus (T2DM) and hypoglycemic therapy on the salivary microbiome in periodontitis patients and identify the potential salivary micro‑biomarker for the early warning of T2DM. Saliva samples were collected from healthy individuals (Health), periodontitis patients (P), T2DM patients, periodontitis patients with T2DM (DAP), and DAP patients treated with Metformin (Met). Samples were determined by16S rRNA gene sequencing. 29 phyla, 322 genera, and 333 species of salivary microbiome were annotated. Compared to the Health group, the P and DAP group showed a signifcantly higher diversity of saliva microbiota, while the T2DM and Met group had no signifcant diference in microbial abundance but showed a trend of increasing diversity. Other than well‑known periodontitis‑inducing pathogens, the proportion of Prevotella copri, Alloprevotella rava, and Ralstonia pickettii, etc. were also signifcantly increased in periodontitis patients with or without T2DM. After efective glycemic control, the abundance of Prevotella copri, Alloprevotella rava, Ralstonia pickettii, etc. decreased in periodontitis patients with companion T2DM. The accuracies of the classifcation models in diferentiating Health‑vs.‑P, DAP‑vs.‑P, and T2DM‑vs.‑P were 100%, 96.3%, and 98.1%, respectively. Hypoglycemic therapy could reconstruct the saliva microbiota and hence improve the localized conditions of diabetes patients with periodontitis. Periodontitis is one of the most frequent bacteria-induced infammatory diseases in the oral cavity.
    [Show full text]
  • Exploring the Connection Between Porphyromonas Gingivalis
    biomolecules Article Exploring the Connection between Porphyromonas gingivalis and Neurodegenerative Diseases: A Pilot Quantitative Study on the Bacterium Abundance in Oral Cavity and the Amount of Antibodies in Serum Raffaella Franciotti 1 , Pamela Pignatelli 2 , Claudia Carrarini 1, Federica Maria Romei 2, Martina Mastrippolito 2, Antonella Gentile 2, Rosa Mancinelli 1, Stefania Fulle 1 , Adriano Piattelli 2,3,4, Marco Onofrj 1 and Maria Cristina Curia 2,* 1 Department of Neuroscience, Imaging and Clinical Sciences, “G. d’Annunzio” University of Chieti-Pescara, 66013 Chieti, Italy; [email protected] (R.F.); [email protected] (C.C.); [email protected] (R.M.); [email protected] (S.F.); [email protected] (M.O.) 2 Department of Medical, Oral and Biotechnological Sciences, “G. d’Annunzio” University of Chieti-Pescara, 66013 Chieti, Italy; [email protected] (P.P.); [email protected] (F.M.R.); [email protected] (M.M.); [email protected] (A.G.); [email protected] (A.P.) 3 Fondazione Villa Serena per la Ricerca, Città S. Angelo, 65013 Pescara, Italy 4 Casa di Cura “Villa Serena” del Dott. L. Petruzzi, Città S. Angelo, 65013 Pescara, Italy * Correspondence: [email protected] Citation: Franciotti, R.; Pignatelli, P.; Abstract: Recent studies support the hypothesis that microbes can seed some Alzheimer’s disease Carrarini, C.; Romei, F.M.; Mastrippolito, M.; Gentile, A.; (AD) cases, leading to inflammation and overproduction of amyloid peptides. Porphyromonas gin- Mancinelli, R.; Fulle, S.; Piattelli, A.; givalis (Pg) is a keystone pathogen of chronic periodontitis and has been identified as risk factor Onofrj, M.; et al.
    [Show full text]
  • Bacteria Evolving: Tracing the Origins of a MRSA Epidemic
    STUDENT VERSION Bacteria Evolving: Tracing the Origins of a MRSA Epidemic PASSAGE FOUR The Human Microbiome To solve the mystery of the origins of USA300, researchers looked to the microbiome that lives on human skin. They knew that within this vast, microscopic ecosystem lives a network of organisms that compete with each other, co-exist with each other and are constantly evolving. If USA300 acquired the speG gene, it was most likely from some other bacterium or organ- ism that is part of this ecosystem. And that is exactly what they found. USA300 had gotten its new abilities from another staph species, Staphylococcus epidermidis. The Source: S. epidermidis Staph epidermidis is a type of Staphylococcus that is closely re- lated to Staphylococcus aureus. Like S. aureus, S. epidermidis has adapted to live on human skin. Although it’s quite common, it usually causes no health problems. One reason that S. epider- midis can colonize human skin so effectively is that it has the ACME region, the mobile element of DNA made of 34 genes. This is the set of genes that includes the speG gene. Thanks to its genome, S. epidermidis is resistant to methicillin and related antibiotics. However, S. epidermidis rarely infects us, so the fact that it is drug resistant is usually not a problem. But what seems to have happened is that S. epidermidis bacteria were living in close contact with S. aureus bacteria on human skin and at some point S. epidermidis transfered the ACME DNA, including the speG gene, to S. aureus. This might have made it possible for S.
