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Xue M, Xie Y, Zang X, Zhong Y, Ma X, Sun H, Liu J. Deciphering functional groups of rumen microbiome and their underlying potentially causal relationships in shaping host traits. IMETA 2024; 3:e225. [PMID: 39135684 PMCID: PMC11316931 DOI: 10.1002/imt2.225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 06/25/2024] [Accepted: 06/26/2024] [Indexed: 08/15/2024]
Abstract
Over the years, microbiome research has achieved tremendous advancements driven by culture-independent meta-omics approaches. Despite extensive research, our understanding of the functional roles and causal effects of the microbiome on phenotypes remains limited. In this study, we focused on the rumen metaproteome, combining it with metatranscriptome and metabolome data to accurately identify the active functional distributions of rumen microorganisms and specific functional groups that influence feed efficiency. By integrating host genetics data, we established the potentially causal relationships between microbes-proteins/metabolites-phenotype, and identified specific patterns in which functional groups of rumen microorganisms influence host feed efficiency. We found a causal link between Selenomonas bovis and rumen carbohydrate metabolism, potentially mediated by bacterial chemotaxis and a two-component regulatory system, impacting feed utilization efficiency of dairy cows. Our study on the nutrient utilization functional groups in the rumen of high-feed-efficiency dairy cows, along with the identification of key microbiota functional proteins and their potentially causal relationships, will help move from correlation to causation in rumen microbiome research. This will ultimately enable precise regulation of the rumen microbiota for optimized ruminant production.
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Affiliation(s)
- Ming‐Yuan Xue
- Institute of Dairy Science, College of Animal SciencesZhejiang UniversityHangzhouChina
- Xianghu LaboratoryHangzhouChina
| | - Yun‐Yi Xie
- Institute of Dairy Science, College of Animal SciencesZhejiang UniversityHangzhouChina
| | - Xin‐Wei Zang
- Institute of Dairy Science, College of Animal SciencesZhejiang UniversityHangzhouChina
| | - Yi‐Fan Zhong
- Institute of Dairy Science, College of Animal SciencesZhejiang UniversityHangzhouChina
| | - Xiao‐Jiao Ma
- Institute of Dairy Science, College of Animal SciencesZhejiang UniversityHangzhouChina
| | - Hui‐Zeng Sun
- Institute of Dairy Science, College of Animal SciencesZhejiang UniversityHangzhouChina
- Ministry of Education Key Laboratory of Molecular Animal NutritionZhejiang UniversityHangzhouChina
| | - Jian‐Xin Liu
- Institute of Dairy Science, College of Animal SciencesZhejiang UniversityHangzhouChina
- Ministry of Education Key Laboratory of Molecular Animal NutritionZhejiang UniversityHangzhouChina
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2
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Algavi YM, Borenstein E. Relative dispersion ratios following fecal microbiota transplant elucidate principles governing microbial migration dynamics. Nat Commun 2024; 15:4447. [PMID: 38789466 PMCID: PMC11126695 DOI: 10.1038/s41467-024-48717-z] [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: 09/12/2023] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Microorganisms frequently migrate from one ecosystem to another. Yet, despite the potential importance of this process in modulating the environment and the microbial ecosystem, our understanding of the fundamental forces that govern microbial dispersion is still lacking. Moreover, while theoretical models and in-vitro experiments have highlighted the contribution of species interactions to community assembly, identifying such interactions in vivo, specifically in communities as complex as the human gut, remains challenging. To address this gap, here we introduce a robust and rigorous computational framework, termed Relative Dispersion Ratio (RDR) analysis, and leverage data from well-characterized fecal microbiota transplant trials, to rigorously pinpoint dependencies between taxa during the colonization of human gastrointestinal tract. Our analysis identifies numerous pairwise dependencies between co-colonizing microbes during migration between gastrointestinal environments. We further demonstrate that identified dependencies agree with previously reported findings from in-vitro experiments and population-wide distribution patterns. Finally, we explore metabolic dependencies between these taxa and characterize the functional properties that facilitate effective dispersion. Collectively, our findings provide insights into the principles and determinants of community dynamics following ecological translocation, informing potential opportunities for precise community design.
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Affiliation(s)
- Yadid M Algavi
- Faculty of Medical & Health Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Elhanan Borenstein
- Faculty of Medical & Health Sciences, Tel Aviv University, Tel Aviv, Israel.
- The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel.
- Santa Fe Institute, Santa Fe, NM, USA.
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3
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Daybog I, Kolodny O. A computational framework for resolving the microbiome diversity conundrum. Nat Commun 2023; 14:7977. [PMID: 38042865 PMCID: PMC10693575 DOI: 10.1038/s41467-023-42768-4] [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: 11/24/2022] [Accepted: 10/20/2023] [Indexed: 12/04/2023] Open
Abstract
Recent empirical studies offer conflicting findings regarding the relation between host fitness and the composition of its microbiome, a conflict which we term 'the microbial β- diversity conundrum'. The microbiome is crucial for host wellbeing and survival. Surprisingly, different healthy individuals' microbiome compositions, even in the same population, often differ dramatically, contrary to the notion that a vital trait should be highly conserved. Moreover, gnotobiotic individuals exhibit highly deleterious phenotypes, supporting the view that the microbiome is paramount to host fitness. However, the introduction of almost arbitrarily selected microbiota into the system often achieves a significant rescue effect of the deleterious phenotypes. This is true even for microbiota from soil or phylogenetically distant host species, highlighting an apparent paradox. We suggest several solutions to the paradox using a computational framework, simulating the population dynamics of hosts and their microbiomes over multiple generations. The answers invoke factors such as host population size, the specific mode of microbial contribution to host fitness, and typical microbiome richness, offering solutions to the conundrum by highlighting scenarios where even when a host's fitness is determined in full by its microbiome composition, this composition has little effect on the natural selection dynamics of the population.
