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Wang S, Jiang Y, Che L, Wang RH, Li SC. Enhancing insights into diseases through horizontal gene transfer event detection from gut microbiome. Nucleic Acids Res 2024; 52:e61. [PMID: 38884260 DOI: 10.1093/nar/gkae515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 04/23/2024] [Accepted: 06/04/2024] [Indexed: 06/18/2024] Open
Abstract
Horizontal gene transfer (HGT) phenomena pervade the gut microbiome and significantly impact human health. Yet, no current method can accurately identify complete HGT events, including the transferred sequence and the associated deletion and insertion breakpoints from shotgun metagenomic data. Here, we develop LocalHGT, which facilitates the reliable and swift detection of complete HGT events from shotgun metagenomic data, delivering an accuracy of 99.4%-verified by Nanopore data-across 200 gut microbiome samples, and achieving an average F1 score of 0.99 on 100 simulated data. LocalHGT enables a systematic characterization of HGT events within the human gut microbiome across 2098 samples, revealing that multiple recipient genome sites can become targets of a transferred sequence, microhomology is enriched in HGT breakpoint junctions (P-value = 3.3e-58), and HGTs can function as host-specific fingerprints indicated by the significantly higher HGT similarity of intra-personal temporal samples than inter-personal samples (P-value = 4.3e-303). Crucially, HGTs showed potential contributions to colorectal cancer (CRC) and acute diarrhoea, as evidenced by the enrichment of the butyrate metabolism pathway (P-value = 3.8e-17) and the shigellosis pathway (P-value = 5.9e-13) in the respective associated HGTs. Furthermore, differential HGTs demonstrated promise as biomarkers for predicting various diseases. Integrating HGTs into a CRC prediction model achieved an AUC of 0.87.
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Affiliation(s)
- Shuai Wang
- City University of Hong Kong Shenzhen Research Institute, Shenzhen, China
- Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong
| | - Yiqi Jiang
- City University of Hong Kong Shenzhen Research Institute, Shenzhen, China
- Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong
| | - Lijia Che
- City University of Hong Kong Shenzhen Research Institute, Shenzhen, China
- Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong
| | - Ruo Han Wang
- City University of Hong Kong Shenzhen Research Institute, Shenzhen, China
- Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong
| | - Shuai Cheng Li
- City University of Hong Kong Shenzhen Research Institute, Shenzhen, China
- Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong
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2
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Sóki J, Wybo I, Baaity Z, Stefán G, Jeverica S, Ulger N, Stingu CS, Mahmood B, Burián K, Nagy E. Detection of the antibiotic resistance genes content of intestinal Bacteroides, Parabacteroides and Phocaeicola isolates from healthy and carbapenem-treated patients from European countries. BMC Microbiol 2024; 24:202. [PMID: 38851699 PMCID: PMC11162026 DOI: 10.1186/s12866-024-03354-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 05/28/2024] [Indexed: 06/10/2024] Open
Abstract
BACKGROUND Bacteroides fragilis group (BFG) species are the most significant anaerobic pathogens and are also the most antibiotic-resistant anaerobic species. Therefore, surveying their antimicrobial resistance levels and investigating their antibiotic resistance mechanisms is recommended. Since their infections are endogenous and they are important constituents of the intestinal microbiota, the properties of the intestinal strains are also important to follow. The aim of this study was to investigate the main antibiotic gene content of microbiota isolates from healthy people and compare them with the gene carriage of strains isolated from infections. RESULTS We detected 13, mainly antibiotic resistance determinants of 184 intestinal BFG strains that were isolated in 5 European countries (Belgium, Germany, Hungary, Slovenia and Turkey) and compared these with values obtained earlier for European clinical strains. Differences were found between the values of this study and an earlier one for antibiotic resistance genes that are considered to be mobile, with higher degrees for cfxA, erm(F) and tet(Q) and with lower degrees for msrSA, erm(B) and erm(G). In addition, a different gene prevalence was found depending on the taxonomical groups, e.g., B. fragilis and NBFB. Some strains with both the cepA and cfiA β-lactamase genes were also detected, which is thought to be exceptional since until now, the B. fragilis genetic divisions were defined by the mutual exclusion of these two genes. CONCLUSIONS Our study detected the prevalences of a series of antibiotic resistance genes in intestinal Bacteroides strains which is a novelty. In addition, based on the current and some previous data we hypothesized that prevalence of some antibiotic resistance genes detected in the clinical and intestinal BFG strains were different, which could be accounted with the differential composition of the Bacteroides microbiota and/or the MGE mobilities at the luminal vs. mucosal sites of the intestine.
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Affiliation(s)
- József Sóki
- Institute of Medical Microbiology, Albert Szent-Györgyi Health Centre and Medical School, University of Szeged, Szeged, Hungary.
| | - Ingrid Wybo
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel, Brussels, Belgium
| | - Zain Baaity
- Institute of Medical Microbiology, Albert Szent-Györgyi Health Centre and Medical School, University of Szeged, Szeged, Hungary
| | - Glória Stefán
- Institute of Medical Microbiology, Albert Szent-Györgyi Health Centre and Medical School, University of Szeged, Szeged, Hungary
- Department of Public Health, Government Office of the Capital City, Budapest, Hungary
| | - Samo Jeverica
- National Laboratory of Health, Environment and Food, Maribor, Slovenia
| | - Nurver Ulger
- Department of Microbiology, Marmara University School of Medicine, Istanbul, Turkey
| | - Catalina-Suzana Stingu
- Institute for Medical Microbiology and Virology, University Hospital of Leipzig, Leipzig, Germany
| | - Bakhtiyar Mahmood
- Institute of Medical Microbiology, Albert Szent-Györgyi Health Centre and Medical School, University of Szeged, Szeged, Hungary
- Department of Biology, University of Garmian, Kalar, Kurdistan Region, Iraq
| | - Katalin Burián
- Institute of Medical Microbiology, Albert Szent-Györgyi Health Centre and Medical School, University of Szeged, Szeged, Hungary
| | - Elisabeth Nagy
- Institute of Medical Microbiology, Albert Szent-Györgyi Health Centre and Medical School, University of Szeged, Szeged, Hungary
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García-Bayona L, Said N, Coyne MJ, Flores K, Elmekki NM, Sheahan ML, Camacho AG, Hutt K, Yildiz FH, Kovács ÁT, Waldor MK, Comstock LE. A pervasive large conjugative plasmid mediates multispecies biofilm formation in the intestinal microbiota increasing resilience to perturbations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.29.590671. [PMID: 38746121 PMCID: PMC11092513 DOI: 10.1101/2024.04.29.590671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Although horizontal gene transfer is pervasive in the intestinal microbiota, we understand only superficially the roles of most exchanged genes and how the mobile repertoire affects community dynamics. Similarly, little is known about the mechanisms underlying the ability of a community to recover after a perturbation. Here, we identified and functionally characterized a large conjugative plasmid that is one of the most frequently transferred elements among Bacteroidales species and is ubiquitous in diverse human populations. This plasmid encodes both an extracellular polysaccharide and fimbriae, which promote the formation of multispecies biofilms in the mammalian gut. We use a hybridization-based approach to visualize biofilms in clarified whole colon tissue with unprecedented 3D spatial resolution. These biofilms increase bacterial survival to common stressors encountered in the gut, increasing strain resiliency, and providing a rationale for the plasmid's recent spread and high worldwide prevalence.
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Koo H, Morrow CD. Bacteroidales-Specific Antimicrobial Genes Can Influence the Selection of the Dominant Fecal Strain of Bacteroides vulgatus and Bacteroides uniformis from the Gastrointestinal Tract Microbial Community. Life (Basel) 2024; 14:555. [PMID: 38792577 PMCID: PMC11121782 DOI: 10.3390/life14050555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/21/2024] [Accepted: 04/23/2024] [Indexed: 05/26/2024] Open
Abstract
Bacteroides vulgatus and Bacteroides uniformis are known to be abundant in the human fecal microbial community. Although these strains typically remain stable over time in humans, disruption of this microbial community following antibiotics resulted in the transient change to new strains suggesting that a complex, dynamic strain community exists in humans. To further study the selection of dominant fecal microbial strains from the gastrointestinal tract (GIT) community, we analyzed three longitudinal metagenomic sequencing data sets using BLAST+ to identify genes encoding Bacteroidales-specific antimicrobial proteins (BSAP) that have known functions to restrict species-specific replication of B. uniformis (BSAP-2) or B. vulgatus (BSAP-3) and have been postulated to provide a competitive advantage in microbial communities. In the HMP (Human Microbiome Project) data set, we found fecal samples from individuals had B. vulgatus or B. uniformis with either complete or deleted BSAP genes that did not change over time. We also examined fecal samples from two separate longitudinal data sets of individuals who had been given either single or multiple antibiotics. The BSAP gene pattern from most individuals given either single or multiple antibiotics recovered to be the same as the pre-antibiotic strain. However, in a few individuals, we found incomplete BSAP-3 genes at early times during the recovery that were replaced by B. vulgatus with the complete BSAP-3 gene, consistent with the function of the BSAP to specifically restrict Bacteroides spp. The results of these studies provide insights into the fluxes that occur in the Bacteroides spp. GIT community following perturbation and the dynamics of the selection of a dominant fecal strain of Bacteroides spp.
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Affiliation(s)
- Hyunmin Koo
- Department of Genetics, Hugh Kaul Precision Medicine Institute, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Casey D. Morrow
- Department of Cell, Developmental and Integrative Biology, Hugh Kaul Precision Medicine Institute, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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Mahmood B, Sárvári KP, Orosz L, Nagy E, Sóki J. Novel and rare β-lactamase genes of Bacteroides fragilis group species: Detection of the genes and characterization of their genetic backgrounds. Anaerobe 2024; 86:102832. [PMID: 38360202 DOI: 10.1016/j.anaerobe.2024.102832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 02/09/2024] [Accepted: 02/12/2024] [Indexed: 02/17/2024]
Abstract
OBJECTIVES This study screened the prevalence of rare β-lactamase genes in Bacteroides fragilis group strains from clinical specimens and normal microbiota and examined the genetic properties of the strains carrying these genes. METHODS blaHGD1, blaOXA347, cblA, crxA, and pbbA were detected by real-time polymerase chain reaction in collections of Bacteroides strains from clinical (n = 406) and fecal (n = 184) samples. To examine the genetic backgrounds of the samples, end-point PCR, FT-IR, and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry were used. RESULTS All B. uniformis isolates were positive for cblA in both collections. Although crxA was B. xylanisolvens-specific and associated with carbapenem resistance, it was only found in six fecal and three clinical B. xylanisolvens strains. Moreover, the crxA-positive strains were not clonal among B. xylanisolvens (contrary to cfiA in B. fragilis), implicating a rate of mobility or emergence by independent evolutionary events. The Phocaeicola (B.) vulgatus/P. dorei-specific gene blaHGD1 was detected among all P. vulgatus/P. dorei isolates from fecal (n = 36) and clinical (n = 26) samples. No blaOXA347-carrying isolate was found from European collections, but all US samples (n = 6) were positive. For three clinical isolates belonging to B. thetaiotaomicron (n = 2) and B. ovatus (n = 1), pbbA was detected on mobile genetic elements, and pbbA-positive strains displayed non-susceptibility to piperacillin or piperacillin/tazobactam phenotypically. CONCLUSIONS Based on these observations, β-lactamases produced by rare β-lactamase genes in B. fragilis group strains should not be overlooked because they could encode important resistance phenotypes.
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Affiliation(s)
- Bakhtiyar Mahmood
- Institute of Medical Microbiology, Albert Szent-Györgyi Health Centre and Medical School, University of Szeged, Szeged, Hungary; Department of Biology, University of Garmian, Kalar, Kurdistan Region, Iraq.
| | - Károly Péter Sárvári
- Institute of Medical Microbiology, Albert Szent-Györgyi Health Centre and Medical School, University of Szeged, Szeged, Hungary
| | - Laszló Orosz
- Institute of Medical Microbiology, Albert Szent-Györgyi Health Centre and Medical School, University of Szeged, Szeged, Hungary
| | - Elisabeth Nagy
- Institute of Medical Microbiology, Albert Szent-Györgyi Health Centre and Medical School, University of Szeged, Szeged, Hungary
| | - József Sóki
- Institute of Medical Microbiology, Albert Szent-Györgyi Health Centre and Medical School, University of Szeged, Szeged, Hungary
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6
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Ortañez J, Degnan PH. Tracking and characterization of a novel conjugative transposon identified by shotgun transposon mutagenesis. Front Microbiol 2024; 15:1241582. [PMID: 38601936 PMCID: PMC11005914 DOI: 10.3389/fmicb.2024.1241582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 03/04/2024] [Indexed: 04/12/2024] Open
Abstract
The horizontal transfer of mobile genetic elements (MGEs) is an essential process determining the functional and genomic diversity of bacterial populations. MGEs facilitate the exchange of fitness determinant genes like antibiotic resistance and virulence factors. Various computational methods exist to identify potential MGEs, but confirming their ability to transfer requires additional experimental approaches. Here, we apply a transposon (Tn) mutagenesis technique for confirming mobilization without the need for targeted mutations. Using this method, we identified two MGEs, including a previously known conjugative transposon (CTn) called BoCTn found in Bacteroides ovatus and a novel CTn, PvCTn, identified in Phocaeicola vulgatus. In addition, Tn mutagenesis and subsequent genetic deletion enabled our characterization of a helix-turn-helix motif gene, BVU3433 which negatively regulates the conjugation efficiency of PvCTn in vitro. Furthermore, our transcriptomics data revealed that BVU3433 plays a crucial role in the repression of PvCTn genes, including genes involved in forming complete conjugation machinery [Type IV Secretion System (T4SS)]. Finally, analysis of individual strain genomes and community metagenomes identified the widespread prevalence of PvCTn-like elements with putative BVU3433 homologs among human gut-associated bacteria. In summary, this Tn mutagenesis mobilization method (TMMM) enables observation of transfer events in vitro and can ultimately be applied in vivo to identify a broader diversity of functional MGEs that may underly the transfer of important fitness determinants.
