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Alencar RM, Martínez JG, Machado VN, Alzate JF, Ortiz-Ojeda CP, Matias RR, Benzaquem DC, Santos MCF, Assunção EN, Lira EC, Astolfi-Filho S, Hrbek T, Farias IP, Fantin C. Preliminary profile of the gut microbiota from amerindians in the Brazilian amazon experiencing a process of transition to urbanization. Braz J Microbiol 2024; 55:2345-2354. [PMID: 38913252 PMCID: PMC11405645 DOI: 10.1007/s42770-024-01413-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: 03/13/2024] [Accepted: 05/31/2024] [Indexed: 06/25/2024] Open
Abstract
The Yanomami are one of the oldest indigenous tribes in the Amazon and are direct descendants of the first people to colonize South America 12,000 years ago. They are located on the border between Venezuela and Brazil, with the Venezuelan side remaining uncontacted. While they maintain a hunter-gatherer society, they are currently experiencing contact with urbanized populations in Brazil. The human gut microbiota of traditional communities has become the subject of recent studies due to the Westernization of their diet and the introduction of antibiotics and other chemicals, which have affected microbial diversity in indigenous populations, thereby threatening their existence. In this study, we preliminarily characterized the diversity of the gut microbiota of the Yanomami, a hunter-gatherer society from the Amazon, experiencing contact with urbanized populations. Similarly, we compared their diversity with the population in Manaus, Amazonas. A metabarcoding approach of the 16 S rRNA gene was carried out on fecal samples. Differences were found between the two populations, particularly regarding the abundance of genera (e.g., Prevotella and Bacteroides) and the higher values of the phyla Bacteroidetes over Firmicutes, which were significant only in the Yanomami. Some bacteria were found exclusively in the Yanomami (Treponema and Succinivibrio). However, diversity was statistically equal between them. In conclusion, the composition of the Yanomami gut microbiota still maintains the profile characteristic of a community with a traditional lifestyle. However, our results suggest an underlying Westernization process of the Yanomami microbiota when compared with that of Manaus, which must be carefully monitored by authorities, as the loss of diversity can be a sign of growing danger to the health of the Yanomami.
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Affiliation(s)
- Rodrigo M Alencar
- Programa de Pós-graduação em Biotecnologia e Recursos Naturais da Amazônia, Universidade do Estado do Amazonas, Manaus, Brazil
| | - José G Martínez
- Programa de Pós-graduação em Biotecnologia e Recursos Naturais da Amazônia, Universidade do Estado do Amazonas, Manaus, Brazil.
- Grupo de investigación Biociencias, Facultad de Ciencias de la Salud, Institución Universitaria Colegio Mayor de Antioquia, Medellín, Colombia.
| | - Valéria N Machado
- Programa de Pós-graduação em Biotecnologia e Recursos Naturais da Amazônia, Universidade do Estado do Amazonas, Manaus, Brazil
- Laboratório de Evolução e Genética Animal, Universidade Federal do Amazonas, Manaus, Brazil
| | - Juan F Alzate
- National Center for Genomic Sequencing, School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Cinthya P Ortiz-Ojeda
- Programa de Pós-graduação em Biotecnologia e Recursos Naturais da Amazônia, Universidade do Estado do Amazonas, Manaus, Brazil
- Universidad Tecnológica del Perú, Lima, Peru
| | - Rosiane R Matias
- Programa de Pós-graduação em Biotecnologia e Recursos Naturais da Amazônia, Universidade do Estado do Amazonas, Manaus, Brazil
| | - Denise C Benzaquem
- Programa de Pós-graduação em Biotecnologia e Recursos Naturais da Amazônia, Universidade do Estado do Amazonas, Manaus, Brazil
| | - Maria C F Santos
- Programa de Pós-graduação em Biotecnologia e Recursos Naturais da Amazônia, Universidade do Estado do Amazonas, Manaus, Brazil
| | - Enedina N Assunção
- Centro de Apoio Multidisciplinar, Universidade Federal do Amazonas, Manaus, Brazil
| | - Evelyn C Lira
- Centro de Apoio Multidisciplinar, Universidade Federal do Amazonas, Manaus, Brazil
| | | | - Tomas Hrbek
- Laboratório de Evolução e Genética Animal, Universidade Federal do Amazonas, Manaus, Brazil
- Department of Biology, Trinity University, San Antonio, USA
| | - Izeni P Farias
- Laboratório de Evolução e Genética Animal, Universidade Federal do Amazonas, Manaus, Brazil
| | - Cleiton Fantin
- Programa de Pós-graduação em Biotecnologia e Recursos Naturais da Amazônia, Universidade do Estado do Amazonas, Manaus, Brazil