    [Show full text]
  • Porphyromonas Gingivalis, Strain F0185 Catalog
    Product Information Sheet for HM-1140 Porphyromonas gingivalis, Strain F0185 immediately upon arrival. For long-term storage, the vapor phase of a liquid nitrogen freezer is recommended. Freeze- thaw cycles should be avoided. Catalog No. HM-1140 Growth Conditions: For research use only. Not for human use. Media: Supplemented Tryptic Soy broth or equivalent Contributor: Tryptic Soy agar with 5% defibrinated sheep blood or Floyd E. Dewhirst, D.D.S., Ph.D., Senior Member of the Staff, Supplemented Tryptic Soy agar or equivalent Department of Microbiology and Jacques Izard, Assistant Incubation: Member of the Staff, Department of Molecular Genetics, The Temperature: 37°C Forsyth Institute, Cambridge, Massachusetts, USA Atmosphere: Anaerobic Propagation: Manufacturer: 1. Keep vial frozen until ready for use, then thaw. BEI Resources 2. Transfer the entire thawed aliquot into a single tube of broth. Product Description: 3. Use several drops of the suspension to inoculate an Bacteria Classification: Porphyromonadaceae, agar slant and/or plate. Porphyromonas 4. Incubate the tube, slant and/or plate at 37°C for 24 to Species: Porphyromonas gingivalis 72 hours. Broth cultures should include shaking. Strain: F0185 Original Source: Porphyromonas gingivalis (P. gingivalis), Citation: strain F0185 was isolated in December 1985 from the Acknowledgment for publications should read “The following tooth of a patient diagnosed with juvenile periodontitis in reagent was obtained through BEI Resources, NIAID, NIH as the United States.1 part of the Human Microbiome Project: Porphyromonas Comments: P. gingivalis, strain F0185 (HMP ID 1988) is a gingivalis, Strain F0185, HM-1140.” reference genome for The Human Microbiome Project (HMP). HMP is an initiative to identify and characterize Biosafety Level: 2 human microbial flora.
    [Show full text]
  • Involvement of Gut Microbiome in Human Health and Disease
    Liang et al. Gut Pathog (2018) 10:3 https://doi.org/10.1186/s13099-018-0230-4 Gut Pathogens REVIEW Open Access Involvement of gut microbiome in human health and disease: brief overview, knowledge gaps and research opportunities Dachao Liang1†, Ross Ka‑Kit Leung2*†, Wenda Guan2 and William W. Au3,4 Abstract The commensal, symbiotic, and pathogenic microbial community which resides inside our body and on our skin (the human microbiome) can perturb host energy metabolism and immunity, and thus signifcantly infuence develop‑ ment of a variety of human diseases. Therefore, the feld has attracted unprecedented attention in the last decade. Although a large amount of data has been generated, there are still many unanswered questions and no universal agreements on how microbiome afects human health have been agreed upon. Consequently, this review was writ‑ ten to provide an updated overview of the rapidly expanding feld, with a focus on revealing knowledge gaps and research opportunities. Specifcally, the review covered animal physiology, optimal microbiome standard, health inter‑ vention by manipulating microbiome, knowledge base building by text mining, microbiota community structure and its implications in human diseases and health monitoring by analyzing microbiome in the blood. The review should enhance interest in conducting novel microbiota investigations that will further improve health and therapy. Keywords: Microbiome, High throughput sequencing, Metagenomics, Human disease causation What is microbiome? collection of bacteria or their genomes, unless otherwise Microorganisms often live in the form of a community. specifed. Furthermore, they can live in close association with com- Microbiome can be found throughout the human plex organisms, such as plants and humans, by establish- body, ranging from the skin to the gut, and to previously ing commensal, ammensal, mutualistic, parasitic and/or considered as sterile environments such as the blood pathogenic relationships with their hosts.