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Affiliation(s)
| | - Patrick H. Degnan
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
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Chiang BH, Vega G, Dunwoody SC, Patnode ML. Bacterial interactions on nutrient-rich surfaces in the gut lumen. Infect Immun 2024:e0048023. [PMID: 38506518 DOI: 10.1128/iai.00480-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024] Open
Abstract
The intestinal lumen is a turbulent, semi-fluid landscape where microbial cells and nutrient-rich particles are distributed with high heterogeneity. Major questions regarding the basic physical structure of this dynamic microbial ecosystem remain unanswered. Most gut microbes are non-motile, and it is unclear how they achieve optimum localization relative to concentrated aggregations of dietary glycans that serve as their primary source of energy. In addition, a random spatial arrangement of cells in this environment is predicted to limit sustained interactions that drive co-evolution of microbial genomes. The ecological consequences of random versus organized microbial localization have the potential to control both the metabolic outputs of the microbiota and the propensity for enteric pathogens to participate in proximity-dependent microbial interactions. Here, we review evidence suggesting that several bacterial species adopt organized spatial arrangements in the gut via adhesion. We highlight examples where localization could contribute to antagonism or metabolic interdependency in nutrient degradation, and we discuss imaging- and sequencing-based technologies that have been used to assess the spatial positions of cells within complex microbial communities.
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Affiliation(s)
- Bo Huey Chiang
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, California, USA
- Graduate Program in Biological Sciences and Engineering, University of California, Santa Cruz, California, USA
| | - Giovanni Vega
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, California, USA
- Graduate Program in Biological Sciences and Engineering, University of California, Santa Cruz, California, USA
| | - Sarah C Dunwoody
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, California, USA
| | - Michael L Patnode
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, California, USA
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8
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González A, Fullaondo A, Odriozola A. Impact of evolution on lifestyle in microbiome. ADVANCES IN GENETICS 2024; 111:149-198. [PMID: 38908899 DOI: 10.1016/bs.adgen.2024.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/24/2024]
Abstract
This chapter analyses the interaction between microbiota and humans from an evolutionary point of view. Long-term interactions between gut microbiota and host have been generated as a result of dietary choices through coevolutionary processes, where mutuality of advantage is essential. Likewise, the characteristics of the intestinal environment have made it possible to describe different intrahost evolutionary mechanisms affecting microbiota. For its part, the intestinal microbiota has been of great importance in the evolution of mammals, allowing the diversification of dietary niches, phenotypic plasticity and the selection of host phenotypes. Although the origin of the human intestinal microbial community is still not known with certainty, mother-offspring transmission plays a key role, and it seems that transmissibility between individuals in adulthood also has important implications. Finally, it should be noted that certain aspects inherent to modern lifestyle, including refined diets, antibiotic intake, exposure to air pollutants, microplastics, and stress, could negatively affect the diversity and composition of our gut microbiota. This chapter aims to combine current knowledge to provide a comprehensive view of the interaction between microbiota and humans throughout evolution.
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Affiliation(s)
- Adriana González
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain.
| | - Asier Fullaondo
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Adrián Odriozola
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain
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Zhang ZJ, Cole CG, Coyne MJ, Lin H, Dylla N, Smith RC, Waligurski E, Ramaswamy R, Woodson C, Burgo V, Little JC, Moran D, Rose A, McMillin M, McSpadden E, Sundararajan A, Sidebottom AM, Pamer EG, Comstock LE. Comprehensive analyses of a large human gut Bacteroidales culture collection reveal species and strain level diversity and evolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.08.584156. [PMID: 38496653 PMCID: PMC10942478 DOI: 10.1101/2024.03.08.584156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Species of the Bacteroidales order are among the most abundant and stable bacterial members of the human gut microbiome with diverse impacts on human health. While Bacteroidales strains and species are genomically and functionally diverse, order-wide comparative analyses are lacking. We cultured and sequenced the genomes of 408 Bacteroidales isolates from healthy human donors representing nine genera and 35 species and performed comparative genomic, gene-specific, mobile gene, and metabolomic analyses. Families, genera, and species could be grouped based on many distinctive features. However, we also show extensive DNA transfer between diverse families, allowing for shared traits and strain evolution. Inter- and intra-specific diversity is also apparent in the metabolomic profiling studies. This highly characterized and diverse Bacteroidales culture collection with strain-resolved genomic and metabolomic analyses can serve as a resource to facilitate informed selection of strains for microbiome reconstitution.
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Affiliation(s)
- Zhenrun J Zhang
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
- Department of Microbiology, Biological Sciences Division, University of Chicago, 5841 South Maryland Ave, Chicago, IL, 60637, USA
| | - Cody G Cole
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
- Department of Microbiology, Biological Sciences Division, University of Chicago, 5841 South Maryland Ave, Chicago, IL, 60637, USA
| | - Michael J Coyne
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
- Department of Microbiology, Biological Sciences Division, University of Chicago, 5841 South Maryland Ave, Chicago, IL, 60637, USA
| | - Huaiying Lin
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
| | - Nicholas Dylla
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
| | - Rita C Smith
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
| | - Emily Waligurski
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
- Department of Microbiology, Biological Sciences Division, University of Chicago, 5841 South Maryland Ave, Chicago, IL, 60637, USA
| | - Ramanujam Ramaswamy
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
| | - Che Woodson
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
| | - Victoria Burgo
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
| | - Jessica C Little
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
| | - David Moran
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
| | - Amber Rose
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
| | - Mary McMillin
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
| | - Emma McSpadden
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
| | - Anitha Sundararajan
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
| | - Ashley M Sidebottom
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
| | - Eric G Pamer
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
- Department of Medicine, Section of Infectious Diseases & Global Health, University of Chicago Medicine, 5841 South Maryland Ave, Chicago, IL, 60637, USA
- Department of Pathology, University of Chicago Medicine, 5841 South Maryland Ave, Chicago, IL, 60637, USA
- Department of Microbiology, Biological Sciences Division, University of Chicago, 5841 South Maryland Ave, Chicago, IL, 60637, USA
| | - Laurie E Comstock
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
- Department of Microbiology, Biological Sciences Division, University of Chicago, 5841 South Maryland Ave, Chicago, IL, 60637, USA
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10
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Liu Z, Good BH. Dynamics of bacterial recombination in the human gut microbiome. PLoS Biol 2024; 22:e3002472. [PMID: 38329938 PMCID: PMC10852326 DOI: 10.1371/journal.pbio.3002472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 12/14/2023] [Indexed: 02/10/2024] Open
Abstract
Horizontal gene transfer (HGT) is a ubiquitous force in microbial evolution. Previous work has shown that the human gut is a hotspot for gene transfer between species, but the more subtle exchange of variation within species-also known as recombination-remains poorly characterized in this ecosystem. Here, we show that the genetic structure of the human gut microbiome provides an opportunity to measure recent recombination events from sequenced fecal samples, enabling quantitative comparisons across diverse commensal species that inhabit a common environment. By analyzing recent recombination events in the core genomes of 29 human gut bacteria, we observed widespread heterogeneities in the rates and lengths of transferred fragments, which are difficult to explain by existing models of ecological isolation or homology-dependent recombination rates. We also show that natural selection helps facilitate the spread of genetic variants across strain backgrounds, both within individual hosts and across the broader population. These results shed light on the dynamics of in situ recombination, which can strongly constrain the adaptability of gut microbial communities.
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Affiliation(s)
- Zhiru Liu
- Department of Applied Physics, Stanford University, Stanford, California, United States of America
| | - Benjamin H. Good
- Department of Applied Physics, Stanford University, Stanford, California, United States of America
- Department of Biology, Stanford University, Stanford, California, United States of America
- Chan Zuckerberg Biohub–San Francisco, San Francisco, California, United States of America
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11
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Wang M, Liu G, Liu M, Tai C, Deng Z, Song J, Ou HY. ICEberg 3.0: functional categorization and analysis of the integrative and conjugative elements in bacteria. Nucleic Acids Res 2024; 52:D732-D737. [PMID: 37870467 PMCID: PMC10767825 DOI: 10.1093/nar/gkad935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 10/07/2023] [Accepted: 10/12/2023] [Indexed: 10/24/2023] Open
Abstract
ICEberg 3.0 (https://tool2-mml.sjtu.edu.cn/ICEberg3/) is an upgraded database that provides comprehensive insights into bacterial integrative and conjugative elements (ICEs). In comparison to the previous version, three key enhancements were introduced: First, through text mining and manual curation, it now encompasses details of 2065 ICEs, 607 IMEs and 275 CIMEs, including 430 with experimental support. Secondly, ICEberg 3.0 systematically categorizes cargo gene functions of ICEs into six groups based on literature curation and predictive analysis, providing a profound understanding of ICEs'diverse biological traits. The cargo gene prediction pipeline is integrated into the online tool ICEfinder 2.0. Finally, ICEberg 3.0 aids the analysis and exploration of ICEs from the human microbiome. Extracted and manually curated from 2405 distinct human microbiome samples, the database comprises 1386 putative ICEs, offering insights into the complex dynamics of Bacteria-ICE-Cargo networks within the human microbiome. With the recent updates, ICEberg 3.0 enhances its capability to unravel the intricacies of ICE biology, particularly in the characterization and understanding of cargo gene functions and ICE interactions within the microbiome. This enhancement may facilitate the investigation of the dynamic landscape of ICE biology and its implications for microbial communities.
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Affiliation(s)
- Meng Wang
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Guitian Liu
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Meng Liu
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Cui Tai
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Jiangning Song
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
- Monash Data Futures Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Hong-Yu Ou
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
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12
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Wang S, Mu L, Yu C, He Y, Hu X, Jiao Y, Xu Z, You S, Liu SL, Bao H. Microbial collaborations and conflicts: unraveling interactions in the gut ecosystem. Gut Microbes 2024; 16:2296603. [PMID: 38149632 PMCID: PMC10761165 DOI: 10.1080/19490976.2023.2296603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 12/14/2023] [Indexed: 12/28/2023] Open
Abstract
The human gut microbiota constitutes a vast and complex community of microorganisms. The myriad of microorganisms present in the intestinal tract exhibits highly intricate interactions, which play a crucial role in maintaining the stability and balance of the gut microbial ecosystem. These interactions, in turn, influence the overall health of the host. The mammalian gut microbes have evolved a wide range of mechanisms to suppress or even eliminate their competitors for nutrients and space. Simultaneously, extensive cooperative interactions exist among different microbes to optimize resource utilization and enhance their own fitness. This review will focus on the competitive mechanisms among members of the gut microorganisms and discuss key modes of actions, including bacterial secretion systems, bacteriocins, membrane vesicles (MVs) etc. Additionally, we will summarize the current knowledge of the often-overlooked positive interactions within the gut microbiota, and showcase representative machineries. This information will serve as a reference for better understanding the complex interactions occurring within the mammalian gut environment. Understanding the interaction dynamics of competition and cooperation within the gut microbiota is crucial to unraveling the ecology of the mammalian gut microbial communities. Targeted interventions aimed at modulating these interactions may offer potential therapeutic strategies for disease conditions.