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Rampelli S, Gallois S, D’Amico F, Turroni S, Fabbrini M, Scicchitano D, Candela M, Henry A. The gut microbiome of Baka forager-horticulturalists from Cameroon is optimized for wild plant foods. iScience 2024; 27:109211. [PMID: 38433907 PMCID: PMC10904984 DOI: 10.1016/j.isci.2024.109211] [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: 10/23/2023] [Revised: 12/21/2023] [Accepted: 02/07/2024] [Indexed: 03/05/2024] Open
Abstract
The human gut microbiome is losing biodiversity, due to the "microbiome modernization process" that occurs with urbanization. To keep track of it, here we applied shotgun metagenomics to the gut microbiome of the Baka, a group of forager-horticulturalists from Cameroon, who combine hunting and gathering with growing a few crops and working for neighboring Bantu-speaking farmers. We analyzed the gut microbiome of individuals with different access to and use of wild plant and processed foods, to explore the variation of their gut microbiome along the cline from hunter-gatherer to agricultural subsistence patterns. We found that 26 species-level genome bins from our cohort were pivotal for the degradation of the wild plant food substrates. These microbes include Old Friend species and are encoded for genes that are no longer present in industrialized gut microbiome. Our results highlight the potential relevance of these genes to human biology and health, in relation to lifestyle.
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Affiliation(s)
- Simone Rampelli
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum – University of Bologna, 40126 Bologna, Italy
| | - Sandrine Gallois
- Department of Archaeological Sciences, Faculty of Archaeology, Leiden University, 2311 Leiden, the Netherlands
- Institute of Environmental Science and Technology, ST, 08193 Bellaterra, Spain
| | - Federica D’Amico
- Microbiomics Unit, Department of Medical and Surgical Sciences (DiMeC), Alma Mater Studiorum – University of Bologna, 40138 Bologna, Italy
| | - Silvia Turroni
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum – University of Bologna, 40126 Bologna, Italy
| | - Marco Fabbrini
- Microbiomics Unit, Department of Medical and Surgical Sciences (DiMeC), Alma Mater Studiorum – University of Bologna, 40138 Bologna, Italy
| | - Daniel Scicchitano
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum – University of Bologna, 40126 Bologna, Italy
| | - Marco Candela
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum – University of Bologna, 40126 Bologna, Italy
| | - Amanda Henry
- Department of Archaeological Sciences, Faculty of Archaeology, Leiden University, 2311 Leiden, the Netherlands
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Giombi F, Pace GM, Pirola F, Cerasuolo M, Ferreli F, Mercante G, Spriano G, Canonica GW, Heffler E, Ferri S, Puggioni F, Paoletti G, Malvezzi L. Airways Type-2 Related Disorders: Multiorgan, Systemic or Syndemic Disease? Int J Mol Sci 2024; 25:730. [PMID: 38255804 PMCID: PMC10815382 DOI: 10.3390/ijms25020730] [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: 12/14/2023] [Revised: 01/03/2024] [Accepted: 01/04/2024] [Indexed: 01/24/2024] Open
Abstract
Chronic rhinosinusitis (CRS) has recently undergone a significant paradigm shift, moving from a phenotypical classification towards an "endotype-based" definition that places more emphasis on clinical and therapeutic aspects. Similar to other airway diseases, like asthma, most cases of CRS in developed countries exhibit a dysregulated type-2 immune response and related cytokines. Consequently, the traditional distinction between upper and lower airways has been replaced by a "united airway" perspective. Additionally, type-2 related disorders extend beyond respiratory boundaries, encompassing conditions beyond the airways, such as atopic dermatitis. This necessitates a multidisciplinary approach. Moreover, consideration of possible systemic implications is crucial, particularly in relation to sleep-related breathing diseases like Obstructive Sleep Apnoea Syndrome (OSAS) and the alteration of systemic inflammatory mediators such as nitric oxide. The trends in epidemiological, economic, and social burden are progressively increasing worldwide, indicating syndemic characteristics. In light of these insights, this narrative review aims to present the latest evidence on respiratory type-2 related disorders, with a specific focus on CRS while promoting a comprehensive perspective on the "united airways". It also introduces a novel concept: viewing these conditions as a multiorgan, systemic, and syndemic disease.