    [Show full text]
  • Molecular Analyses of Changes Induced in the Microbial Populations of Murine Colon After As(III) Exposure Rishu Dheer
    Duquesne University Duquesne Scholarship Collection Electronic Theses and Dissertations Summer 2011 Molecular Analyses of Changes Induced in the Microbial Populations of Murine Colon After As(III) Exposure Rishu Dheer Follow this and additional works at: https://dsc.duq.edu/etd Recommended Citation Dheer, R. (2011). Molecular Analyses of Changes Induced in the Microbial Populations of Murine Colon After As(III) Exposure (Doctoral dissertation, Duquesne University). Retrieved from https://dsc.duq.edu/etd/484 This Immediate Access is brought to you for free and open access by Duquesne Scholarship Collection. It has been accepted for inclusion in Electronic Theses and Dissertations by an authorized administrator of Duquesne Scholarship Collection. For more information, please contact [email protected]. MOLECULAR ANALYSES OF CHANGES INDUCED IN THE MICROBIAL POPULATIONS OF MURINE COLON AFTER As (III) EXPOSURE A Dissertation Submitted to Bayer School of Natural and Environmental Sciences Duquesne University In partial fulfillment of the requirements for the degree of Doctor of Philosophy By Rishu Dheer August, 2011 Copyright by Rishu Dheer 2011 MOLECULAR ANALYSES OF CHANGES INDUCED IN THE MICROBIAL POPULATIONS OF MURINE COLON AFTER As (III) EXPOSURE By Rishu Dheer Approved June 14, 2011 ________________________________ ________________________________ Dr. John F. Stolz Dr. Aaron Barchowsky Director, Center of Environmental Associate Professor of Biology Research and Education (Committee Member) Professor of Biology (Committee Chair) ________________________________
    [Show full text]
  • Evolutionary Dynamics of Bacteria in the Gut Microbiome Within and Across Hosts
    bioRxiv preprint doi: https://doi.org/10.1101/210955; this version posted September 14, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. preprint Evolutionary dynamics of bacteria in the gut microbiome within and across hosts Nandita R. Garud1Y*, Benjamin H. Good2,3,5,Y*, Oskar Hallatschek2,4,5, Katherine S. Pollard1,6,7 1 Gladstone Institutes, San Francisco, California, United States of America 2 Department of Physics, University of California, Berkeley, California, United States of America 3 Department of Bioengineering, University of California, Berkeley, California, United States of America 4 Department of Integrative Biology, University of California, Berkeley, California, United States of America 5 Kavli Institute for Theoretical Physics, University of California, Santa Barbara, California, United States of America 6 Department of Epidemiology & Biostatistics, Institute for Human Genetics, Quantitative Biology Institute, and Institute for Computational Health Sciences, University of California, San Francisco, California, United States of America 7 Chan-Zuckerberg Biohub, San Francisco, California, United States of America YThese authors contributed equally and are ordered alphabetically * [email protected] (B.H.G.), [email protected] (N.R.G.) Abstract Gut microbiota are shaped by a combination of ecological and evolutionary forces. While the ecological dynamics have been extensively studied, much less is known about how species of gut bacteria evolve over time. Here we introduce a model-based framework for quantifying evolutionary dynamics within and across hosts using a panel of metagenomic samples. We use this approach to study evolution in ∼30 prevalent species in the human gut.
    [Show full text]
  • Vaginal Microbiome Lactobacillus Crispatus Is Heritable Among European American Women
    ARTICLE https://doi.org/10.1038/s42003-021-02394-6 OPEN Vaginal microbiome Lactobacillus crispatus is heritable among European American women Michelle L. Wright 1,2,10, Jennifer M. Fettweis3,4,5,10, Lindon J. Eaves6, Judy L. Silberg6,7, Michael C. Neale 6, Myrna G. Serrano 3,5, Nicole R. Jimenez3,5, Elizabeth Prom-Wormley8, Philippe H. Girerd4,5, ✉ Joseph F. Borzelleca Jr.4, Kimberly K. Jefferson3,5, Jerome F. Strauss III4,5, Timothy P. York 4,6,11 & Gregory A. Buck 3,5,9,11 The diversity and dominant bacterial taxa in the vagina are reported to be influenced by multiple intrinsic and extrinsic factors, including but not limited to pregnancy, contraceptive use, pathogenic states, socioeconomic status, and ancestry. However, the extent to which 1234567890():,; host genetic factors influence variation in the vaginal microbiota is unclear. We used a biometrical genetic approach to determine whether host genetic factors contribute to inter- individual differences in taxa from a sample of 332 twins who self-identified as being of African (44 pairs) or European ancestry (122 pairs). Lactobacillus crispatus, a major deter- minant of vaginal health, was identified as heritable among European American women (narrow-sense heritability = 34.7%, P-value = 0.018). Heritability of L. crispatus is consistent with the reduced prevalence of adverse reproductive disorders, including bacterial vaginosis and preterm birth, among women of European ancestry. 1 School of Nursing, The University of Texas at Austin, Austin, TX, USA. 2 Department of Women’s Health, Dell Medical School, The University of Texas at Austin, Austin, TX, USA. 3 Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA.
    [Show full text]
  • Impact of Occupational Exposure on Human Microbiota
    HHS Public Access Author manuscript Author ManuscriptAuthor Manuscript Author Curr Opin Manuscript Author Allergy Clin Manuscript Author Immunol. Author manuscript; available in PMC 2020 April 01. Published in final edited form as: Curr Opin Allergy Clin Immunol. 2019 April ; 19(2): 86–91. doi:10.1097/ACI.0000000000000502. Impact of occupational exposure on human microbiota Peggy S. Lai1,2,3 and David C. Christiani1,2,3 1Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA, United States of America 2Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, United States of America 3Harvard Medical School, Boston, MA, United States of America Abstract Purpose of review—Recent evidence suggests that environmental exposures change the adult human microbiome. Here we review recent evidence on the impact of the work microbiome and work-related chemical, metal, and particulate exposures on the human microbiome. Recent findings—Prior literature on occupational microbial exposures have focused mainly on the respiratory effects of endotoxin, but a recent study suggests that not all endotoxin is the same; endotoxin from some species is pro-inflammatory, while endotoxin from other species is anti- inflammatory. Work with animals can change the adult human microbiome, likely through colonization. Early studies in military personnel and animal models of gulf war illness show that military exposures changes the gut microbiome and increases gut permeability. Heavy metal and particulate matter exposure, which are often elevated in occupational settings, also changes the gut microbiome. Summary—An emerging body of literature shows that work-related exposures can change the human microbiome.
    [Show full text]