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Affiliation(s)
- Shuang Wang
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- Department of Biopharmaceutical Sciences (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), College of Pharmacy, Harbin Medical University, Harbin, China
- National Key Laboratory of Frigid Zone Cardiovascular Diseases (NKLFZCD) College of Pharmacy, Harbin Medical University, Harbin, China
| | - Lingyi Mu
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
| | - Chong Yu
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- National Key Laboratory of Frigid Zone Cardiovascular Diseases (NKLFZCD) College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Yuting He
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- National Key Laboratory of Frigid Zone Cardiovascular Diseases (NKLFZCD) College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Xinliang Hu
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- National Key Laboratory of Frigid Zone Cardiovascular Diseases (NKLFZCD) College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Yanlei Jiao
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- National Key Laboratory of Frigid Zone Cardiovascular Diseases (NKLFZCD) College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Ziqiong Xu
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- National Key Laboratory of Frigid Zone Cardiovascular Diseases (NKLFZCD) College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Shaohui You
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- National Key Laboratory of Frigid Zone Cardiovascular Diseases (NKLFZCD) College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Shu-Lin Liu
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- National Key Laboratory of Frigid Zone Cardiovascular Diseases (NKLFZCD) College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Hongxia Bao
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- National Key Laboratory of Frigid Zone Cardiovascular Diseases (NKLFZCD) College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
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13
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Diebold PJ, Rhee MW, Shi Q, Trung NV, Umrani F, Ahmed S, Kulkarni V, Deshpande P, Alexander M, Thi Hoa N, Christakis NA, Iqbal NT, Ali SA, Mathad JS, Brito IL. Clinically relevant antibiotic resistance genes are linked to a limited set of taxa within gut microbiome worldwide. Nat Commun 2023; 14:7366. [PMID: 37963868 PMCID: PMC10645880 DOI: 10.1038/s41467-023-42998-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 10/27/2023] [Indexed: 11/16/2023] Open
Abstract
The acquisition of antimicrobial resistance (AR) genes has rendered important pathogens nearly or fully unresponsive to antibiotics. It has been suggested that pathogens acquire AR traits from the gut microbiota, which collectively serve as a global reservoir for AR genes conferring resistance to all classes of antibiotics. However, only a subset of AR genes confers resistance to clinically relevant antibiotics, and, although these AR gene profiles are well-characterized for common pathogens, less is known about their taxonomic associations and transfer potential within diverse members of the gut microbiota. We examined a collection of 14,850 human metagenomes and 1666 environmental metagenomes from 33 countries, in addition to nearly 600,000 isolate genomes, to gain insight into the global prevalence and taxonomic range of clinically relevant AR genes. We find that several of the most concerning AR genes, such as those encoding the cephalosporinase CTX-M and carbapenemases KPC, IMP, NDM, and VIM, remain taxonomically restricted to Proteobacteria. Even cfiA, the most common carbapenemase gene within the human gut microbiome, remains tightly restricted to Bacteroides, despite being found on a mobilizable plasmid. We confirmed these findings in gut microbiome samples from India, Honduras, Pakistan, and Vietnam, using a high-sensitivity single-cell fusion PCR approach. Focusing on a set of genes encoding carbapenemases and cephalosporinases, thus far restricted to Bacteroides species, we find that few mutations are required for efficacy in a different phylum, raising the question of why these genes have not spread more widely. Overall, these data suggest that globally prevalent, clinically relevant AR genes have not yet established themselves across diverse commensal gut microbiota.
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Affiliation(s)
- Peter J Diebold
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Matthew W Rhee
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Qiaojuan Shi
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Nguyen Vinh Trung
- Oxford University Clinical Research Unit (OUCRU) in Ho Chi Minh City, Ho Chi Minh city, Viet Nam
| | | | | | - Vandana Kulkarni
- Johns Hopkins University Clinical Trials Unit, Byramjee Jeejeebhoy Government Medical College, Pune, Maharashtra, India
| | - Prasad Deshpande
- Johns Hopkins University Clinical Trials Unit, Byramjee Jeejeebhoy Government Medical College, Pune, Maharashtra, India
| | - Mallika Alexander
- Johns Hopkins University Clinical Trials Unit, Byramjee Jeejeebhoy Government Medical College, Pune, Maharashtra, India
| | - Ngo Thi Hoa
- Oxford University Clinical Research Unit (OUCRU) in Ho Chi Minh City, Ho Chi Minh city, Viet Nam
- Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Microbiology Department and Center for Tropical Medicine Research, Ngoc Thach University of Medicine, Ho Chi Minh city, Vietnam
| | | | | | | | | | - Ilana L Brito
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA.
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14
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Nishida AH, Ochman H. Origins and Evolution of Novel Bacteroides in Captive Apes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.20.563286. [PMID: 37961372 PMCID: PMC10634691 DOI: 10.1101/2023.10.20.563286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Bacterial strains evolve in response to the gut environment of their hosts, with genomic changes that influence their interactions with hosts as well as with other members of the gut community. Great apes in captivity have acquired strains of Bacteroides xylanisolvens, which are common within gut microbiome of humans but not typically found other apes, thereby enabling characterization of strain evolution following colonization. Here, we isolate, sequence and reconstruct the history of gene gain and loss events in numerous captive-ape-associated strains since their divergence from their closest human-associated strains. We show that multiple captive-ape-associated B. xylanisolvens lineages have independently acquired gene complexes that encode functions related to host mucin metabolism. Our results support the finding of high genome fluidity in Bacteroides, in that several strains, in moving from humans to captive apes, have rapidly gained large genomic regions that augment metabolic properties not previously present in their relatives.
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Affiliation(s)
- Alexandra H. Nishida
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712 USA
| | - Howard Ochman
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712 USA
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15
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Sheng H, Wu S, Xue Y, Zhao W, Caplan AB, Hovde CJ, Minnich SA. Engineering conjugative CRISPR-Cas9 systems for the targeted control of enteric pathogens and antibiotic resistance. PLoS One 2023; 18:e0291520. [PMID: 37699034 PMCID: PMC10497133 DOI: 10.1371/journal.pone.0291520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 08/30/2023] [Indexed: 09/14/2023] Open
Abstract
Pathogenic Escherichia coli and Salmonella enterica pose serious public health threats due to their ability to cause severe gastroenteritis and life-threatening sequela, particularly in young children. Moreover, the emergence and dissemination of antibiotic resistance in these bacteria have complicated control of infections. Alternative strategies that effectively target these enteric pathogens and negate or reduce the need of antibiotics are urgently needed. Such an alternative is the CRISPR-Cas9 system because it can generate sequence-specific lethal double stranded DNA breaks. In this study, two self-transmissible broad host range conjugative plasmids, pRK24 and pBP136, were engineered to deliver multiplexed CRSIPR-Cas9 systems that specifically target Enterohemorrhagic and Enteropathogenic strains of E. coli (EHEC and EPEC), S. enterica, and blaCMY-2 antibiotic resistance plasmids. Using in vitro mating assays, we show that the conjugative delivery of pRK24-CRISPR-Cas9 carrying guide RNAs to the EPEC/EHEC eae (intimin) gene can selectively kill enterohemorrhagic E. coli O157 eae+ cells (3 log kill at 6 h) but does not kill the isogenic Δeae mutant (P<0.001). Similar results were also obtained with a pBP136 derivative, pTF16, carrying multiplexed guide RNAs targeting E. coli eae and the S. enterica ssaN gene coding for the type III secretion ATPase. Another pBP136 derivative, TF18, carries guide RNAs targeting S. enterica ssaN and the antibiotic resistance gene, blaCMY-2, carried on the multi-drug resistant pAR06302. Introduction of pTF18 into bacteria harboring pAR06302 showed plasmids were cured at an efficiency of 53% (P<0.05). Using a murine neonate EPEC infection model, pTF16 was delivered by a murine derived E. coli strain to EPEC infected mice and showed significant reductions of intestinal EPEC (P<0.05). These results suggest that establishing conjugative CRISPR-Cas9 antimicrobials in the intestinal microbiome may provide protection from enteric pathogens and reduce antibiotic resistance without disrupting the normal microbiota.
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Affiliation(s)
- Haiqing Sheng
- Animal, Veterinary and Food Science, University of Idaho, Moscow, Idaho, United States of America
- Department of Chemical and Biological Engineering, University of Idaho, Moscow, Idaho, United States of America
| | - Sarah Wu
- Department of Chemical and Biological Engineering, University of Idaho, Moscow, Idaho, United States of America
| | - Yansong Xue
- Animal, Veterinary and Food Science, University of Idaho, Moscow, Idaho, United States of America
| | - Wei Zhao
- Animal, Veterinary and Food Science, University of Idaho, Moscow, Idaho, United States of America
| | - Allan B. Caplan
- Department of Plant Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Carolyn J. Hovde
- Animal, Veterinary and Food Science, University of Idaho, Moscow, Idaho, United States of America
| | - Scott A. Minnich
- Animal, Veterinary and Food Science, University of Idaho, Moscow, Idaho, United States of America
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16
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Abstract
A massive number of microorganisms, belonging to different species, continuously divide inside the guts of animals and humans. The large size of these communities and their rapid division times imply that we should be able to watch microbial evolution in the gut in real time, in a similar manner to what has been done in vitro. Here, we review recent findings on how natural selection shapes intrahost evolution (also known as within-host evolution), with a focus on the intestines of mice and humans. The microbiota of a healthy host is not as static as initially thought from the information measured at only one genomic marker. Rather, the genomes of each gut-colonizing species can be highly dynamic, and such dynamism seems to be related to the microbiota species diversity. Genetic and bioinformatic tools, and analysis of time series data, allow quantification of the selection strength on emerging mutations and horizontal transfer events in gut ecosystems. The drivers and functional consequences of gut evolution can now begin to be grasped. The rules of this intrahost microbiota evolution, and how they depend on the biology of each species, need to be understood for more effective development of microbiota therapies to help maintain or restore host health.
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Affiliation(s)
| | - Isabel Gordo
- Instituto Gulbenkian de Ciência, Oeiras, Portugal.
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17
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Bosch DE, Abbasian R, Parajuli B, Peterson SB, Mougous JD. Structural disruption of Ntox15 nuclease effector domains by immunity proteins protects against type VI secretion system intoxication in Bacteroidales. mBio 2023; 14:e0103923. [PMID: 37345922 PMCID: PMC10470768 DOI: 10.1128/mbio.01039-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 05/03/2023] [Indexed: 06/23/2023] Open
Abstract
Bacteroidales use type VI secretion systems (T6SS) to competitively colonize and persist in the colon. We identify a horizontally transferred T6SS with Ntox15 family nuclease effector (Tde1) that mediates interbacterial antagonism among Bacteroidales, including several derived from a single human donor. Expression of cognate (Tdi1) or orphan immunity proteins in acquired interbacterial defense systems protects against Tde1-dependent attack. We find that immunity protein interaction induces a large effector conformational change in Tde nucleases, disrupting the active site and altering the DNA-binding site. Crystallographic snapshots of isolated Tde1, the Tde1/Tdi1 complex, and homologs from Phocaeicola vulgatus (Tde2/Tdi2) illustrate a conserved mechanism of immunity inserting into the central core of Tde, splitting the nuclease fold into two subdomains. The Tde/Tdi interface and immunity mechanism are distinct from all other polymorphic toxin-immunity interactions of known structure. Bacteroidales abundance has been linked to inflammatory bowel disease activity in prior studies, and we demonstrate that Tde and T6SS structural genes are each enriched in fecal metagenomes from ulcerative colitis subjects. Genetically mobile Tde1-encoding T6SS in Bacteroidales mediate competitive growth and may be involved in inflammatory bowel disease. Broad immunity is conferred by Tdi1 homologs through a fold-disrupting mechanism unique among polymorphic effector-immunity pairs of known structure. IMPORTANCE Bacteroidales are related to inflammatory bowel disease severity and progression. We identify type VI secretion system (T6SS) nuclease effectors (Tde) which are enriched in ulcerative colitis and horizontally transferred on mobile genetic elements. Tde-encoding T6SSs mediate interbacterial competition. Orphan and cognate immunity proteins (Tdi) prevent intoxication by multiple Tde through a new mechanism among polymorphic toxin systems. Tdi inserts into the effector central core, splitting Ntox15 into two subdomains and disrupting the active site. This mechanism may allow for evolutionary diversification of the Tde/Tdi interface as observed in colicin nuclease-immunity interactions, promoting broad neutralization of Tde by orphan Tdi. Tde-dependent T6SS interbacterial antagonism may contribute to Bacteroidales diversity in the context of ulcerative colitis.
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Affiliation(s)
- Dustin E. Bosch
- Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Romina Abbasian
- Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Bishal Parajuli
- Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - S. Brook Peterson
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington, USA
| | - Joseph D. Mougous
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington, USA
- Microbial Interactions and Microbiome Center, University of Washington, Seattle, Washington, USA
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18
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Koo H, Morrow CD. Identification of donor Bacteroides vulgatus genes encoding proteins that correlate with early colonization following fecal transplant of patients with recurrent Clostridium difficile. Sci Rep 2023; 13:14112. [PMID: 37644161 PMCID: PMC10465488 DOI: 10.1038/s41598-023-41128-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 08/22/2023] [Indexed: 08/31/2023] Open
Abstract
Due to suppressive antibiotics, patients with recurrent Clostridium difficile have gut microbial communities that are devoid of most commensal microbes. Studies have shown that most of the failures using fecal microbe transplantation (FMT) for recurrent C. difficile occur during the first 4 weeks following transplantation. To identify features of donor Bacteroides vulgatus that lead to early colonization, we used two data sets that collected fecal samples from recipients at early times points post FMT. The first analysis used the shotgun metagenomic DNA sequencing data set from Aggarwala et al. consisting of 7 FMT donors and 13 patients with recurrent C. difficile with fecal samples taken as early as 24 h post FMT. We identified 2 FMT donors in which colonization of recipients by donor B. vulgatus was detected as early as 24 h post FMT. We examined a second data set from Hourigan et al. that collected fecal samples from C. difficile infected children and identified 1 of 3 FMT that also had early colonization of the donor B. vulgatus. We found 19 genes out of 4911 encoding proteins were unique to the 3 donors that had early colonization. A gene encoding a putative chitobiase was identified that was in a gene complex that had been previously identified to enhance colonization in mice. A gene encoding a unique fimbrillin (i.e., pili) family protein and 17 genes encoding hypothetical proteins were also specific for early colonizing donors. Most of the genes encoding hypothetical proteins had neighboring genes that encoded proteins involved in mobilization or transposition. Finally, analysis of 42 paired fecal samples from the human microbiome project (HMP) found no individuals had all 19 genes while 2 individuals had none of the 19 genes. Based on the results from our study, consideration should be given to the screening of FMT donors for these B. vulgatus genes found to enhance early colonization that would be of benefit to promote colonization following FMT.