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Affiliation(s)
- Francesco Giombi
- Otorhinolaryngology Head & Neck Surgery Unit, IRCCS Humanitas Research Hospital, Via Manzoni 56, Rozzano, 20089 Milan, Italy; (F.G.); (F.P.); (M.C.); (F.F.); (G.M.); (G.S.); (L.M.)
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele, 20090 Milan, Italy; (G.W.C.); (E.H.); (S.F.); (F.P.); (G.P.)
| | - Gian Marco Pace
- Otorhinolaryngology Head & Neck Surgery Unit, IRCCS Humanitas Research Hospital, Via Manzoni 56, Rozzano, 20089 Milan, Italy; (F.G.); (F.P.); (M.C.); (F.F.); (G.M.); (G.S.); (L.M.)
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele, 20090 Milan, Italy; (G.W.C.); (E.H.); (S.F.); (F.P.); (G.P.)
| | - Francesca Pirola
- Otorhinolaryngology Head & Neck Surgery Unit, IRCCS Humanitas Research Hospital, Via Manzoni 56, Rozzano, 20089 Milan, Italy; (F.G.); (F.P.); (M.C.); (F.F.); (G.M.); (G.S.); (L.M.)
| | - Michele Cerasuolo
- Otorhinolaryngology Head & Neck Surgery Unit, IRCCS Humanitas Research Hospital, Via Manzoni 56, Rozzano, 20089 Milan, Italy; (F.G.); (F.P.); (M.C.); (F.F.); (G.M.); (G.S.); (L.M.)
- Otorhinolaryngology Head & Neck Surgery Unit, Casa di Cura Humanitas San Pio X, Via Francesco Nava 31, 20159 Milan, Italy
| | - Fabio Ferreli
- Otorhinolaryngology Head & Neck Surgery Unit, IRCCS Humanitas Research Hospital, Via Manzoni 56, Rozzano, 20089 Milan, Italy; (F.G.); (F.P.); (M.C.); (F.F.); (G.M.); (G.S.); (L.M.)
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele, 20090 Milan, Italy; (G.W.C.); (E.H.); (S.F.); (F.P.); (G.P.)
| | - Giuseppe Mercante
- Otorhinolaryngology Head & Neck Surgery Unit, IRCCS Humanitas Research Hospital, Via Manzoni 56, Rozzano, 20089 Milan, Italy; (F.G.); (F.P.); (M.C.); (F.F.); (G.M.); (G.S.); (L.M.)
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele, 20090 Milan, Italy; (G.W.C.); (E.H.); (S.F.); (F.P.); (G.P.)
| | - Giuseppe Spriano
- Otorhinolaryngology Head & Neck Surgery Unit, IRCCS Humanitas Research Hospital, Via Manzoni 56, Rozzano, 20089 Milan, Italy; (F.G.); (F.P.); (M.C.); (F.F.); (G.M.); (G.S.); (L.M.)