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Affiliation(s)
- Itay Daybog
- Department of Ecology, Evolution and Behavior, The A. Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel.
| | - Oren Kolodny
- Department of Ecology, Evolution and Behavior, The A. Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel.
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4
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Suez J, Cohen Y, Valdés-Mas R, Mor U, Dori-Bachash M, Federici S, Zmora N, Leshem A, Heinemann M, Linevsky R, Zur M, Ben-Zeev Brik R, Bukimer A, Eliyahu-Miller S, Metz A, Fischbein R, Sharov O, Malitsky S, Itkin M, Stettner N, Harmelin A, Shapiro H, Stein-Thoeringer CK, Segal E, Elinav E. Personalized microbiome-driven effects of non-nutritive sweeteners on human glucose tolerance. Cell 2022; 185:3307-3328.e19. [PMID: 35987213 DOI: 10.1016/j.cell.2022.07.016] [Citation(s) in RCA: 112] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 04/26/2022] [Accepted: 07/18/2022] [Indexed: 02/06/2023]
Abstract
Non-nutritive sweeteners (NNS) are commonly integrated into human diet and presumed to be inert; however, animal studies suggest that they may impact the microbiome and downstream glycemic responses. We causally assessed NNS impacts in humans and their microbiomes in a randomized-controlled trial encompassing 120 healthy adults, administered saccharin, sucralose, aspartame, and stevia sachets for 2 weeks in doses lower than the acceptable daily intake, compared with controls receiving sachet-contained vehicle glucose or no supplement. As groups, each administered NNS distinctly altered stool and oral microbiome and plasma metabolome, whereas saccharin and sucralose significantly impaired glycemic responses. Importantly, gnotobiotic mice conventionalized with microbiomes from multiple top and bottom responders of each of the four NNS-supplemented groups featured glycemic responses largely reflecting those noted in respective human donors, which were preempted by distinct microbial signals, as exemplified by sucralose. Collectively, human NNS consumption may induce person-specific, microbiome-dependent glycemic alterations, necessitating future assessment of clinical implications.
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Affiliation(s)
- Jotham Suez
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Yotam Cohen
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Rafael Valdés-Mas
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Uria Mor
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Mally Dori-Bachash
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sara Federici
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Niv Zmora
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel; Research Center for Digestive Tract and Liver Diseases, Tel Aviv Sourasky Medical Center, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6423906, Israel; Internal Medicine Department, Tel Aviv Sourasky Medical Center, Tel Aviv 6423906, Israel
| | - Avner Leshem
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel; Department of Surgery, Tel Aviv Sourasky Medical Center, Tel Aviv 6423906, Israel
| | - Melina Heinemann
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Raquel Linevsky
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Maya Zur
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Rotem Ben-Zeev Brik
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Aurelie Bukimer
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Shimrit Eliyahu-Miller
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Alona Metz
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ruthy Fischbein
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Olga Sharov
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sergey Malitsky
- Department of Biological Services, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Maxim Itkin
- Department of Biological Services, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Noa Stettner
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Alon Harmelin
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Hagit Shapiro
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Christoph K Stein-Thoeringer
- Microbiome & Cancer Division, DKFZ, Heidelberg, Germany; National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 7610001, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Eran Elinav
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel; Microbiome & Cancer Division, DKFZ, Heidelberg, Germany.
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5
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Lawrence D, Campbell DE, Schriefer LA, Rodgers R, Walker FC, Turkin M, Droit L, Parkes M, Handley SA, Baldridge MT. Single-cell genomics for resolution of conserved bacterial genes and mobile genetic elements of the human intestinal microbiota using flow cytometry. Gut Microbes 2022; 14:2029673. [PMID: 35130125 PMCID: PMC8824198 DOI: 10.1080/19490976.2022.2029673] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 12/03/2021] [Accepted: 01/07/2022] [Indexed: 02/04/2023] Open
Abstract
As our understanding of the importance of the human microbiota in health and disease grows, so does our need to carefully resolve and delineate its genomic content. 16S rRNA gene-based analyses yield important insights into taxonomic composition, and metagenomics-based approaches reveal the functional potential of microbial communities. However, these methods generally fail to directly link genetic features, including bacterial genes and mobile genetic elements, to each other and to their source bacterial genomes. Further, they are inadequate to capture the microdiversity present within a genus, species, or strain of bacteria within these complex communities. Here, we present a method utilizing fluorescence-activated cell sorting for isolation of single bacterial cells, amplifying their genomes, screening them by 16S rRNA gene analysis, and selecting cells for genomic sequencing. We apply this method to both a cultured laboratory strain of Escherichia coli and human stool samples. Our analyses reveal the capacity of this method to provide nearly complete coverage of bacterial genomes when applied to isolates and partial genomes of bacterial species recovered from complex communities. Additionally, this method permits exploration and comparison of conserved and variable genomic features between individual cells. We generate assemblies of novel genomes within the Ruminococcaceae family and the Holdemanella genus by combining several 16S rRNA gene-matched single cells, and report novel prophages and conjugative transposons for both Bifidobacterium and Ruminococcaceae. Thus, we demonstrate an approach for flow cytometric separation and sequencing of single bacterial cells from the human microbiota, which yields a variety of critical insights into both the functional potential of individual microbes and the variation among those microbes. This method definitively links a variety of conserved and mobile genomic features, and can be extended to further resolve diverse elements present in the human microbiota.