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Affiliation(s)
- Hyunmin Koo
- Department of Genetics, Hugh Kaul Precision Medicine Institute, University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Casey D Morrow
- Department of Cell, Developmental and Integrative Biology, Hugh Kaul Precision Medicine Institute, University of Alabama at Birmingham, Birmingham, AL, USA.
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19
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Smith WPJ, Wucher BR, Nadell CD, Foster KR. Bacterial defences: mechanisms, evolution and antimicrobial resistance. Nat Rev Microbiol 2023:10.1038/s41579-023-00877-3. [PMID: 37095190 DOI: 10.1038/s41579-023-00877-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2023] [Indexed: 04/26/2023]
Abstract
Throughout their evolutionary history, bacteria have faced diverse threats from other microorganisms, including competing bacteria, bacteriophages and predators. In response to these threats, they have evolved sophisticated defence mechanisms that today also protect bacteria against antibiotics and other therapies. In this Review, we explore the protective strategies of bacteria, including the mechanisms, evolution and clinical implications of these ancient defences. We also review the countermeasures that attackers have evolved to overcome bacterial defences. We argue that understanding how bacteria defend themselves in nature is important for the development of new therapies and for minimizing resistance evolution.
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Affiliation(s)
- William P J Smith
- Division of Genomics, Infection and Evolution, University of Manchester, Manchester, UK.
- Department of Biology, University of Oxford, Oxford, UK.
- Department of Biochemistry, University of Oxford, Oxford, UK.
| | - Benjamin R Wucher
- Department of Biological sciences, Dartmouth College, Hanover, NH, USA
| | - Carey D Nadell
- Department of Biological sciences, Dartmouth College, Hanover, NH, USA
| | - Kevin R Foster
- Department of Biology, University of Oxford, Oxford, UK.
- Department of Biochemistry, University of Oxford, Oxford, UK.
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20
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Ding D, Wang B, Zhang X, Zhang J, Zhang H, Liu X, Gao Z, Yu Z. The spread of antibiotic resistance to humans and potential protection strategies. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 254:114734. [PMID: 36950985 DOI: 10.1016/j.ecoenv.2023.114734] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 02/26/2023] [Accepted: 03/03/2023] [Indexed: 06/18/2023]
Abstract
Antibiotic resistance is currently one of the greatest threats to human health. Widespread use and residues of antibiotics in humans, animals, and the environment can exert selective pressure on antibiotic resistance bacteria (ARB) and antibiotic resistance gene (ARG), accelerating the flow of antibiotic resistance. As ARG spreads to the population, the burden of antibiotic resistance in humans increases, which may have potential health effects on people. Therefore, it is critical to mitigate the spread of antibiotic resistance to humans and reduce the load of antibiotic resistance in humans. This review briefly described the information of global antibiotic consumption information and national action plans (NAPs) to combat antibiotic resistance and provided a set of feasible control strategies for the transmission of ARB and ARG to humans in three areas including (a) Reducing the colonization capacity of exogenous ARB, (b) Enhancing human colonization resistance and mitigating the horizontal gene transfer (HGT) of ARG, (c) Reversing ARB antibiotic resistance. With the hope of achieving interdisciplinary one-health prevention and control of bacterial resistance.
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Affiliation(s)
- Dong Ding
- The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China; College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Bin Wang
- College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Xiaoan Zhang
- The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Junxi Zhang
- NHC Key Laboratory of Birth Defects Prevention & Henan Key Laboratory of Population Defects Prevention, Zhengzhou, China
| | - Huanhuan Zhang
- College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Xinxin Liu
- College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Zhan Gao
- The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
| | - Zengli Yu
- College of Public Health, Zhengzhou University, Zhengzhou, China; The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
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21
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Weltzer ML, Wall D. Social Diversification Driven by Mobile Genetic Elements. Genes (Basel) 2023; 14:648. [PMID: 36980919 PMCID: PMC10047993 DOI: 10.3390/genes14030648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/17/2023] [Accepted: 02/28/2023] [Indexed: 03/08/2023] Open
Abstract
Social diversification in microbes is an evolutionary process where lineages bifurcate into distinct populations that cooperate with themselves but not with other groups. In bacteria, this is frequently driven by horizontal transfer of mobile genetic elements (MGEs). Here, the resulting acquisition of new genes changes the recipient's social traits and consequently how they interact with kin. These changes include discriminating behaviors mediated by newly acquired effectors. Since the producing cell is protected by cognate immunity factors, these selfish elements benefit from selective discrimination against recent ancestors, thus facilitating their proliferation and benefiting the host. Whether social diversification benefits the population at large is less obvious. The widespread use of next-generation sequencing has recently provided new insights into population dynamics in natural habitats and the roles MGEs play. MGEs belong to accessory genomes, which often constitute the majority of the pangenome of a taxon, and contain most of the kin-discriminating loci that fuel rapid social diversification. We further discuss mechanisms of diversification and its consequences to populations and conclude with a case study involving myxobacteria.
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Affiliation(s)
- Michael L Weltzer
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
| | - Daniel Wall
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
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22
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Boiten KE, Kuijper EJ, Schuele L, van Prehn J, Bode LGM, Maat I, van Asten SAV, Notermans DW, Rossen JWA, Veloo ACM. Characterization of mobile genetic elements in multidrug-resistant Bacteroides fragilis isolates from different hospitals in the Netherlands. Anaerobe 2023; 81:102722. [PMID: 37001724 DOI: 10.1016/j.anaerobe.2023.102722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 03/16/2023] [Accepted: 03/17/2023] [Indexed: 03/31/2023]
Abstract
OBJECTIVES Five human clinical multidrug-resistant (MDR) Bacteroides fragilis isolates, including resistance to meropenem and metronidazole, were recovered at different hospitals in the Netherlands between 2014 and 2020 and sent to the anaerobic reference laboratory for full characterization. METHODS Isolates were recovered from a variety of clinical specimens from patients with unrelated backgrounds. Long- and short-read sequencing was performed, followed by a hybrid assembly to study the presence of mobile genetic elements (MGEs) and antimicrobial resistance genes (ARGs). RESULTS A cfxA gene was present on a transposon (Tn) similar to Tn4555 in two isolates. In two isolates a novel Tn was present with the cfxA gene. Four isolates harbored a nimE gene, located on a pBFS01_2 plasmid. One isolate contained a novel plasmid carrying a nimA gene with IS1168. The tetQ gene was present on novel conjugative transposons (CTns) belonging to the CTnDOT family. Two isolates harbored a novel plasmid with tetQ. Other ARGs in these isolates, but not on an MGE, were: cfiA, ermF, mef(EN2), and sul2. ARGs harboured differed between isolates and corresponded with the observed phenotypic resistance. CONCLUSIONS Novel CTns, Tns, and plasmids were encountered in the five MDR B. fragilis isolates, complementing our knowledge on MDR and horizontal gene transfer in anaerobic bacteria.
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Affiliation(s)
- K E Boiten
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands.
| | - E J Kuijper
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands; Department of Medical Microbiology, Leiden University Center for Infectious Diseases, Leiden University Medical Center (LUMC), Leiden, the Netherlands
| | - L Schuele
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands
| | - J van Prehn
- Department of Medical Microbiology, Leiden University Center for Infectious Diseases, Leiden University Medical Center (LUMC), Leiden, the Netherlands
| | - L G M Bode
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center (Erasmus MC), Rotterdam, the Netherlands
| | - I Maat
- Radboud University Medical Center, Department of Medical Microbiology, Nijmegen, the Netherlands
| | - S A V van Asten
- Haga Ziekenhuis, Department of Medical Microbiology, Den Haag, the Netherlands
| | - D W Notermans
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - J W A Rossen
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands; Laboratory of Medical Microbiology and Infectious Diseases, Isala Hospital, Zwolle, the Netherlands; Department of Pathology, University of Utah School of Medicine, Salt Lake City, USA
| | - A C M Veloo
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands
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Singh RP, Kumari K. Bacterial type VI secretion system (T6SS): an evolved molecular weapon with diverse functionality. Biotechnol Lett 2023; 45:309-331. [PMID: 36683130 DOI: 10.1007/s10529-023-03354-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 12/14/2022] [Accepted: 01/05/2023] [Indexed: 01/24/2023]
Abstract
Bacterial secretion systems are nanomolecular complexes that release a diverse set of virulence factors/or proteins into its surrounding or translocate to their target host cells. Among these systems, type VI secretion system 'T6SS' is a recently discovered molecular secretion system which is widely distributed in Gram-negative (-ve) bacteria, and shares structural similarity with the puncturing device of bacteriophages. The presence of T6SS is an advantage to many bacteria as it delivers toxins to its neighbour pathogens for competitive survival, and also translocates protein effectors to the host cells, leading to disruption of lipid membranes, cell walls, and cytoskeletons etc. Recent studies have characterized both anti-prokaryotic and anti-eukaryotic effectors, where T6SS is involved in diverse cellular functions including favouring colonization, enhancing the survival, adhesive modifications, internalization, and evasion of the immune system. With the evolution of advanced genomics and proteomics tools, there has been an increase in the number of characterized T6SS effector arsenals and also more clear information about the adaptive significance of this complex system. The functions of T6SS are generally regulated at the transcription, post-transcription and post-translational levels through diverse mechanisms. In the present review, we aimed to provide information about the distribution of T6SS in diverse bacteria, any structural similarity/or dissimilarity, effectors proteins, functional significance, and regulatory mechanisms. We also tried to provide information about the diverse roles played by T6SS in its natural environments and hosts, and further any changes in the microbiome.
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Affiliation(s)
- Rajnish Prakash Singh
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India.
| | - Kiran Kumari
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
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24
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Qusa MH, Abdelwahed KS, Hill RA, El Sayed KA. S-(-)-Oleocanthal Ex Vivo Modulatory Effects on Gut Microbiota. Nutrients 2023; 15:nu15030618. [PMID: 36771326 PMCID: PMC9920009 DOI: 10.3390/nu15030618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 01/27/2023] Open
Abstract
Compelling evidence points to the critical role of bioactive extra-virgin olive oil (EVOO) phenolics and gut microbiota (GM) interplay, but reliable models for studying the consequences thereof remain to be developed. Herein, we report an optimized ex vivo fecal anaerobic fermentation model to study the modulation of GM by the most bioactive EVOO phenolic S-(-)-oleocanthal (OC), and impacts therefrom, focusing on OC biotransformation in the gut. This model will also be applicable for characterization of GM interactions with other EVOO phenolics, and moreover, for a broadly diverse range of bioactive natural products. The fecal fermentation media and time, and mouse type and gender, were the major factors varied and optimized to provide better understanding of GM-OC interplay. A novel resin entrapment technique (solid-phase extraction) served to selectively entrap OC metabolites, degradation products, and any remaining fraction of OC while excluding interfering complex fecal medium constituents. The effects of OC on GM compositions were investigated via shallow shotgun DNA sequencing. Robust metabolome analyses identified GM bacterial species selectively altered (population numbers/fraction) by OC. Finally, the topmost OC-affected gut bacterial species of the studied mice were compared with those known to be extant in humans and distributions of these bacteria at different human body sites. OC intake caused significant quantitative and qualitative changes to mice GM, which was also comparable with human GM. Results clearly highlight the potential positive health outcomes of OC as a prospective nutraceutical.
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25
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Dhariwal A, Haugli Bråten LC, Sturød K, Salvadori G, Bargheet A, Åmdal H, Junges R, Berild D, Zwart JA, Storheim K, Petersen FC. Differential response to prolonged amoxicillin treatment: long-term resilience of the microbiome versus long-lasting perturbations in the gut resistome. Gut Microbes 2023; 15:2157200. [PMID: 36576106 PMCID: PMC9809947 DOI: 10.1080/19490976.2022.2157200] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The collateral impact of antibiotics on the microbiome has attained increasing attention. However, the ecological consequences of long-term antibiotic exposure on the gut microbiome, including antibiotic resistance, are still limited. Here, we investigated long-term exposure effects to amoxicillin on the human gut microbiome and resistome. Fecal samples were collected from 20 patients receiving 3-months of amoxicillin or placebo treatment as part of a Norwegian multicenter clinical trial on chronic low back pain (AIM study). Samples were collected at baseline, last day of treatment, and 9 months after antibiotic cessation. The abundance and diversity of microbial and resistome composition were characterized using whole shotgun and functional metagenomic sequencing data. While the microbiome profiles of placebo subjects were stable over time, discernible changes in diversity and overall microbiome composition were observed after amoxicillin treatment. In particular, health-associated short-chain fatty acid producing species significantly decreased in proportion. However, these changes were short-lived as the microbiome showed overall recovery 9 months post-treatment. On the other hand, exposure to long-term amoxicillin was associated with an increase in total antimicrobial resistance gene load and diversity of antimicrobial resistance genes, with persistent changes even at 9 months post-treatment. Additionally, beta-lactam resistance was the most affected antibiotic class, suggesting a targeted response to amoxicillin, although changes at the gene level varied across individuals. Overall, our results suggest that the impact of prolonged amoxicillin exposure was more explicit and long-lasting in the fecal resistome than in microbiome composition. Such information is relevant for designing rational administration guidelines for antibiotic therapies.