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele, 20090 Milan, Italy; (G.W.C.); (E.H.); (S.F.); (F.P.); (G.P.)
| | - Giorgio Walter Canonica
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele, 20090 Milan, Italy; (G.W.C.); (E.H.); (S.F.); (F.P.); (G.P.)
- Personalized Medicine, Asthma and Allergy, IRCCS Humanitas Research Hospital, Via Manzoni 56, Rozzano, 20089 Milan, Italy
| | - Enrico Heffler
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele, 20090 Milan, Italy; (G.W.C.); (E.H.); (S.F.); (F.P.); (G.P.)
- Personalized Medicine, Asthma and Allergy, IRCCS Humanitas Research Hospital, Via Manzoni 56, Rozzano, 20089 Milan, Italy
| | - Sebastian Ferri
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele, 20090 Milan, Italy; (G.W.C.); (E.H.); (S.F.); (F.P.); (G.P.)
- Personalized Medicine, Asthma and Allergy, IRCCS Humanitas Research Hospital, Via Manzoni 56, Rozzano, 20089 Milan, Italy
| | - Francesca Puggioni
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele, 20090 Milan, Italy; (G.W.C.); (E.H.); (S.F.); (F.P.); (G.P.)
- Personalized Medicine, Asthma and Allergy, IRCCS Humanitas Research Hospital, Via Manzoni 56, Rozzano, 20089 Milan, Italy
| | - Giovanni Paoletti
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele, 20090 Milan, Italy; (G.W.C.); (E.H.); (S.F.); (F.P.); (G.P.)
- Personalized Medicine, Asthma and Allergy, IRCCS Humanitas Research Hospital, Via Manzoni 56, Rozzano, 20089 Milan, Italy
| | - Luca Malvezzi
- Otorhinolaryngology Head & Neck Surgery Unit, IRCCS Humanitas Research Hospital, Via Manzoni 56, Rozzano, 20089 Milan, Italy; (F.G.); (F.P.); (M.C.); (F.F.); (G.M.); (G.S.); (L.M.)
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele, 20090 Milan, Italy; (G.W.C.); (E.H.); (S.F.); (F.P.); (G.P.)
- Otorhinolaryngology Head & Neck Surgery Unit, Casa di Cura Humanitas San Pio X, Via Francesco Nava 31, 20159 Milan, Italy
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Basak S, Hridayanka KSN, Duttaroy AK. Bioactives and their roles in bone metabolism of osteoarthritis: evidence and mechanisms on gut-bone axis. Front Immunol 2024; 14:1323233. [PMID: 38235147 PMCID: PMC10792057 DOI: 10.3389/fimmu.2023.1323233] [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: 10/17/2023] [Accepted: 12/11/2023] [Indexed: 01/19/2024] Open
Abstract
Bioactives significantly modify and maintain human health. Available data suggest that Bioactives might play a beneficial role in chronic inflammatory diseases. Although promised, defining their mechanisms and opting to weigh their benefits and limitations is imperative. Detailed mechanisms by which critical Bioactives, including probiotics and prebiotics such as dietary lipids (DHA, EPA, alpha LA), vitamin D, polysaccharides (fructooligosaccharide), polyphenols (curcumin, resveratrol, and capsaicin) potentially modulate inflammation and bone metabolism is limited. Certain dietary bioactive significantly impact the gut microbiota, immune system, and pain response via the gut-immune-bone axis. This narrative review highlights a recent update on mechanistic evidence that bioactive is demonstrated demonstrated to reduce osteoarthritis pathophysiology.