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Affiliation(s)
- Dylan Lawrence
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Danielle E. Campbell
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Lawrence A. Schriefer
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Rachel Rodgers
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Forrest C. Walker
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Marissa Turkin
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Lindsay Droit
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Miles Parkes
- Division of Gastroenterology Addenbrooke’s Hospital and Department of Medicine, University of Cambridge, Cambridge, UK
| | - Scott A. Handley
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Megan T. Baldridge
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
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6
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Eng A, Hayden HS, Pope CE, Brittnacher MJ, Vo AT, Weiss EJ, Hager KR, Leung DH, Heltshe SL, Raftery D, Miller SI, Hoffman LR, Borenstein E. Infants with cystic fibrosis have altered fecal functional capacities with potential clinical and metabolic consequences. BMC Microbiol 2021; 21:247. [PMID: 34525965 PMCID: PMC8444586 DOI: 10.1186/s12866-021-02305-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 08/20/2021] [Indexed: 12/11/2022] Open
Abstract
Background Infants with cystic fibrosis (CF) suffer from gastrointestinal (GI) complications, including pancreatic insufficiency and intestinal inflammation, which have been associated with impaired nutrition and growth. Recent evidence identified altered fecal microbiota taxonomic compositions in infants with CF relative to healthy infants that were characterized by differences in the abundances of taxa associated with GI health and nutrition. Furthermore, these taxonomic differences were more pronounced in low length infants with CF, suggesting a potential link to linear growth failure. We hypothesized that these differences would entail shifts in the microbiome’s functional capacities that could contribute to inflammation and nutritional failure in infants with CF. Results To test this hypothesis, we compared fecal microbial metagenomic content between healthy infants and infants with CF, supplemented with an analysis of fecal metabolomes in infants with CF. We identified notable differences in CF fecal microbial functional capacities, including metabolic and environmental response functions, compared to healthy infants that intensified during the first year of life. A machine learning-based longitudinal metagenomic age analysis of healthy and CF fecal metagenomic functional profiles further demonstrated that these differences are characterized by a CF-associated delay in the development of these functional capacities. Moreover, we found metagenomic differences in functions related to metabolism among infants with CF that were associated with diet and antibiotic exposure, and identified several taxa as potential drivers of these functional differences. An integrated metagenomic and metabolomic analysis further revealed that abundances of several fecal GI metabolites important for nutrient absorption, including three bile acids, correlated with specific microbes in infants with CF. Conclusions Our results highlight several metagenomic and metabolomic factors, including bile acids and other microbial metabolites, that may impact nutrition, growth, and GI health in infants with CF. These factors could serve as promising avenues for novel microbiome-based therapeutics to improve health outcomes in these infants. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02305-z.
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Affiliation(s)
- Alexander Eng
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Hillary S Hayden
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | | | | | - Anh T Vo
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Eli J Weiss
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Kyle R Hager
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Daniel H Leung
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Sonya L Heltshe
- Department of Pediatrics, University of Washington, Seattle, WA, USA.,Cystic Fibrosis Foundation Therapeutics Development Network Coordinating Center, Seattle Children's Research Institute, Seattle, WA, USA
| | - Daniel Raftery
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA, USA
| | - Samuel I Miller
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.,Department of Microbiology, University of Washington, Seattle, WA, USA.,Department of Medicine, University of Washington, Seattle, WA, USA
| | - Lucas R Hoffman
- Department of Microbiology, University of Washington, Seattle, WA, USA. .,Department of Pediatrics, University of Washington, Seattle, WA, USA. .,Pulmonary and Sleep Medicine, Seattle Children's Hospital, Seattle, WA, USA.
| | - Elhanan Borenstein
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel. .,Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel. .,Santa Fe Institute, Santa Fe, NM, USA.