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Affiliation(s)
- Achal Dhariwal
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Lars Christian Haugli Bråten
- Department of Research and Innovation, Division of Clinical Neuroscience, Oslo University Hospital HF, Oslo, Norway
| | - Kjersti Sturød
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Gabriela Salvadori
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Ahmed Bargheet
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Heidi Åmdal
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Roger Junges
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Dag Berild
- Department of Infectious Diseases, Oslo University Hospital HF, Oslo, Norway,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - John-Anker Zwart
- Department of Research and Innovation, Division of Clinical Neuroscience, Oslo University Hospital HF, Oslo, Norway,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Kjersti Storheim
- Department of Research and Innovation, Division of Clinical Neuroscience, Oslo University Hospital HF, Oslo, Norway,Department of Physiotherapy, Faculty of Health Science, Oslo Metropolitan University, Oslo, Norway
| | - Fernanda Cristina Petersen
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway,CONTACT Fernanda Cristina Petersen Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
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Vatanen T, Jabbar KS, Ruohtula T, Honkanen J, Avila-Pacheco J, Siljander H, Stražar M, Oikarinen S, Hyöty H, Ilonen J, Mitchell CM, Yassour M, Virtanen SM, Clish CB, Plichta DR, Vlamakis H, Knip M, Xavier RJ. Mobile genetic elements from the maternal microbiome shape infant gut microbial assembly and metabolism. Cell 2022; 185:4921-4936.e15. [PMID: 36563663 PMCID: PMC9869402 DOI: 10.1016/j.cell.2022.11.023] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 09/30/2022] [Accepted: 11/11/2022] [Indexed: 12/24/2022]
Abstract
The perinatal period represents a critical window for cognitive and immune system development, promoted by maternal and infant gut microbiomes and their metabolites. Here, we tracked the co-development of microbiomes and metabolomes from late pregnancy to 1 year of age using longitudinal multi-omics data from a cohort of 70 mother-infant dyads. We discovered large-scale mother-to-infant interspecies transfer of mobile genetic elements, frequently involving genes associated with diet-related adaptations. Infant gut metabolomes were less diverse than maternal but featured hundreds of unique metabolites and microbe-metabolite associations not detected in mothers. Metabolomes and serum cytokine signatures of infants who received regular-but not extensively hydrolyzed-formula were distinct from those of exclusively breastfed infants. Taken together, our integrative analysis expands the concept of vertical transmission of the gut microbiome and provides original insights into the development of maternal and infant microbiomes and metabolomes during late pregnancy and early life.
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Affiliation(s)
- Tommi Vatanen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Liggins Institute, University of Auckland, Auckland, New Zealand
| | | | - Terhi Ruohtula
- New Children's Hospital, Helsinki University Hospital, Helsinki, Finland
| | - Jarno Honkanen
- New Children's Hospital, Helsinki University Hospital, Helsinki, Finland
| | | | - Heli Siljander
- New Children's Hospital, Helsinki University Hospital, Helsinki, Finland; Centre for Military Medicine, Finnish Defence Forces, Riihimäki, Finland
| | - Martin Stražar
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sami Oikarinen
- Department of Virology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Heikki Hyöty
- Department of Virology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland; Fimlab Laboratories, Tampere, Finland
| | - Jorma Ilonen
- Immunogenetics Laboratory, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Caroline M Mitchell
- Vincent Obstetrics & Gynecology Department, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Moran Yassour
- Microbiology & Molecular Genetics Department, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel; The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Suvi M Virtanen
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland; Unit of Health Sciences, Faculty of Social Sciences, Tampere University, Tampere, Finland; Center for Child Health Research and Development and Innovation Center, Tampere University Hospital, Tampere, Finland
| | - Clary B Clish
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Damian R Plichta
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA 02139, USA
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA 02139, USA
| | - Mikael Knip
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland; New Children's Hospital, Helsinki University Hospital, Helsinki, Finland; Tampere Center for Child Health Research, Tampere University Hospital, Tampere, Finland
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA 02139, USA; Center for Computational and Integrative Biology, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
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27
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Robinson L, Liaw J, Omole Z, Corcionivoschi N, Hachani A, Gundogdu O. In silico investigation of the genus Campylobacter type VI secretion system reveals genetic diversity in organization and putative effectors. Microb Genom 2022; 8:mgen000898. [PMID: 36314601 PMCID: PMC9676060 DOI: 10.1099/mgen.0.000898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 09/11/2022] [Indexed: 01/25/2023] Open
Abstract
Bacterial type VI secretion systems (T6SSs) are contractile nanomachines that deliver proteinic substrates into target prokaryotic or eukaryotic cells and the surrounding milieu. The genus Campylobacter encompasses 39 recognized species and 13 subspecies, with many belonging to a group known as ‘emerging Campylobacter pathogens’. Within Campylobacter , seven species have been identified to harbour a complete T6SS cluster but have yet to be comparatively assessed. In this study, using systematic bioinformatics approaches and the T6SS-positive Campylobacter jejuni 488 strain as a reference, we explored the genus-wide prevalence, similarity and make-up of the T6SS amongst 372 publicly available ‘complete’ Campylobacter genomes. Our analyses predict that approximately one-third of Campylobacter species possess a T6SS. We also putatively report the first identification of a T6SS in four species: Campylobacter cuniculorum, Campylobacter helveticus, Campylobacter armoricus and Campylobacter ornithocola . The Campylobacter T6SSs cluster into three distinct organizations (I–III), of which two break down into further variants. Thirty T6SS-containing genomes were found to harbour more than one vgrG gene, with Campylobacter lari strain NCTC 11845 possessing five. Analysis of the C. jejuni Pathogenicity Island-1 confirmed its conservation amongst T6SS-positive C. jejuni strains, as well as highlighting its diverse genetic composition, including additional putative effector–immunity pairs (e.g. PoNe and DUF1911 domains). Effector–immunity pairs were also observed neighbouring vgrG s in several other Campylobacter species, in addition to putative genes encoding nucleases, lysozymes, ATPases and a ferric ATP-binding cassette uptake system. These observations highlight the diverse genetic make-up of the T6SS within Campylobacter and provide further evidence of its role in pathogenesis.
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Affiliation(s)
- Luca Robinson
- National Heart and Lung Institute, Imperial College London, London, UK
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Janie Liaw
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Zahra Omole
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Nicolae Corcionivoschi
- Bacteriology Branch, Veterinary Sciences Division, Agri-Food and Biosciences Institute, Belfast, UK
- Bioengineering of Animal Resources, University of Life Sciences – King Mihai I of Romania from Timisoara, Timisoara, Romania
| | - Abderrahman Hachani
- The Peter Doherty Institute for Infection and Immunity, Department of Microbiology and Immunology, University of Melbourne, Melbourne, VIC, Australia
| | - Ozan Gundogdu
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
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28
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Koo H, Morrow CD. Time series strain tracking analysis post fecal transplantation identifies individual specific patterns of fecal dominant donor, recipient, and unrelated microbial strains. PLoS One 2022; 17:e0274633. [PMID: 36107983 PMCID: PMC9477264 DOI: 10.1371/journal.pone.0274633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 08/31/2022] [Indexed: 11/21/2022] Open
Abstract
Background Fecal microbial transplantation (FMT) has been used with the therapeutic intent to change the functions of the gut microbial community in metabolism and host immunity. For most of these therapies, the recipients are not given antibiotics to eliminate the microbial community prior to transplant with donor fecal microbes resulting in the initial gut microbial community following FMT consisting of a consortium of donor and recipient microbes. The detailed analysis of the fecal samples from these FMT over time provides a unique opportunity to study the changes in the gut microbial strain community that occurs following the introduction of new microbial strains (donor) into an established community (recipient). Methods In this study, we have metagenomic data set consisting of 5 FMT that contained donor, recipient and recipient post FMT taken multiple times for periods up to 535 days after the FMT. We used two established strain tracking methods, Window-based Single Nucleotide Variant (SNV) Similarity (WSS) and StrainPhlAn, to determine the presence of donor and recipient microbial strains following FMT. To assess recombination between donor and recipient strains of Bacteroides vulgatus post FMT, we used BLAST+ to analyze the data sets for Bacteroidales-specific antimicrobial proteins (BSAP-3) that have known functions to restrict species specific replication. Results We found that Alistipes onderdonkii, Alistipes shahii, Alistipes putredinis, and Parabacteroides merdae, all had patterns post FMT consisting of either dominant donor or recipient microbial strains in the feces. In contrast, the analysis of Bacteroides spp. in five FMT pairs revealed inter-individual oscillation over time with the appearance of either donor or recipient fecal strain dominance. In some instances, B. vulgatus and B. uniformis were also identified after FMT that were not related to either the donor or recipient. Finally, in one of the FMT, we identified a distinct B. vulgatus strain post-FMT that matched the pre-FMT strain but was BSAP-3 positive, suggesting a possible recombination event between the donor and recipient strains. Conclusion The complex oscillating patterns of the appearance of fecal dominant donor, recipient or unrelated strains following extended times post FMT provide new insights into the dynamics of the microbial community interactions with the recipients following FMT. The result from our analysis has implications for the use of FMT to predictably change the biological functions of the gut community in metabolism and host immunity.
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Affiliation(s)
- Hyunmin Koo
- Department of Genetics, Hugh Kaul Precision Medicine Institute, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- * E-mail: (HK); (CDM)
| | - Casey D. Morrow
- Department of Cell, Developmental and Integrative Biology, Hugh Kaul Precision Medicine Institute, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- * E-mail: (HK); (CDM)
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29
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Analysis of Effector and Immunity Proteins of the GA2 Type VI Secretion Systems of Gut Bacteroidales. J Bacteriol 2022; 204:e0012222. [PMID: 35735993 PMCID: PMC9295542 DOI: 10.1128/jb.00122-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Three distinct genetic architectures (GAs) of Type VI secretion systems (T6SSs) have been described in gut Bacteroidales species, each with unique genes and characteristics. Unlike the GA3 T6SSs, potent antagonism has not yet been demonstrated for the GA1 or GA2 T6SSs. We previously showed that the GA2 T6SS loci are contained on integrative and conjugative elements and that there are five subtypes. Collectively, GA2 are the most prevalent Bacteroidales T6SSs in the human populations analyzed. In this study, we provide a comprehensive bioinformatic analysis of the three variable regions of GA2 T6SS loci, which encode toxic effector and immunity proteins. In total, we identified 63 distinct effectors encoded within 31 nonredundant GA2 loci, 18 of which do not have described motifs or predicted functions. We provide experimental evidence for toxin activity for four different GA2 effectors, showing that each functions only when present in the periplasm, and experimentally confirm their cognate immunity proteins. Our data demonstrate that each GA2 locus encodes at least three distinct effectors with targets in both the cytoplasm and the periplasm. The data also suggest that the effectors of a given locus are loaded onto the tube by different mechanisms, which may allow all three effectors encoded within a single GA2 locus with distinct antibacterial activity to be loaded onto a single T6 tube, increasing the antagonistic effect. IMPORTANCE Humans are colonized with many gut Bacteroidales species at high density, allowing for extensive opportunities for contact-dependent antagonism. To begin to understand the antagonistic potential of the GA2 T6SSs of the gut Bacteroidales, we performed bioinformatic and experimental analyses of the three divergent regions containing the toxin effector and immunity genes. We show that each GA2 T6SS locus encodes at least three distinct toxic effectors including toxins linked to Rhs and Hcp with cytoplasmic targets, and unlinked effectors with targets in the periplasm. The diversity and modality of effectors exceeds that of the GA1 or GA3 T6SS loci (M. J. Coyne, K. G. Roelofs, and L. E. Comstock, BMC Genomics 17:58, 2016, https://doi.org/10.1186/s12864-016-2377-z) and suggests that these T6SSs have the potential to be potent antibacterial weapons in the human gut.
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30
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Conteville LC, Vicente ACP. A plasmid network from the gut microbiome of semi-isolated human groups reveals unique and shared metabolic and virulence traits. Sci Rep 2022; 12:12102. [PMID: 35840779 PMCID: PMC9287393 DOI: 10.1038/s41598-022-16392-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 07/08/2022] [Indexed: 11/29/2022] Open
Abstract
The plasmids in gut microbiomes have the potential to contribute to the microbiome community, as well as human health and physiology. Nevertheless, this niche remains poorly explored. In general, most microbiome studies focus on urban-industrialized groups, but here, we studied semi-isolated groups from South America and Africa, which would represent a link between ancestral and modern human groups. Based on open metagenomic data, we characterized the set of plasmids, including their genes and functions, from the gut microbiome of the Hadza, Matses, Tunapuco, and Yanomami, semi-isolated groups with a hunter, gather or subsistence lifestyle. Unique plasmid clusters and gene functions for each human group were identified. Moreover, a dozen plasmid clusters circulating in other niches worldwide are shared by these distinct groups. In addition, novel and unique plasmids harboring resistance (encompassing six antibiotic classes and multiple metals) and virulence (as type VI secretion systems) genes were identified. Functional analysis revealed pathways commonly associated with urban-industrialized groups, such as lipopolysaccharide biosynthesis that was characterized in the Hadza gut plasmids. These results demonstrate the richness of plasmids in semi-isolated human groups’ gut microbiome, which represents an important source of information with biotechnological/pharmaceutical potential, but also on the spread of resistance/virulence genes to semi-isolated groups.