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Affiliation(s)
- Sanjay Basak
- Molecular Biology Division, National Institute of Nutrition, Indian Council of Medical Research, Hyderabad, India
| | - Kota Sri Naga Hridayanka
- Molecular Biology Division, National Institute of Nutrition, Indian Council of Medical Research, Hyderabad, India
| | - Asim K. Duttaroy
- Department of Nutrition, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
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5
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Zhang ZJ, Cole C, Lin H, Wu C, Haro F, McSpadden E, van der Donk WA, Pamer EG. Exposure and resistance to lantibiotics impact microbiota composition and function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.30.573728. [PMID: 38234830 PMCID: PMC10793476 DOI: 10.1101/2023.12.30.573728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
The intestinal microbiota is composed of hundreds of distinct microbial species that interact with each other and their mammalian host. Antibiotic exposure dramatically impacts microbiota compositions and leads to acquisition of antibiotic-resistance genes. Lantibiotics are ribosomally synthesized and post-translationally modified peptides produced by some bacterial strains to inhibit the growth of competing bacteria. Nisin A is a lantibiotic produced by Lactococcus lactis that is commonly added to food products to reduce contamination with Gram-positive pathogens. Little is known, however, about lantibiotic-resistance of commensal bacteria inhabiting the human intestine. Herein, we demonstrate that Nisin A administration to mice alters fecal microbiome compositions and the concentration of taurine-conjugated primary bile acids. Lantibiotic Resistance System genes (LRS) are encoded by lantibiotic-producing bacterial strains but, we show, are also prevalent in microbiomes across human cohorts spanning vastly different lifestyles and 5 continents. Bacterial strains encoding LRS have enhanced in vivo fitness upon dietary exposure to Nisin A but reduced fitness in the absence of lantibiotic pressure. Differential binding of host derived, secreted IgA contributes to fitness discordance between bacterial strains encoding or lacking LRS. Although LRS are associated with mobile genetic elements, sequence comparisons of LRS encoded by distinct bacterial species suggest they have been long-term components of their respective genomes. Our study reveals the prevalence, abundance and physiologic significance of an underappreciated subset of antimicrobial resistance genes encoded by commensal bacterial species constituting the human gut microbiome, and provides insights that will guide development of microbiome augmenting strategies.
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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 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
| | - Huaiying Lin
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL 60637, USA
| | - Chunyu Wu
- Department of Chemistry, University of Illinois Urbana-Champaign, IL 61801, USA
| | - Fidel Haro
- 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
| | - Wilfred A van der Donk
- Department of Chemistry, University of Illinois Urbana-Champaign, IL 61801, USA; Howard Hughes Medical Institute, University of Illinois Urbana-Champaign, IL 61801, 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 Microbiology, Biological Sciences Division, University of Chicago, 5841 South Maryland Ave, Chicago, IL 60637, USA
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6
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Conteville LC, Oliveira-Ferreira J, Vicente ACP. Heavy metal resistance in the Yanomami and Tunapuco microbiome. Mem Inst Oswaldo Cruz 2023; 118:e230086. [PMID: 37971084 PMCID: PMC10641926 DOI: 10.1590/0074-02760230086] [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: 05/14/2023] [Accepted: 10/05/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND The Amazon Region hosts invaluable and unique biodiversity as well as mineral resources. Consequently, large illegal and artisanal gold mining areas exist in indigenous territories. Mercury has been used in gold mining, and some has been released into the environment and atmosphere, primarily affecting indigenous people such as the Yanomami. In addition, other heavy metals have been associated with gold mining and other metal-dispersing activities in the region. OBJECTIVE Investigate the gut microbiome of two semi-isolated groups from the Amazon, focusing on metal resistance. METHODS Metagenomic data from the Yanomami and Tunapuco gut microbiome were assembled into contigs, and their putative proteins were searched against a database of metal resistance proteins. FINDINGS Proteins associated with mercury resistance were exclusive in the Yanomami, while proteins associated with silver resistance were exclusive in the Tunapuco. Both groups share 77 non-redundant metal resistance (MR) proteins, mostly associated with multi-MR and operons with potential resistance to arsenic, nickel, zinc, copper, copper/silver, and cobalt/nickel. Although both groups harbour operons related to copper resistance, only the Tunapuco group had the pco operon. CONCLUSION The Yanomami and Tunapuco gut microbiome shows that these people have been exposed directly or indirectly to distinct scenarios concerning heavy metals.