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7
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Rapp JZ, Sullivan MB, Deming JW. Divergent Genomic Adaptations in the Microbiomes of Arctic Subzero Sea-Ice and Cryopeg Brines. Front Microbiol 2021; 12:701186. [PMID: 34367102 PMCID: PMC8339730 DOI: 10.3389/fmicb.2021.701186] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 06/29/2021] [Indexed: 11/16/2022] Open
Abstract
Subzero hypersaline brines are liquid microbial habitats within otherwise frozen environments, where concentrated dissolved salts prevent freezing. Such extreme conditions presumably require unique microbial adaptations, and possibly altered ecologies, but specific strategies remain largely unknown. Here we examined prokaryotic taxonomic and functional diversity in two seawater-derived subzero hypersaline brines: first-year sea ice, subject to seasonally fluctuating conditions; and ancient cryopeg, under relatively stable conditions geophysically isolated in permafrost. Overall, both taxonomic composition and functional potential were starkly different. Taxonomically, sea-ice brine communities (∼105 cells mL–1) had greater richness, more diversity and were dominated by bacterial genera, including Polaribacter, Paraglaciecola, Colwellia, and Glaciecola, whereas the more densely inhabited cryopeg brines (∼108 cells mL–1) lacked these genera and instead were dominated by Marinobacter. Functionally, however, sea ice encoded fewer accessory traits and lower average genomic copy numbers for shared traits, though DNA replication and repair were elevated; in contrast, microbes in cryopeg brines had greater genetic versatility with elevated abundances of accessory traits involved in sensing, responding to environmental cues, transport, mobile elements (transposases and plasmids), toxin-antitoxin systems, and type VI secretion systems. Together these genomic features suggest adaptations and capabilities of sea-ice communities manifesting at the community level through seasonal ecological succession, whereas the denser cryopeg communities appear adapted to intense bacterial competition, leaving fewer genera to dominate with brine-specific adaptations and social interactions that sacrifice some members for the benefit of others. Such cryopeg genomic traits provide insight into how long-term environmental stability may enable life to survive extreme conditions.
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Affiliation(s)
- Josephine Z Rapp
- School of Oceanography, University of Washington, Seattle, WA, United States
| | - Matthew B Sullivan
- Byrd Polar and Climate Research Center, Ohio State University, Columbus, OH, United States.,Department of Microbiology, Ohio State University, Columbus, OH, United States.,Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH, United States.,Center of Microbiome Science, Ohio State University, Columbus, OH, United States
| | - Jody W Deming
- School of Oceanography, University of Washington, Seattle, WA, United States
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8
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Pinna NK, Anjana RM, Saxena S, Dutta A, Gnanaprakash V, Rameshkumar G, Aswath S, Raghavan S, Rani CSS, Radha V, Balasubramanyam M, Pant A, Nielsen T, Jørgensen T, Færch K, Kashani A, Silva MCA, Vestergaard H, Hansen TH, Hansen T, Arumugam M, Nair GB, Das B, Pedersen O, Mohan V, Mande SS. Trans-ethnic gut microbial signatures of prediabetic subjects from India and Denmark. Genome Med 2021; 13:36. [PMID: 33658065 PMCID: PMC7931552 DOI: 10.1186/s13073-021-00851-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 02/11/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Recent studies have indicated an association of gut microbiota and microbial metabolites with type 2 diabetes mellitus (T2D). However, large-scale investigation of the gut microbiota of "prediabetic" (PD) subjects has not been reported. Identifying robust gut microbiome signatures of prediabetes and characterizing early prediabetic stages is important for the understanding of disease development and could be crucial in early diagnosis and prevention. METHODS The current study performed amplification and sequencing on the variable regions (V1-V5) of the 16S rRNA genes to profile and compare gut microbiota of prediabetic individuals (N = 262) with normoglycemic individuals (N = 275) from two cohorts in India and Denmark. Similarly, fasting serum inflammatory biomarkers were profiled from the study participants. RESULTS After correcting for strong country-specific cohort effect, 16 operational taxonomic units (OTUs) including members from the genera Prevotella9, Phascolarctobacterium, Barnesiella, Flavonifractor, Tyzzerella_4, Bacteroides, Faecalibacterium, and Agathobacter were identified as enriched in normoglycaemic subjects with respect to the subjects with prediabetes using a negative binomial Wald test. We also identified 144 OTUs enriched in the prediabetic subjects, which included members from the genera Megasphaera, Streptococcus, Prevotella9, Alistipes, Mitsuokella, Escherichia/Shigella, Prevotella2, Vibrio, Lactobacillus, Alloprevotella, Rhodococcus, and Klebsiella. Comparative analyses of relative abundance of bacterial taxa revealed that the Streptococcus, Escherichia/Shigella, Prevotella2, Vibrio, and Alloprevotella OTUs exhibited more than fourfold enrichment in the gut microbiota of prediabetic subjects. When considering subjects from the two geographies separately, we were able to identify additional gut microbiome signatures of prediabetes. The study reports a probable association of Megasphaera OTU(s) with impaired glucose tolerance, which is significantly pronounced in Indian subjects. While the overall results confirm a state of proinflammation as early as in prediabetes, the Indian cohort exhibited a characteristic pattern of abundance of inflammatory markers indicating low-grade intestinal inflammation at an overall population level, irrespective of glycemic status. CONCLUSIONS The results present trans-ethnic gut microbiome and inflammation signatures associated with prediabetes, in Indian and Danish populations. The identified associations may be explored further as potential early indicators for individuals at risk of dysglycemia.