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Affiliation(s)
- Liliane Costa Conteville
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil.
| | - Ana Carolina Paulo Vicente
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
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31
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Ott LC, Mellata M. Models for Gut-Mediated Horizontal Gene Transfer by Bacterial Plasmid Conjugation. Front Microbiol 2022; 13:891548. [PMID: 35847067 PMCID: PMC9280185 DOI: 10.3389/fmicb.2022.891548] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
The emergence of new antimicrobial resistant and virulent bacterial strains may pose a threat to human and animal health. Bacterial plasmid conjugation is a significant contributor to rapid microbial evolutions that results in the emergence and spread of antimicrobial resistance (AR). The gut of animals is believed to be a potent reservoir for the spread of AR and virulence genes through the horizontal exchange of mobile genetic elements such as plasmids. The study of the plasmid transfer process in the complex gut environment is limited due to the confounding factors that affect colonization, persistence, and plasmid conjugation. Furthermore, study of plasmid transfer in the gut of humans is limited to observational studies, leading to the need to identify alternate models that provide insight into the factors regulating conjugation in the gut. This review discusses key studies on the current models for in silico, in vitro, and in vivo modeling of bacterial conjugation, and their ability to reflect the gut of animals. We particularly emphasize the use of computational and in vitro models that may approximate aspects of the gut, as well as animal models that represent in vivo conditions to a greater extent. Directions on future research studies in the field are provided.
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Affiliation(s)
- Logan C. Ott
- Department of Food Science and Human Nutrition, Iowa State University, Ames, IA, United States
- Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA, United States
| | - Melha Mellata
- Department of Food Science and Human Nutrition, Iowa State University, Ames, IA, United States
- Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA, United States
- *Correspondence: Melha Mellata,
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32
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Fansler RT, Zhu W. Mind the Gap: Bridging the Divide from Sequencing Data to Empiric Phenotypes in the Human Gut Microbiota. mSystems 2022; 7:e0020722. [PMID: 35695430 PMCID: PMC9239041 DOI: 10.1128/msystems.00207-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The gut microbiome exerts a powerful influence on human health and disease. Elucidating the underlying mechanisms of the microbiota's influence is hindered by the immense complexity of the gut microbial community and the glycans they forage. Despite a wealth of genomic and metagenomic sequencing information, there remains a lack of informative phenotypic measurements. Pudlo NA, Urs K, Crawford R, Pirani A, et al. (mSystems 7: e00947-21, 2022, https://doi.org/10.1128/msystems.00947-21) decode this complexity by introducing a scalable assay to measure specific carbohydrate utilization in the dominant microbiota phylum Bacteroidetes. The results reveal a mosaic structure of glycan utilization, both genetic and functional, underpinning niche construction in the human gastrointestinal tract. This Commentary highlights the significance of their findings in connection to the field's growing appreciation for competition, cooperation, and horizontal gene transfer in shaping the highly complex microbial community.
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Affiliation(s)
- Ryan T. Fansler
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, Tennessee, USA
| | - Wenhan Zhu
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, Tennessee, USA
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Chen DW, Garud NR. Rapid evolution and strain turnover in the infant gut microbiome. Genome Res 2022; 32:1124-1136. [PMID: 35545448 DOI: 10.1101/gr.276306.121] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 05/06/2022] [Indexed: 11/25/2022]
Abstract
While the ecological dynamics of the infant gut microbiome have been intensely studied, relatively little is known about evolutionary dynamics in the infant gut microbiome. Here we analyze longitudinal fecal metagenomic data from >700 infants and their mothers over the first year of life and find that the evolutionary dynamics in infant gut microbiomes are distinct from that of adults. We find evidence for more than 10-fold increase in the rate of evolution and strain turnover in the infant gut compared to healthy adults, with the mother-infant transition at delivery being a particularly dynamic period in which gene loss dominates. Within a few months after birth, these dynamics stabilize, and gene gains become increasingly frequent as the microbiome matures. We furthermore find that evolutionary changes in infants show signatures of being seeded by a mixture of de novo mutations and transmissions of pre-evolved lineages from the broader family. Several of these evolutionary changes occur in parallel across infants, highlighting candidate genes that may play important roles in the development of the infant gut microbiome. Our results point to a picture of a volatile infant gut microbiome characterized by rapid evolutionary and ecological change in the early days of life.
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Affiliation(s)
- Daisy W Chen
- University of California, Los Angeles, University of California, San Diego
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Crits-Christoph A, Hallowell HA, Koutouvalis K, Suez J. Good microbes, bad genes? The dissemination of antimicrobial resistance in the human microbiome. Gut Microbes 2022; 14:2055944. [PMID: 35332832 PMCID: PMC8959533 DOI: 10.1080/19490976.2022.2055944] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
A global rise in antimicrobial resistance among pathogenic bacteria has proved to be a major public health threat, with the rate of multidrug-resistant bacterial infections increasing over time. The gut microbiome has been studied as a reservoir of antibiotic resistance genes (ARGs) that can be transferred to bacterial pathogens via horizontal gene transfer (HGT) of conjugative plasmids and mobile genetic elements (the gut resistome). Advances in metagenomic sequencing have facilitated the identification of resistome modulators, including live microbial therapeutics such as probiotics and fecal microbiome transplantation that can either expand or reduce the abundances of ARG-carrying bacteria in the gut. While many different gut microbes encode for ARGs, they are not uniformly distributed across, or transmitted by, various members of the microbiome, and not all are of equal clinical relevance. Both experimental and theoretical approaches in microbial ecology have been applied to understand differing frequencies of ARG horizontal transfer between commensal microbes as well as between commensals and pathogens. In this commentary, we assess the evidence for the role of commensal gut microbes in encoding antimicrobial resistance genes, the degree to which they are shared both with other commensals and with pathogens, and the host and environmental factors that can impact resistome dynamics. We further discuss novel sequencing-based approaches for identifying ARGs and predicting future transfer events of clinically relevant ARGs from commensals to pathogens.
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Affiliation(s)
- Alexander Crits-Christoph
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Haley Anne Hallowell
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Kalia Koutouvalis
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Jotham Suez
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA,CONTACT Jotham Suez Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, 615 N Wolfe St, Baltimore, Maryland, USA, 21205
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35
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Unni R, Pintor KL, Diepold A, Unterweger D. Presence and absence of type VI secretion systems in bacteria. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35467500 DOI: 10.1099/mic.0.001151] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The type VI secretion system (T6SS) is a molecular puncturing device that enables Gram-negative bacteria to kill competitors, manipulate host cells and take up nutrients. Who would want to miss such superpowers? Indeed, many studies show how widespread the secretion apparatus is among microbes. However, it is becoming evident that, on multiple taxonomic levels, from phyla to species and strains, some bacteria lack a T6SS. Here, we review who does and does not have a type VI secretion apparatus and speculate on the dynamic process of gaining and losing the secretion system to better understand its spread and distribution across the microbial world.
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Affiliation(s)
- Rahul Unni
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Straße 2, 24306 Plön, Germany.,Institute for Experimental Medicine, Kiel University, Michaelisstraße 5, 24105 Kiel, Germany
| | - Katherine L Pintor
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Andreas Diepold
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Daniel Unterweger
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Straße 2, 24306 Plön, Germany.,Institute for Experimental Medicine, Kiel University, Michaelisstraße 5, 24105 Kiel, Germany
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36
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Serapio-Palacios A, Woodward SE, Vogt SL, Deng W, Creus-Cuadros A, Huus KE, Cirstea M, Gerrie M, Barcik W, Yu H, Finlay BB. Type VI secretion systems of pathogenic and commensal bacteria mediate niche occupancy in the gut. Cell Rep 2022; 39:110731. [PMID: 35476983 DOI: 10.1016/j.celrep.2022.110731] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 02/04/2022] [Accepted: 04/01/2022] [Indexed: 12/18/2022] Open
Abstract
The type VI secretion system (T6SS) is a contractile nanomachine widely distributed among pathogenic and commensal Gram-negative bacteria. The T6SS is used for inter-bacterial competition to directly kill competing species; however, its importance during bacterial infection in vivo remains poorly understood. We report that the murine pathogen Citrobacter rodentium, used as a model for human pathogenic Escherichia coli, harbors two functional T6SSs. C. rodentium employs its T6SS-1 to colonize the murine gastrointestinal tract by targeting commensal Enterobacteriaceae. We identify VgrG1 as a C. rodentium T6SS antibacterial effector, which exhibits toxicity in E. coli. Conversely, commensal prey species E. coli Mt1B1 employs two T6SSs of its own to counter C. rodentium colonization. Collectively, these data demonstrate that the T6SS is a potent weapon during bacterial competition and is used by both invading pathogens and resident microbiota to fight for a niche in the hostile gut environment.
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Affiliation(s)
- Antonio Serapio-Palacios
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Microbiology and Immunology, University of British Columbia, BC V6T 1Z3, Canada
| | - Sarah E Woodward
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Microbiology and Immunology, University of British Columbia, BC V6T 1Z3, Canada
| | - Stefanie L Vogt
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Microbiology and Immunology, University of British Columbia, BC V6T 1Z3, Canada
| | - Wanyin Deng
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Anna Creus-Cuadros
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Microbiology and Immunology, University of British Columbia, BC V6T 1Z3, Canada
| | - Kelsey E Huus
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Microbiology and Immunology, University of British Columbia, BC V6T 1Z3, Canada
| | - Mihai Cirstea
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Microbiology and Immunology, University of British Columbia, BC V6T 1Z3, Canada
| | - Madeleine Gerrie
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Weronika Barcik
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Microbiology and Immunology, University of British Columbia, BC V6T 1Z3, Canada
| | - Hongbing Yu
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - B Brett Finlay
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Microbiology and Immunology, University of British Columbia, BC V6T 1Z3, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
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37
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Backes N, Phillips GJ. Repurposing CRISPR-Cas Systems as Genetic Tools for the Enterobacteriales. EcoSal Plus 2021; 9:eESP00062020. [PMID: 34125584 PMCID: PMC11163844 DOI: 10.1128/ecosalplus.esp-0006-2020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 03/22/2021] [Indexed: 11/20/2022]
Abstract
Over the last decade, the study of CRISPR-Cas systems has progressed from a newly discovered bacterial defense mechanism to a diverse suite of genetic tools that have been applied across all domains of life. While the initial applications of CRISPR-Cas technology fulfilled a need to more precisely edit eukaryotic genomes, creative "repurposing" of this adaptive immune system has led to new approaches for genetic analysis of microorganisms, including improved gene editing, conditional gene regulation, plasmid curing and manipulation, and other novel uses. The main objective of this review is to describe the development and current state-of-the-art use of CRISPR-Cas techniques specifically as it is applied to members of the Enterobacteriales. While many of the applications covered have been initially developed in Escherichia coli, we also highlight the potential, along with the limitations, of this technology for expanding the availability of genetic tools in less-well-characterized non-model species, including bacterial pathogens.
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Affiliation(s)
- Nicholas Backes
- Department of Veterinary Microbiology, Iowa State University, Ames, Iowa, USA
| | - Gregory J. Phillips
- Department of Veterinary Microbiology, Iowa State University, Ames, Iowa, USA
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38
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Frye KA, Piamthai V, Hsiao A, Degnan PH. Mobilization of vitamin B12 transporters alters competitive dynamics in a human gut microbe. Cell Rep 2021; 37:110164. [PMID: 34965410 PMCID: PMC8759732 DOI: 10.1016/j.celrep.2021.110164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/29/2021] [Accepted: 12/02/2021] [Indexed: 02/07/2023] Open
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Gallegos-Monterrosa R, Coulthurst SJ. The ecological impact of a bacterial weapon: microbial interactions and the Type VI secretion system. FEMS Microbiol Rev 2021; 45:fuab033. [PMID: 34156081 PMCID: PMC8632748 DOI: 10.1093/femsre/fuab033] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 06/20/2021] [Indexed: 12/13/2022] Open
Abstract
Bacteria inhabit all known ecological niches and establish interactions with organisms from all kingdoms of life. These interactions are mediated by a wide variety of mechanisms and very often involve the secretion of diverse molecules from the bacterial cells. The Type VI secretion system (T6SS) is a bacterial protein secretion system that uses a bacteriophage-like machinery to secrete a diverse array of effectors, usually translocating them directly into neighbouring cells. These effectors display toxic activity in the recipient cell, making the T6SS an effective weapon during inter-bacterial competition and interactions with eukaryotic cells. Over the last two decades, microbiology research has experienced a shift towards using systems-based approaches to study the interactions between diverse organisms and their communities in an ecological context. Here, we focus on this aspect of the T6SS. We consider how our perspective of the T6SS has developed and examine what is currently known about the impact that bacteria deploying the T6SS can have in diverse environments, including niches associated with plants, insects and mammals. We consider how T6SS-mediated interactions can affect host organisms by shaping their microbiota, as well as the diverse interactions that can be established between different microorganisms through the deployment of this versatile secretion system.