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Affiliation(s)
- Liliane Costa Conteville
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Genética Molecular de Microrganismos, Rio de Janeiro, RJ, Brasil
- Embrapa Pecuária Sudeste, São Carlos, SP, Brasil
| | - Joseli Oliveira-Ferreira
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Imunoparasitologia, Rio de Janeiro, RJ, Brasil
| | - Ana Carolina P Vicente
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Genética Molecular de Microrganismos, Rio de Janeiro, RJ, Brasil
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Carter MM, Olm MR, Merrill BD, Dahan D, Tripathi S, Spencer SP, Yu FB, Jain S, Neff N, Jha AR, Sonnenburg ED, Sonnenburg JL. Ultra-deep sequencing of Hadza hunter-gatherers recovers vanishing gut microbes. Cell 2023; 186:3111-3124.e13. [PMID: 37348505 PMCID: PMC10330870 DOI: 10.1016/j.cell.2023.05.046] [Citation(s) in RCA: 44] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 02/12/2023] [Accepted: 05/26/2023] [Indexed: 06/24/2023]
Abstract
The gut microbiome modulates immune and metabolic health. Human microbiome data are biased toward industrialized populations, limiting our understanding of non-industrialized microbiomes. Here, we performed ultra-deep metagenomic sequencing on 351 fecal samples from the Hadza hunter-gatherers of Tanzania and comparative populations in Nepal and California. We recovered 91,662 genomes of bacteria, archaea, bacteriophages, and eukaryotes, 44% of which are absent from existing unified datasets. We identified 124 gut-resident species vanishing in industrialized populations and highlighted distinct aspects of the Hadza gut microbiome related to in situ replication rates, signatures of selection, and strain sharing. Industrialized gut microbes were found to be enriched in genes associated with oxidative stress, possibly a result of microbiome adaptation to inflammatory processes. This unparalleled view of the Hadza gut microbiome provides a valuable resource, expands our understanding of microbes capable of colonizing the human gut, and clarifies the extensive perturbation induced by the industrialized lifestyle.
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Affiliation(s)
- Matthew M Carter
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Matthew R Olm
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Bryan D Merrill
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Dylan Dahan
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Surya Tripathi
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Sean P Spencer
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Feiqiao B Yu
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Sunit Jain
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Norma Neff
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Aashish R Jha
- Genetic Heritage Group, Program in Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Erica D Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA.
| | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Center for Human Microbiome Studies, Stanford University School of Medicine, Stanford, CA 94304, USA.