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Affiliation(s)
- Nishal Kumar Pinna
- TCS Research, Tata Consultancy Services Limited, 54B Hadapsar Industrial Estate, Pune, 411013, India
| | - Ranjit Mohan Anjana
- Madras Diabetes Research Foundation, No. 4, Conran Smith Road, Gopalapuram, Chennai, 600 086, India
| | - Shruti Saxena
- Molecular Genetics Laboratory, Infections and Immunology, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad - Gurgaon Expressway, PO box #04, Faridabad, 121001, India
| | - Anirban Dutta
- TCS Research, Tata Consultancy Services Limited, 54B Hadapsar Industrial Estate, Pune, 411013, India
| | - Visvanathan Gnanaprakash
- Madras Diabetes Research Foundation, No. 4, Conran Smith Road, Gopalapuram, Chennai, 600 086, India
| | - Gnanavadivel Rameshkumar
- Madras Diabetes Research Foundation, No. 4, Conran Smith Road, Gopalapuram, Chennai, 600 086, India
| | - Sukumaran Aswath
- Madras Diabetes Research Foundation, No. 4, Conran Smith Road, Gopalapuram, Chennai, 600 086, India
| | - Srividhya Raghavan
- Madras Diabetes Research Foundation, No. 4, Conran Smith Road, Gopalapuram, Chennai, 600 086, India
| | | | - Venkatesan Radha
- Madras Diabetes Research Foundation, No. 4, Conran Smith Road, Gopalapuram, Chennai, 600 086, India
| | - Muthuswamy Balasubramanyam
- Madras Diabetes Research Foundation, No. 4, Conran Smith Road, Gopalapuram, Chennai, 600 086, India.,Present address: SRM Medical College Hospital & Research Centre, SRM Institute of Science & Technology (SRMIST), Kattankulathur, Chennai, India
| | - Archana Pant
- Molecular Genetics Laboratory, Infections and Immunology, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad - Gurgaon Expressway, PO box #04, Faridabad, 121001, India
| | - Trine Nielsen
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Blegdamsvej 3B, Maersk Tower, Building: 07-8-55, DK-2200, Copenhagen N, Denmark
| | - Torben Jørgensen
- Center for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospitals, University of Copenhagen, Copenhagen, Denmark
| | | | - Alireza Kashani
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Blegdamsvej 3B, Maersk Tower, Building: 07-8-55, DK-2200, Copenhagen N, Denmark.,Current affiliation: Qbiom, Microbiome Consultancy Service, Copenhagen, Denmark
| | - Maria Camila Alvarez Silva
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Blegdamsvej 3B, Maersk Tower, Building: 07-8-55, DK-2200, Copenhagen N, Denmark
| | - Henrik Vestergaard
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Blegdamsvej 3B, Maersk Tower, Building: 07-8-55, DK-2200, Copenhagen N, Denmark
| | - Tue Haldor Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Blegdamsvej 3B, Maersk Tower, Building: 07-8-55, DK-2200, Copenhagen N, Denmark.,Department of Cardiology and Endocrinology, Slagelse Hospital, Slagelse, Denmark
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Blegdamsvej 3B, Maersk Tower, Building: 07-8-55, DK-2200, Copenhagen N, Denmark
| | - Manimozhiyan Arumugam
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Blegdamsvej 3B, Maersk Tower, Building: 07-8-55, DK-2200, Copenhagen N, Denmark
| | - Gopinath Balakrish Nair
- Molecular Genetics Laboratory, Infections and Immunology, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad - Gurgaon Expressway, PO box #04, Faridabad, 121001, India
| | - Bhabatosh Das
- Molecular Genetics Laboratory, Infections and Immunology, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad - Gurgaon Expressway, PO box #04, Faridabad, 121001, India.
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Blegdamsvej 3B, Maersk Tower, Building: 07-8-55, DK-2200, Copenhagen N, Denmark.
| | - Viswanathan Mohan
- Madras Diabetes Research Foundation, No. 4, Conran Smith Road, Gopalapuram, Chennai, 600 086, India.
| | - Sharmila Shekhar Mande
- TCS Research, Tata Consultancy Services Limited, 54B Hadapsar Industrial Estate, Pune, 411013, India.
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9
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Tian L, Wang XW, Wu AK, Fan Y, Friedman J, Dahlin A, Waldor MK, Weinstock GM, Weiss ST, Liu YY. Deciphering functional redundancy in the human microbiome. Nat Commun 2020; 11:6217. [PMID: 33277504 PMCID: PMC7719190 DOI: 10.1038/s41467-020-19940-1] [Citation(s) in RCA: 118] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 11/04/2020] [Indexed: 02/07/2023] Open
Abstract
Although the taxonomic composition of the human microbiome varies tremendously across individuals, its gene composition or functional capacity is highly conserved - implying an ecological property known as functional redundancy. Such functional redundancy has been hypothesized to underlie the stability and resilience of the human microbiome, but this hypothesis has never been quantitatively tested. The origin of functional redundancy is still elusive. Here, we investigate the basis for functional redundancy in the human microbiome by analyzing its genomic content network - a bipartite graph that links microbes to the genes in their genomes. We find that this network exhibits several topological features that favor high functional redundancy. Furthermore, we develop a simple genome evolution model to generate genomic content network, finding that moderate selection pressure and high horizontal gene transfer rate are necessary to generate genomic content networks with key topological features that favor high functional redundancy. Finally, we analyze data from two published studies of fecal microbiota transplantation (FMT), finding that high functional redundancy of the recipient's pre-FMT microbiota raises barriers to donor microbiota engraftment. This work elucidates the potential ecological and evolutionary processes that create and maintain functional redundancy in the human microbiome and contribute to its resilience.