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Affiliation(s)
| | - Sarah J Coulthurst
- School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
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40
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Zhang Y, Xu S, Yang Y, Chou SH, He J. A 'time bomb' in the human intestine-the multiple emergence and spread of antibiotic-resistant bacteria. Environ Microbiol 2021; 24:1231-1246. [PMID: 34632679 DOI: 10.1111/1462-2920.15795] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/21/2021] [Accepted: 09/28/2021] [Indexed: 11/30/2022]
Abstract
Antibiotics have a strong killing effect on bacteria and are the first choice for the prevention and treatment of bacterial infectious diseases. Therefore, they have been widely used in the medical field, animal husbandry and planting industry. However, with the massive use of antibiotics, more and more antibiotic-resistant bacteria (ARB) have emerged. Because human intestines are rich in nutrients, have suitable temperature, and are high in bacterial abundance, they can easily become a hotbed for the spread of ARB and antibiotic-resistant genes (ARGs). When opportunistic pathogenic bacteria in the intestine acquire ARGs, the infectious diseases caused by such opportunistic pathogens will become more difficult to treat, or even impossible to cure. Therefore, ARB in the human intestine are like a 'time bomb'. In this review, we discuss the sources of intestinal ARB and the transmission routes of ARGs in the human intestine from the perspective of One Health. Further, we describe various methods to prevent the emergence of ARB and inhibit the spread of ARGs in the human intestine. Finally, we may be able to overcome ARB in the human intestine using an interdisciplinary 'One Health' approach.
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Affiliation(s)
- Yuling Zhang
- State Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Siyang Xu
- State Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Yijun Yang
- State Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Shan-Ho Chou
- State Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Jin He
- State Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
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41
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McKee LS, La Rosa SL, Westereng B, Eijsink VG, Pope PB, Larsbrink J. Polysaccharide degradation by the Bacteroidetes: mechanisms and nomenclature. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:559-581. [PMID: 34036727 DOI: 10.1111/1758-2229.12980] [Citation(s) in RCA: 109] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 05/22/2021] [Accepted: 05/23/2021] [Indexed: 06/12/2023]
Abstract
The Bacteroidetes phylum is renowned for its ability to degrade a wide range of complex carbohydrates, a trait that has enabled its dominance in many diverse environments. The best studied species inhabit the human gut microbiome and use polysaccharide utilization loci (PULs), discrete genetic structures that encode proteins involved in the sensing, binding, deconstruction, and import of target glycans. In many environmental species, polysaccharide degradation is tightly coupled to the phylum-exclusive type IX secretion system (T9SS), which is used for the secretion of certain enzymes and is linked to gliding motility. In addition, within specific species these two adaptive systems (PULs and T9SS) are intertwined, with PUL-encoded enzymes being secreted by the T9SS. Here, we discuss the most noteworthy PUL and non-PUL mechanisms that confer specific and rapid polysaccharide degradation capabilities to the Bacteroidetes in a range of environments. We also acknowledge that the literature showcasing examples of PULs is rapidly expanding and developing a set of assumptions that can be hard to track back to original findings. Therefore, we present a simple universal description of conserved PUL functions and how they are determined, while proposing a common nomenclature describing PULs and their components, to simplify discussion and understanding of PUL systems.
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Affiliation(s)
- Lauren S McKee
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, 106 91, Sweden
- Wallenberg Wood Science Center, Stockholm, 100 44, Sweden
| | | | - Bjørge Westereng
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Vincent G Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Phillip B Pope
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Johan Larsbrink
- Wallenberg Wood Science Center, Stockholm, 100 44, Sweden
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, 412 96, Sweden
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42
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Defending against the Type Six Secretion System: beyond Immunity Genes. Cell Rep 2021; 33:108259. [PMID: 33053336 DOI: 10.1016/j.celrep.2020.108259] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 07/10/2020] [Accepted: 09/21/2020] [Indexed: 02/07/2023] Open
Abstract
The bacterial type six secretion system (T6SS) delivers toxic effector proteins into neighboring cells, but bacteria must protect themselves against their own T6SS. Immunity genes are the best-characterized defenses, protecting against specific cognate effectors. However, the prevalence of the T6SS and the coexistence of species with heterologous T6SSs suggest evolutionary pressure selecting for additional defenses against it. Here we review defenses against the T6SS beyond self-associated immunity genes, such as diverse stress responses that can recognize T6SS-inflicted damage and coordinate induction of molecular armor, repair pathways, and overall survival. Some of these stress responses are required for full survival even in the presence of immunity genes. Finally, we propose that immunity gene-independent protection is, mechanistically, bacterial innate immunity and that such defenses and the T6SS have co-evolved and continue to shape one another in polymicrobial communities.
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43
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Kern L, Abdeen SK, Kolodziejczyk AA, Elinav E. Commensal inter-bacterial interactions shaping the microbiota. Curr Opin Microbiol 2021; 63:158-171. [PMID: 34365152 DOI: 10.1016/j.mib.2021.07.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/15/2021] [Accepted: 07/16/2021] [Indexed: 12/14/2022]
Abstract
The gut microbiota, a complex ecosystem of microorganisms of different kingdoms, impacts host physiology and disease. Within this ecosystem, inter-bacterial interactions and their impacts on microbiota community structure and the eukaryotic host remain insufficiently explored. Microbiota-related inter-bacterial interactions range from symbiotic interactions, involving exchange of nutrients, enzymes, and genetic material; competition for nutrients and space, mediated by biophysical alterations and secretion of toxins and anti-microbials; to predation of overpopulating bacteria. Collectively, these understudied interactions hold important clues as to forces shaping microbiota diversity, niche formation, and responses to signals perceived from the host, incoming pathogens and the environment. In this review, we highlight the roles and mechanisms of selected inter-bacterial interactions in the microbiota, and their potential impacts on the host and pathogenic infection. We discuss challenges in mechanistically decoding these complex interactions, and prospects of harnessing them as future targets for rational microbiota modification in a variety of diseases.
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Affiliation(s)
- Lara Kern
- Immunology Department, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Suhaib K Abdeen
- Immunology Department, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | | | - Eran Elinav
- Immunology Department, Weizmann Institute of Science, Rehovot, 7610001, Israel; Cancer-Microbiota Division Deutsches Krebsforschungszentrum (DKFZ), Neuenheimer Feld 280, 69120 Heidelberg, Germany.
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44
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Dong X, Zhang C, Li W, Weng S, Song W, Li J, Wang Y. Functional diversity of microbial communities in inactive seafloor sulfide deposits. FEMS Microbiol Ecol 2021; 97:6327547. [PMID: 34302348 DOI: 10.1093/femsec/fiab108] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 07/22/2021] [Indexed: 11/12/2022] Open
Abstract
The seafloor sulfide structures of inactive vents are known to host abundant and diverse microorganisms potentially supported by mineralogy of sulfides. However, little is known about the diversity and distribution of microbial functions. Here, we used genome-resolved metagenomics to predict microbial metabolic functions and the contribution of horizontal gene transfer to the functionality of microorganisms inhabiting several hydrothermally inactive seafloor deposits among globally distributed deep-sea vent fields. Despite of geographically distant vent fields, similar microbial community patterns were observed with the dominance of Gammaproteobacteria, Bacteroidota and previously overlooked Candidatus Patescibacteria. Metabolically flexible Gammaproteobacteria are major potential primary producers utilizing mainly sulfur, iron and hydrogen as electron donors coupled with oxygen and nitrate respiration for chemolithoautotrophic growth. In addition to heterotrophic microorganisms like free-living Bacteroidota, Ca. Patescibacteria potentially perform fermentative recycling of organic carbon. Finally, we provided evidence that many functional genes that are central to energy metabolism have been laterally transferred among members within the community and largely within the same class. Taken together, these findings shed light on microbial ecology and evolution in inactive seafloor sulfide deposits after the cessation of hydrothermal activities.
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Affiliation(s)
- Xiyang Dong
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China
| | - Chuwen Zhang
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Wenli Li
- Department of Life Science, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China
| | - Shengze Weng
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Weizhi Song
- Centre for Marine Science & Innovation, University of New South Wales, 2052 Sydney, Australia
| | - Jiangtao Li
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
| | - Yong Wang
- Department of Life Science, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China
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45
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Sun P, Yang J, Wang B, Ma H, Zhang Y, Guo J, Chen X, Zhao J, Sun H, Yang J, Yang H, Cui Y. The effects of combined environmental factors on the intestinal flora of mice based on ground simulation experiments. Sci Rep 2021; 11:11373. [PMID: 34059794 PMCID: PMC8166921 DOI: 10.1038/s41598-021-91077-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 05/17/2021] [Indexed: 11/09/2022] Open
Abstract
The composition and function of intestinal microbial communities are important for human health. However, these intestinal floras are sensitive to changes in the environment. Adverse changes to intestinal flora can affect the health of astronauts, resulting in difficulties in implementing space missions. We randomly divided mice into three groups and placed each group in either a normal environment, simulated microgravity environment or a combined effects environment, which included simulated microgravity, low pressure and noise. Fecal samples of the mice were collected for follow-up analysis based on metagenomics technology. With the influence of different space environmental factors, the species composition at the phylum and genus levels were significantly affected by the combined effects environment, especially the abundance of the Firmicutes and Bacteroidetes. Furthermore, screening was conducted to identify biomarkers that could be regarded as environmental markers. And there have also been some noticeable changes in the function of intestinal floras. Moreover, the abundance of antibiotic resistance genes (ARGs) was also found to be changed under different environmental conditions, such as bacitracin and vancomycin. The combined effects environment could significantly affect the species composition, function, and the expression of ARGs of intestinal flora of mice which may provide a theoretical basis for space medical supervision and healthcare.
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Affiliation(s)
- Peiming Sun
- Department of General Surgery, Strategic Support Force Medical Center, Chaoyang District, Beijing, 100101, China
| | - Jiaqi Yang
- Department of General Surgery, Strategic Support Force Medical Center, Chaoyang District, Beijing, 100101, China
- Department of General Surgery, The 306th Hospital of Chinese PLA-Peking University Teaching Hospital, Chaoyang District, Beijing, 100101, China
| | - Bo Wang
- China Astronaut Research and Training Center, Haidian District, Beijing, 100094, China
| | - Huan Ma
- Ministry of Education (MOE) Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Haizhu District, Guangzhou, 510006, China
| | - Yin Zhang
- Ministry of Education (MOE) Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Haizhu District, Guangzhou, 510006, China
| | - Jinhu Guo
- Ministry of Education (MOE) Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Haizhu District, Guangzhou, 510006, China
| | - Xiaoping Chen
- China Astronaut Research and Training Center, Haidian District, Beijing, 100094, China
| | - Jianwei Zhao
- China Astronaut Research and Training Center, Haidian District, Beijing, 100094, China
| | - Hongwei Sun
- Department of General Surgery, Strategic Support Force Medical Center, Chaoyang District, Beijing, 100101, China
| | - Jianwu Yang
- Department of General Surgery, Strategic Support Force Medical Center, Chaoyang District, Beijing, 100101, China
| | - Heming Yang
- Department of General Surgery, Strategic Support Force Medical Center, Chaoyang District, Beijing, 100101, China.
| | - Yan Cui
- Department of General Surgery, Strategic Support Force Medical Center, Chaoyang District, Beijing, 100101, China.
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46
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Campbell DE, Ly LK, Ridlon JM, Hsiao A, Whitaker RJ, Degnan PH. Infection with Bacteroides Phage BV01 Alters the Host Transcriptome and Bile Acid Metabolism in a Common Human Gut Microbe. Cell Rep 2021; 32:108142. [PMID: 32937127 PMCID: PMC8354205 DOI: 10.1016/j.celrep.2020.108142] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 07/07/2020] [Accepted: 08/21/2020] [Indexed: 12/16/2022] Open
Abstract
Gut-associated phages are hypothesized to alter the abundance and activity of their bacterial hosts, contributing to human health and disease. Although temperate phages constitute a significant fraction of the gut virome, the effects of lysogenic infection are underexplored. We report that the temperate phage, Bacteroides phage BV01, broadly alters its host's transcriptome, the prominent human gut symbiont Bacteroides vulgatus. This alteration occurs through phage-induced repression of a tryptophan-rich sensory protein (TspO) and represses bile acid deconjugation. Because microbially modified bile acids are important signals for the mammalian host, this is a mechanism by which a phage may influence mammalian phenotypes. Furthermore, BV01 and its relatives in the proposed phage family Salyersviridae are ubiquitous in human gut metagenomes, infecting a broad range of Bacteroides hosts. These results demonstrate the complexity of phage-bacteria-mammal relationships and emphasize a need to better understand the role of temperate phages in the gut microbiome.
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Affiliation(s)
| | - Lindsey K Ly
- Division of Nutritional Sciences, University of Illinois, Urbana, IL 61801, USA; Department of Animal Sciences, University of Illinois, Urbana, IL 61801, USA
| | - Jason M Ridlon
- Division of Nutritional Sciences, University of Illinois, Urbana, IL 61801, USA; Department of Animal Sciences, University of Illinois, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA
| | - Ansel Hsiao
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA 92521, USA
| | - Rachel J Whitaker
- Department of Microbiology, University of Illinois, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA
| | - Patrick H Degnan
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA 92521, USA.