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8
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Chaiyasut C, Sivamaruthi BS, Lailerd N, Sirilun S, Thangaleela S, Khongtan S, Bharathi M, Kesika P, Saelee M, Choeisoongnern T, Fukngoen P, Peerajan S, Sittiprapaporn P. Influence of Bifidobacterium breve on the Glycaemic Control, Lipid Profile and Microbiome of Type 2 Diabetic Subjects: A Preliminary Randomized Clinical Trial. Pharmaceuticals (Basel) 2023; 16:ph16050695. [PMID: 37242478 DOI: 10.3390/ph16050695] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/14/2023] [Accepted: 04/27/2023] [Indexed: 05/28/2023] Open
Abstract
Type 2 diabetes mellitus (T2DM) is one of the most highly prevalent metabolic disorders worldwide. Uncontrolled T2DM can lead to other health threats such as cardiac arrest, lower-limb amputation, blindness, stroke, impaired kidney function, and microvascular and macrovascular complications. Many studies have demonstrated the association between gut microbiota and diabetes development and probiotic supplementation in improving glycemic properties in T2DM. The study aimed to evaluate the influence of Bifidobacterium breve supplementation on glycemic control, lipid profile, and microbiome of T2DM subjects. Forty participants were randomly divided into two groups, and they received probiotics (50 × 109 CFU/day) or placebo interventions (corn starch; 10 mg/day) for 12 weeks. The changes in the blood-urea nitrogen (BUN), aspartate aminotransferase (AST), alanine transaminase (ALT), alkaline phosphatase (ALP), fasting blood sugar (FBS), glycated hemoglobin (HbA1c), total cholesterol (TC), triglycerides (TG), high-density lipoprotein (HDL), low-density lipoprotein (LDL), creatinine levels, and other factors such as body-mass index, visceral fat, body fat, and body weight were assessed at baseline and after 12 weeks. B. breve supplementation significantly reduced BUN, creatinine, LDL, TG, and HbA1c levels compared to the placebo group. Significant changes were observed in the microbiome of the probiotic-treated group compared to the placebo group. Firmicutes and proteobacteria were predominant in the placebo and probiotic-treated groups. Genera Streptococcus, Butyricicoccus, and species Eubacterium hallii were significantly reduced in the probiotic-treated group compared to the placebo. Overall results suggested that B. breve supplementation could prevent worsening of representative clinical parameters in T2DM subjects. The current study has limitations, including fewer subjects, a single probiotic strain, and fewer metagenomic samples for microbiome analysis. Therefore, the results of the current study require further validation using more experimental subjects.
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Affiliation(s)
- Chaiyavat Chaiyasut
- Innovation Center for Holistic Health, Nutraceuticals, and Cosmeceuticals, Faculty of Pharmacy, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Bhagavathi Sundaram Sivamaruthi
- Innovation Center for Holistic Health, Nutraceuticals, and Cosmeceuticals, Faculty of Pharmacy, Chiang Mai University, Chiang Mai 50200, Thailand
- Office of Research Administration, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Narissara Lailerd
- Innovation Center for Holistic Health, Nutraceuticals, and Cosmeceuticals, Faculty of Pharmacy, Chiang Mai University, Chiang Mai 50200, Thailand
- Department of Physiology, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Sasithorn Sirilun
- Innovation Center for Holistic Health, Nutraceuticals, and Cosmeceuticals, Faculty of Pharmacy, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Subramanian Thangaleela
- Innovation Center for Holistic Health, Nutraceuticals, and Cosmeceuticals, Faculty of Pharmacy, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Suchanat Khongtan
- Innovation Center for Holistic Health, Nutraceuticals, and Cosmeceuticals, Faculty of Pharmacy, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Muruganantham Bharathi
- Innovation Center for Holistic Health, Nutraceuticals, and Cosmeceuticals, Faculty of Pharmacy, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Periyanaina Kesika
- Innovation Center for Holistic Health, Nutraceuticals, and Cosmeceuticals, Faculty of Pharmacy, Chiang Mai University, Chiang Mai 50200, Thailand
- Office of Research Administration, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Manee Saelee
- Neuropsychological Research Laboratory, Neuroscience Research Center, School of Anti-Aging and Regenerative Medicine, Mae Fah Luang University, Bangkok 10110, Thailand
| | - Thiwanya Choeisoongnern
- Neuropsychological Research Laboratory, Neuroscience Research Center, School of Anti-Aging and Regenerative Medicine, Mae Fah Luang University, Bangkok 10110, Thailand
| | - Pranom Fukngoen
- Innovation Center for Holistic Health, Nutraceuticals, and Cosmeceuticals, Faculty of Pharmacy, Chiang Mai University, Chiang Mai 50200, Thailand