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Affiliation(s)
- Liang Tian
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
- Department of Physics, Hong Kong Baptist University, Hong Kong SAR, China
- Institute of Computational and Theoretical Studies, Hong Kong Baptist University, Hong Kong SAR, China
- State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong SAR, China
| | - Xu-Wen Wang
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Ang-Kun Wu
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
- Department of Physics and Astronomy, Rutgers University, Piscataway, NJ, 08854, USA
| | - Yuhang Fan
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Jonathan Friedman
- Faculty of Agriculture, Food and Environment, Department of Plant Pathology and Microbiology, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Amber Dahlin
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Matthew K Waldor
- Division of Infectious Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | | | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Yang-Yu Liu
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
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10
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Eng A, Verster AJ, Borenstein E. MetaLAFFA: a flexible, end-to-end, distributed computing-compatible metagenomic functional annotation pipeline. BMC Bioinformatics 2020; 21:471. [PMID: 33087062 PMCID: PMC7579964 DOI: 10.1186/s12859-020-03815-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/13/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Microbial communities have become an important subject of research across multiple disciplines in recent years. These communities are often examined via shotgun metagenomic sequencing, a technology which can offer unique insights into the genomic content of a microbial community. Functional annotation of shotgun metagenomic data has become an increasingly popular method for identifying the aggregate functional capacities encoded by the community's constituent microbes. Currently available metagenomic functional annotation pipelines, however, suffer from several shortcomings, including limited pipeline customization options, lack of standard raw sequence data pre-processing, and insufficient capabilities for integration with distributed computing systems. RESULTS Here we introduce MetaLAFFA, a functional annotation pipeline designed to take unfiltered shotgun metagenomic data as input and generate functional profiles. MetaLAFFA is implemented as a Snakemake pipeline, which enables convenient integration with distributed computing clusters, allowing users to take full advantage of available computing resources. Default pipeline settings allow new users to run MetaLAFFA according to common practices while a Python module-based configuration system provides advanced users with a flexible interface for pipeline customization. MetaLAFFA also generates summary statistics for each step in the pipeline so that users can better understand pre-processing and annotation quality. CONCLUSIONS MetaLAFFA is a new end-to-end metagenomic functional annotation pipeline with distributed computing compatibility and flexible customization options. MetaLAFFA source code is available at https://github.com/borenstein-lab/MetaLAFFA and can be installed via Conda as described in the accompanying documentation.
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Affiliation(s)
- Alexander Eng
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Adrian J Verster
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA.,Bureau of Food Surveillance and Science Integration, Food Directorate, Health Canada, Ottawa, ON, K1A 0K9, Canada
| | - Elhanan Borenstein
- Blavatnik School of Computer Science, Tel Aviv University, 6997801, Tel Aviv, Israel. .,Sackler Faculty of Medicine, Tel Aviv University, 6997801, Tel Aviv, Israel. .,Santa Fe Institute, Santa Fe, NM, 87501, USA.
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11
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Blanco-Míguez A, Fdez-Riverola F, Sánchez B, Lourenço A. Resources and tools for the high-throughput, multi-omic study of intestinal microbiota. Brief Bioinform 2020; 20:1032-1056. [PMID: 29186315 DOI: 10.1093/bib/bbx156] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 10/23/2017] [Indexed: 12/18/2022] Open
Abstract
The human gut microbiome impacts several aspects of human health and disease, including digestion, drug metabolism and the propensity to develop various inflammatory, autoimmune and metabolic diseases. Many of the molecular processes that play a role in the activity and dynamics of the microbiota go beyond species and genic composition and thus, their understanding requires advanced bioinformatics support. This article aims to provide an up-to-date view of the resources and software tools that are being developed and used in human gut microbiome research, in particular data integration and systems-level analysis efforts. These efforts demonstrate the power of standardized and reproducible computational workflows for integrating and analysing varied omics data and gaining deeper insights into microbe community structure and function as well as host-microbe interactions.
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Affiliation(s)
| | | | | | - Anália Lourenço
- Dpto. de Informática - Universidade de Vigo, ESEI - Escuela Superior de Ingeniería Informática, Edificio politécnico, Campus Universitario As Lagoas s/n, 32004 Ourense, Spain
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12
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Suez J, Zmora N, Zilberman-Schapira G, Mor U, Dori-Bachash M, Bashiardes S, Zur M, Regev-Lehavi D, Ben-Zeev Brik R, Federici S, Horn M, Cohen Y, Moor AE, Zeevi D, Korem T, Kotler E, Harmelin A, Itzkovitz S, Maharshak N, Shibolet O, Pevsner-Fischer M, Shapiro H, Sharon I, Halpern Z, Segal E, Elinav E. Post-Antibiotic Gut Mucosal Microbiome Reconstitution Is Impaired by Probiotics and Improved by Autologous FMT. Cell 2019; 174:1406-1423.e16. [PMID: 30193113 DOI: 10.1016/j.cell.2018.08.047] [Citation(s) in RCA: 654] [Impact Index Per Article: 130.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 06/05/2018] [Accepted: 08/20/2018] [Indexed: 02/06/2023]
Abstract
Probiotics are widely prescribed for prevention of antibiotics-associated dysbiosis and related adverse effects. However, probiotic impact on post-antibiotic reconstitution of the gut mucosal host-microbiome niche remains elusive. We invasively examined the effects of multi-strain probiotics or autologous fecal microbiome transplantation (aFMT) on post-antibiotic reconstitution of the murine and human mucosal microbiome niche. Contrary to homeostasis, antibiotic perturbation enhanced probiotics colonization in the human mucosa but only mildly improved colonization in mice. Compared to spontaneous post-antibiotic recovery, probiotics induced a markedly delayed and persistently incomplete indigenous stool/mucosal microbiome reconstitution and host transcriptome recovery toward homeostatic configuration, while aFMT induced a rapid and near-complete recovery within days of administration. In vitro, Lactobacillus-secreted soluble factors contributed to probiotics-induced microbiome inhibition. Collectively, potential post-antibiotic probiotic benefits may be offset by a compromised gut mucosal recovery, highlighting a need of developing aFMT or personalized probiotic approaches achieving mucosal protection without compromising microbiome recolonization in the antibiotics-perturbed host.