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García-Bayona L, Coyne MJ, Comstock LE. Mobile Type VI secretion system loci of the gut Bacteroidales display extensive intra-ecosystem transfer, multi-species spread and geographical clustering. PLoS Genet 2021; 17:e1009541. [PMID: 33901198 PMCID: PMC8102008 DOI: 10.1371/journal.pgen.1009541] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 05/06/2021] [Accepted: 04/08/2021] [Indexed: 02/07/2023] Open
Abstract
The human gut microbiota is a dense microbial ecosystem with extensive opportunities for bacterial contact-dependent processes such as conjugation and Type VI secretion system (T6SS)-dependent antagonism. In the gut Bacteroidales, two distinct genetic architectures of T6SS loci, GA1 and GA2, are contained on Integrative and Conjugative Elements (ICE). Despite intense interest in the T6SSs of the gut Bacteroidales, there is only a superficial understanding of their evolutionary patterns, and of their dissemination among Bacteroidales species in human gut communities. Here, we combine extensive genomic and metagenomic analyses to better understand their ecological and evolutionary dynamics. We identify new genetic subtypes, document extensive intrapersonal transfer of these ICE to Bacteroidales species within human gut microbiomes, and most importantly, reveal frequent population fixation of these newly armed strains in multiple species within a person. We further show the distribution of each of the distinct T6SSs in human populations and show there is geographical clustering. We reveal that the GA1 T6SS ICE integrates at a minimal recombination site leading to their integration throughout genomes and their frequent interruption of genes, whereas the GA2 T6SS ICE integrate at one of three different tRNA genes. The exclusion of concurrent GA1 and GA2 T6SSs in individual strains is associated with intact T6SS loci and with an ICE-encoded gene. By performing a comprehensive analysis of mobile genetic elements (MGE) in co-resident Bacteroidales species in numerous human gut communities, we identify 74 MGE that transferred to multiple Bacteroidales species within individual gut microbiomes. We further show that only three other MGE demonstrate multi-species spread in human gut microbiomes to the degree demonstrated by the GA1 and GA2 ICE. These data underscore the ubiquity and dissemination of mobile T6SS loci within Bacteroidales communities and across human populations.
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Affiliation(s)
- Leonor García-Bayona
- Division of Infectious Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Michael J. Coyne
- Division of Infectious Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Laurie E. Comstock
- Division of Infectious Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
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Groussin M, Poyet M, Sistiaga A, Kearney SM, Moniz K, Noel M, Hooker J, Gibbons SM, Segurel L, Froment A, Mohamed RS, Fezeu A, Juimo VA, Lafosse S, Tabe FE, Girard C, Iqaluk D, Nguyen LTT, Shapiro BJ, Lehtimäki J, Ruokolainen L, Kettunen PP, Vatanen T, Sigwazi S, Mabulla A, Domínguez-Rodrigo M, Nartey YA, Agyei-Nkansah A, Duah A, Awuku YA, Valles KA, Asibey SO, Afihene MY, Roberts LR, Plymoth A, Onyekwere CA, Summons RE, Xavier RJ, Alm EJ. Elevated rates of horizontal gene transfer in the industrialized human microbiome. Cell 2021; 184:2053-2067.e18. [PMID: 33794144 DOI: 10.1016/j.cell.2021.02.052] [Citation(s) in RCA: 154] [Impact Index Per Article: 51.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 10/27/2020] [Accepted: 02/24/2021] [Indexed: 12/16/2022]
Abstract
Industrialization has impacted the human gut ecosystem, resulting in altered microbiome composition and diversity. Whether bacterial genomes may also adapt to the industrialization of their host populations remains largely unexplored. Here, we investigate the extent to which the rates and targets of horizontal gene transfer (HGT) vary across thousands of bacterial strains from 15 human populations spanning a range of industrialization. We show that HGTs have accumulated in the microbiome over recent host generations and that HGT occurs at high frequency within individuals. Comparison across human populations reveals that industrialized lifestyles are associated with higher HGT rates and that the functions of HGTs are related to the level of host industrialization. Our results suggest that gut bacteria continuously acquire new functionality based on host lifestyle and that high rates of HGT may be a recent development in human history linked to industrialization.
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Affiliation(s)
- Mathieu Groussin
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA; The Broad Institute of MIT and Harvard, Cambridge, MA, USA; The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Mathilde Poyet
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA; The Broad Institute of MIT and Harvard, Cambridge, MA, USA; The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Ainara Sistiaga
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Earth, Atmospheric and Planetary Science, Massachusetts Institute of Technology, Cambridge, MA, USA; GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Sean M Kearney
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Katya Moniz
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA; The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mary Noel
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Chief Dull Knife College, Lame Deer, MT, USA
| | - Jeff Hooker
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Chief Dull Knife College, Lame Deer, MT, USA
| | - Sean M Gibbons
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Institute for Systems Biology, Seattle, WA, USA; Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Laure Segurel
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; UMR7206 Eco-anthropologie, CNRS-MNHN-Univ Paris Diderot-Sorbonne, Paris, France
| | - Alain Froment
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Institut de Recherche pour le Développement UMR 208, Muséum National d'Histoire Naturelle, Paris, France
| | - Rihlat Said Mohamed
- SA MRC / Wits Developmental Pathways for Health Research Unit, Department of Paediatrics, School of Clinical Medicine, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
| | - Alain Fezeu
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Institut de Recherche pour le Développement, Yaounde, Cameroon
| | - Vanessa A Juimo
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Institut de Recherche pour le Développement, Yaounde, Cameroon
| | - Sophie Lafosse
- UMR7206 Eco-anthropologie, CNRS-MNHN-Univ Paris Diderot-Sorbonne, Paris, France
| | - Francis E Tabe
- Faculté de Médecine et des Sciences Biomédicales, Université Yaoundé 1, Yaoundé, Cameroun
| | - Catherine Girard
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Université de Montréal, Département de sciences biologiques, C.P. 6128, succursale Centre-ville, Montréal, QC, Canada; Centre d'études nordiques, Département de biochimie, de microbiologie et de bio-informatique, Université Laval, 1030 rue de la Médecine, Québec, QC, Canada
| | - Deborah Iqaluk
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Resolute Bay, Nunavut, Canada
| | - Le Thanh Tu Nguyen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA; The Broad Institute of MIT and Harvard, Cambridge, MA, USA; The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - B Jesse Shapiro
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Université de Montréal, Département de sciences biologiques, C.P. 6128, succursale Centre-ville, Montréal, QC, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada; McGill Genome Centre, McGill University, Montreal, QC, Canada
| | - Jenni Lehtimäki
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental sciences, University of Helsinki, Helsinki, Finland; Environmental Policy Centre, Finnish Environment Institute SYKE, Helsinki, Finland
| | - Lasse Ruokolainen
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental sciences, University of Helsinki, Helsinki, Finland
| | - Pinja P Kettunen
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental sciences, University of Helsinki, Helsinki, Finland
| | - Tommi Vatanen
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA; The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; The Liggins Institute, University of Auckland, Auckland 1023, New Zealand
| | - Shani Sigwazi
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Tumaini University Makumira, Arusha, Tanzania
| | - Audax Mabulla
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Archaeology and Heritage Studies, University of Dar es Salaam, Tanzania
| | - Manuel Domínguez-Rodrigo
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Prehistory Unit, Department of History and Philosophy, University of Alcalá, Alcalá de Henares, Madrid, Spain; Institute of Evolution in Africa, University of Alcalá de Henares, Madrid, Spain
| | - Yvonne A Nartey
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Adwoa Agyei-Nkansah
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Medicine and Therapeutics, University of Ghana Medical School and Korle Bu Teaching Hospital, Accra, Ghana
| | - Amoako Duah
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Medicine, St. Dominic Hospital, Akwatia, Ghana
| | - Yaw A Awuku
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Internal Medicine and Therapeutics, School of Medical Sciences University of Cape Coast, Cape Coast, Ghana
| | - Kenneth A Valles
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Medical Scientist Training Program, Mayo Clinic, Rochester, 55905, USA
| | - Shadrack O Asibey
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Catholic University College, Sunyani, Ghana
| | - Mary Y Afihene
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Lewis R Roberts
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN, USA
| | - Amelie Plymoth
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Charles A Onyekwere
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Medicine, Lagos State University College of Medicine, Lagos, Nigeria
| | - Roger E Summons
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Earth, Atmospheric and Planetary Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ramnik J Xavier
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA; The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Eric J Alm
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA; The Broad Institute of MIT and Harvard, Cambridge, MA, USA; The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA.
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Zimmermann M, Patil KR, Typas A, Maier L. Towards a mechanistic understanding of reciprocal drug-microbiome interactions. Mol Syst Biol 2021; 17:e10116. [PMID: 33734582 PMCID: PMC7970330 DOI: 10.15252/msb.202010116] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/10/2021] [Accepted: 01/25/2021] [Indexed: 02/06/2023] Open
Abstract
Broad-spectrum antibiotics target multiple gram-positive and gram-negative bacteria, and can collaterally damage the gut microbiota. Yet, our knowledge of the extent of damage, the antibiotic activity spectra, and the resistance mechanisms of gut microbes is sparse. This limits our ability to mitigate microbiome-facilitated spread of antibiotic resistance. In addition to antibiotics, non-antibiotic drugs affect the human microbiome, as shown by metagenomics as well as in vitro studies. Microbiome-drug interactions are bidirectional, as microbes can also modulate drugs. Chemical modifications of antibiotics mostly function as antimicrobial resistance mechanisms, while metabolism of non-antibiotics can also change the drugs' pharmacodynamic, pharmacokinetic, and toxic properties. Recent studies have started to unravel the extensive capacity of gut microbes to metabolize drugs, the mechanisms, and the relevance of such events for drug treatment. These findings raise the question whether and to which degree these reciprocal drug-microbiome interactions will differ across individuals, and how to take them into account in drug discovery and precision medicine. This review describes recent developments in the field and discusses future study areas that will benefit from systems biology approaches to better understand the mechanistic role of the human gut microbiota in drug actions.
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Affiliation(s)
- Michael Zimmermann
- Structural and Computational Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
| | - Kiran Raosaheb Patil
- Structural and Computational Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
- The Medical Research Council Toxicology UnitUniversity of CambridgeCambridgeUK
| | - Athanasios Typas
- Structural and Computational Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
- Genome Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
| | - Lisa Maier
- Interfaculty Institute of Microbiology and Infection MedicineUniversity of TübingenTübingenGermany
- Cluster of Excellence ‘Controlling Microbes to Fight Infections’University of TübingenTübingenGermany
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50
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In Vitro Assessment of Antimicrobial Resistance Dissemination Dynamics during Multidrug-Resistant-Bacterium Invasion Events by Using a Continuous-Culture Device. Appl Environ Microbiol 2021; 87:AEM.02659-20. [PMID: 33361364 DOI: 10.1128/aem.02659-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 12/11/2020] [Indexed: 11/20/2022] Open
Abstract
Antimicrobial-resistant pathogens display significant public health threats by causing difficulties in clinical treatment of bacterial infection. Antimicrobial resistance (AMR) is transmissible between bacteria, significantly increasing the appearance of antimicrobial-resistant pathogens and aggravating the AMR problem. In this work, the dissemination dynamics of AMR from invading multidrug-resistant (MDR) Escherichia coli to a community of pathogenic Salmonella enterica was investigated using a continuous-culture device, and the behaviors of dissemination dynamics under different levels of antibiotic stress were investigated. Three MDR E. coli invasion events were analyzed in this work: MDR E. coli-S. enterica cocolonization, MDR E. coli invasion after antibiotic treatment of S. enterica, and MDR E. coli invasion before antibiotic treatment of S. enterica It was found that both horizontal gene transfer (HGT) and vertical gene transfer (VGT) play significant roles in AMR dissemination, although different processes contribute differently under different circumstances, that environmental levels of antibiotics promote AMR dissemination by enhancing HGT rather than leading to selective advantage for resistant bacteria, and that early invasion of MDR E. coli completely and quickly sabotages the effectiveness of antibiotic treatment. These findings contribute to understanding the drivers of AMR dissemination under different antibiotic stresses, the detrimental impact of environmental tetracycline contamination, and the danger of nosocomial presence and dissemination of MDR nonpathogens.IMPORTANCE Antimicrobial resistance poses a grave threat to public health and reduces the effectiveness of antimicrobial drugs in treating bacterial infections. Antimicrobial resistance is transmissible, either by horizontal gene transfer between bacteria or by vertical gene transfer following inheritance of genetic traits. The dissemination dynamics and behaviors of this threat, however, have not been rigorously investigated. In this work, with a continuous-culture device, we studied antimicrobial resistance dissemination processes by simulating antimicrobial-resistant Escherichia coli invasion to a pathogenic Salmonella enterica community. Using this novel tool, we provide evidence on the drivers of antimicrobial resistance dissemination, on the detrimental impact of environmental antibiotic contamination, and on the danger of antimicrobial resistance in hospitals, even if what harbors the antimicrobial resistance is not a pathogen. This work furthers our understanding of antimicrobial resistance and its dissemination between bacteria and of antibiotic therapy, our most powerful tool against bacterial infection.
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