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Affiliation(s)
- Jotham Suez
- Immunology Department, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Niv Zmora
- Immunology Department, Weizmann Institute of Science, 7610001 Rehovot, Israel; Internal Medicine Department, Tel Aviv Sourasky Medical Center, 6423906 Tel Aviv, Israel
| | | | - Uria Mor
- Immunology Department, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Mally Dori-Bachash
- Immunology Department, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Stavros Bashiardes
- Immunology Department, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Maya Zur
- Immunology Department, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Dana Regev-Lehavi
- Immunology Department, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Rotem Ben-Zeev Brik
- Immunology Department, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Sara Federici
- Immunology Department, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Max Horn
- Immunology Department, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Yotam Cohen
- Immunology Department, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Andreas E Moor
- Department of Molecular Cell Biology, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - David Zeevi
- Department of Molecular Cell Biology, Weizmann Institute of Science, 7610001 Rehovot, Israel; Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Tal Korem
- Department of Molecular Cell Biology, Weizmann Institute of Science, 7610001 Rehovot, Israel; Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Eran Kotler
- Department of Molecular Cell Biology, Weizmann Institute of Science, 7610001 Rehovot, Israel; Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Alon Harmelin
- Department of Veterinary Resources, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Shalev Itzkovitz
- Department of Molecular Cell Biology, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Nitsan Maharshak
- Department of Gastroenterology and Liver Diseases, Tel Aviv Sourasky Medical Center, 6423906 Tel Aviv, Israel; Research Center for Digestive tract and Liver Diseases, Tel Aviv Sourasky Medical Center, 6423906 Tel Aviv, Israel; Sackler Faculty of Medicine, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Oren Shibolet
- Department of Gastroenterology and Liver Diseases, Tel Aviv Sourasky Medical Center, 6423906 Tel Aviv, Israel; Research Center for Digestive tract and Liver Diseases, Tel Aviv Sourasky Medical Center, 6423906 Tel Aviv, Israel; Sackler Faculty of Medicine, Tel Aviv University, 6997801 Tel Aviv, Israel
| | | | - Hagit Shapiro
- Immunology Department, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Itai Sharon
- Migal Galilee Research Institute, 11016 Kiryat Shmona, Israel; Tel Hai College, Upper Galilee, 1220800, Israel
| | - Zamir Halpern
- Department of Gastroenterology and Liver Diseases, Tel Aviv Sourasky Medical Center, 6423906 Tel Aviv, Israel; Research Center for Digestive tract and Liver Diseases, Tel Aviv Sourasky Medical Center, 6423906 Tel Aviv, Israel; Sackler Faculty of Medicine, Tel Aviv University, 6997801 Tel Aviv, Israel.
| | - Eran Segal
- Department of Molecular Cell Biology, Weizmann Institute of Science, 7610001 Rehovot, Israel; Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, 7610001 Rehovot, Israel.
| | - Eran Elinav
- Immunology Department, Weizmann Institute of Science, 7610001 Rehovot, Israel.
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13
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Kwon M, Seo SS, Kim MK, Lee DO, Lim MC. Compositional and Functional Differences between Microbiota and Cervical Carcinogenesis as Identified by Shotgun Metagenomic Sequencing. Cancers (Basel) 2019; 11:cancers11030309. [PMID: 30841606 PMCID: PMC6468638 DOI: 10.3390/cancers11030309] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 02/27/2019] [Accepted: 02/28/2019] [Indexed: 12/15/2022] Open
Abstract
Recent studies have reported the potential role of microbiomes in cervical disease. However, little is known about the microbiome composition and function in cervical carcinogenesis. We aimed to identify the compositional and functional alterations of cervical microbiomes in cases of cervical carcinogenesis of Korean women using shotgun metagenomic sequencing. In this study, using shotgun sequencing, we sequenced the cervical metagenomes of cervical intraneoplasia 2/3 (n = 17), cervical cancer (n = 12), and normal controls (n = 18) to identify the microbial abundances and enriched metabolic functions in cervical metagenomes. At the genus level, the microbiota of cervical cancer were differentially enriched with genera Alkaliphilus, Pseudothermotoga, and Wolbachia. Cervical intraepithelial neoplasia (CIN) 2/3 were enriched with Lactobacillus, Staphylococcus, and Candidatus Endolissoclinum. The normal group was enriched with Pseudoalteromonas and Psychrobacter. Further characterization of the functionalities of the metagenomes may suggest that six Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologies (KOs) that are involved in 10 pathways are associated with an increased risk of CIN2/3 and cervical cancer. Specifically, cervical metagenomes were enriched in the course of peptidoglycan synthesis and depleted by dioxin degradation and 4-oxalocrotonate tautomerase. The Cluster of Orthologous Groups (COG) category ‘Defense mechanisms’ was depleted in cervical cancer patients. Our findings based on shotgun metagenomic sequencing suggest that cervical microbiome community compositions and their metagenomics profiles differed between cervical lesions and normal subjects. Future studies should have larger sample sizes and/or aggregate their results to have sufficient power to detect reproducible and significant associations.
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Affiliation(s)
- Minji Kwon
- Division of Cancer Epidemiology and Prevention, National Cancer Center, 323, Ilsan-ro, Ilsandong-gu, Goyang-si 10408, Korea.
| | - Sang-Soo Seo
- Center for Uterine Cancer, National Cancer Center, 323, Ilsan-ro, Ilsandong-gu, Goyang-si 10408, Korea.
| | - Mi Kyung Kim
- Division of Cancer Epidemiology and Prevention, National Cancer Center, 323, Ilsan-ro, Ilsandong-gu, Goyang-si 10408, Korea.
| | - Dong Ock Lee
- Center for Uterine Cancer, National Cancer Center, 323, Ilsan-ro, Ilsandong-gu, Goyang-si 10408, Korea.
| | - Myoung Cheol Lim
- Center for Uterine Cancer, National Cancer Center, 323, Ilsan-ro, Ilsandong-gu, Goyang-si 10408, Korea.
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14
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A review of 10 years of human microbiome research activities at the US National Institutes of Health, Fiscal Years 2007-2016. MICROBIOME 2019; 7:31. [PMID: 30808411 PMCID: PMC6391833 DOI: 10.1186/s40168-019-0620-y] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 01/03/2019] [Indexed: 05/26/2023]
Abstract
The National Institutes of Health (NIH) is the primary federal government agency for biomedical research in the USA. NIH provides extensive support for human microbiome research with 21 of 27 NIH Institutes and Centers (ICs) currently funding this area through their extramural research programs. This analysis of the NIH extramural portfolio in human microbiome research briefly reviews the early history of this field at NIH, summarizes the program objectives and the resources developed in the recently completed 10-year (fiscal years 2007-2016) $215 M Human Microbiome Project (HMP) program, evaluates the scope and range of the $728 M NIH investment in extramural human microbiome research activities outside of the HMP over fiscal years 2012-2016, and highlights some specific areas of research which emerged from this investment. This analysis closes with a few comments on the technical needs and knowledge gaps which remain for this field to be able to advance over the next decade and for the outcomes of this research to be able to progress to microbiome-based interventions for treating disease and supporting health.
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15
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Personalized Gut Mucosal Colonization Resistance to Empiric Probiotics Is Associated with Unique Host and Microbiome Features. Cell 2018; 174:1388-1405.e21. [DOI: 10.1016/j.cell.2018.08.041] [Citation(s) in RCA: 725] [Impact Index Per Article: 120.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2016] [Revised: 06/05/2018] [Accepted: 08/20/2018] [Indexed: 12/17/2022]
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16
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Heintz-Buschart A, Wilmes P. Human Gut Microbiome: Function Matters. Trends Microbiol 2018; 26:563-574. [DOI: 10.1016/j.tim.2017.11.002] [Citation(s) in RCA: 296] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 10/29/2017] [Accepted: 11/03/2017] [Indexed: 12/16/2022]
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17
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McNally CP, Eng A, Noecker C, Gagne-Maynard WC, Borenstein E. BURRITO: An Interactive Multi-Omic Tool for Visualizing Taxa-Function Relationships in Microbiome Data. Front Microbiol 2018; 9:365. [PMID: 29545787 PMCID: PMC5837987 DOI: 10.3389/fmicb.2018.00365] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 02/15/2018] [Indexed: 01/21/2023] Open
Abstract
The abundance of both taxonomic groups and gene categories in microbiome samples can now be easily assayed via various sequencing technologies, and visualized using a variety of software tools. However, the assemblage of taxa in the microbiome and its gene content are clearly linked, and tools for visualizing the relationship between these two facets of microbiome composition and for facilitating exploratory analysis of their co-variation are lacking. Here we introduce BURRITO, a web tool for interactive visualization of microbiome multi-omic data with paired taxonomic and functional information. BURRITO simultaneously visualizes the taxonomic and functional compositions of multiple samples and dynamically highlights relationships between taxa and functions to capture the underlying structure of these data. Users can browse for taxa and functions of interest and interactively explore the share of each function attributed to each taxon across samples. BURRITO supports multiple input formats for taxonomic and metagenomic data, allows adjustment of data granularity, and can export generated visualizations as static publication-ready formatted figures. In this paper, we describe the functionality of BURRITO, and provide illustrative examples of its utility for visualizing various trends in the relationship between the composition of taxa and functions in complex microbiomes.
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Affiliation(s)
- Colin P. McNally
- Department of Genome Sciences, University of Washington, Seattle, WA, United States
| | - Alexander Eng
- Department of Genome Sciences, University of Washington, Seattle, WA, United States
| | - Cecilia Noecker
- Department of Genome Sciences, University of Washington, Seattle, WA, United States
| | | | - Elhanan Borenstein
- Department of Genome Sciences, University of Washington, Seattle, WA, United States
- Department of Computer Science and Engineering, University of Washington, Seattle, WA, United States
- Santa Fe Institute, Santa Fe, NM, United States
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