| | | | - Phakkharawat Sittiprapaporn
- Neuropsychological Research Laboratory, Neuroscience Research Center, School of Anti-Aging and Regenerative Medicine, Mae Fah Luang University, Bangkok 10110, Thailand
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9
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Lan LY, Hong QX, Gao SM, Li Q, You YY, Chen W, Fan PF. Gut microbiota of skywalker hoolock gibbons (Hoolock tianxing) from different habitats and in captivity: Implications for gibbon health. Am J Primatol 2023; 85:e23468. [PMID: 36691713 DOI: 10.1002/ajp.23468] [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] [Received: 04/05/2022] [Revised: 01/10/2023] [Accepted: 01/12/2023] [Indexed: 01/25/2023]
Abstract
The gut microbiota plays an integral role in the metabolism and immunity of animal hosts, and provides insights into the health and habitat assessment of threatened animals. The skywalker hoolock gibbon (Hoolock tianxing) is a newly described gibbon species, and is considered an endangered species. Here, we used 16S rRNA amplicon sequencing to describe the fecal bacterial community of skywalker hoolock gibbons from different habitats and in captivity. Fecal samples (n = 5) from two captive gibbons were compared with wild populations (N = 6 gibbons, n = 33 samples). At the phylum level, Spirochetes, Proteobacteria, Firmicutes, Bacteroidetes dominated in captive gibbons, while Firmicutes, Bacteroidetes, and Tenericutes dominated in wild gibbons. At the genus level, captive gibbons were dominated by Treponema-2, followed by Succinivibrio and Cerasicoccus, while wild gibbons were dominated by Anaeroplasma, Prevotellaceae UCG-001, and Erysipelotrichaceae UCG-004. Captive rearing was significantly associated with lower taxonomic alpha-diversity, and different relative abundance of some dominant bacteria compared to wild gibbons. Predicted Kyoto Encyclopedia of Genes and Genomes pathway analyses showed that captive gibbons have significantly lower total pathway diversity and higher relative abundance of bacterial functions involved in "drug resistance: antimicrobial" and "carbohydrate metabolism" than wild gibbons. This study reveals the potential influence of captivity and habitat on the gut bacterial community of gibbons and provides a basis for guiding the conservation management of captive populations.
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Affiliation(s)
- Li-Ying Lan
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Qi-Xuan Hong
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shao-Ming Gao
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Qi Li
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yu-Yan You
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China
| | - Wu Chen
- Guangzhou Zoo, Guangzhou, China
| | - Peng-Fei Fan
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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10
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Ruxton CHS, Kajita C, Rocca P, Pot B. Microbiota and probiotics: chances and challenges - a symposium report. GUT MICROBIOME (CAMBRIDGE, ENGLAND) 2023; 4:e6. [PMID: 39295904 PMCID: PMC11406417 DOI: 10.1017/gmb.2023.4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 03/14/2023] [Accepted: 03/16/2023] [Indexed: 09/21/2024]
Abstract
The 10th International Yakult Symposium was held in Milan, Italy, on 13-14 October 2022. Two keynote lectures covered the crewed journey to space and its implications for the human microbiome, and how current regulatory systems can be adapted and updated to ensure the safety of microorganisms used as probiotics or food processing ingredients. The remaining lectures were split into sections entitled "Chances" and "Challenges." The "Chances" section explored opportunities for the science of probiotics and fermented foods to contribute to diverse areas of health such as irritable bowel syndrome, major depression, Parkinson's disease, immune dysfunction, infant colic, intensive care, respiratory infections, and promoting healthy longevity. The "Challenges" section included selecting appropriate clinical trial participants and methodologies to minimise heterogeneity in responses, how to view probiotics in the context of One Health, adapting regulatory frameworks, and understanding how substances of bacterial origin can cross the blood-brain barrier. The symposium provided evidence from cutting-edge research that gut eubiosis is vital for human health and, like space, the microbiota deserves further exploration of its vast potential.
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Affiliation(s)
| | | | | | - Bruno Pot
- Yakult Europe BV, Almere, Netherlands
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11
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Kann S, Eberhardt K, Hinz R, Schwarz NG, Dib JC, Aristizabal A, Mendoza GAC, Hagen RM, Frickmann H, Barrantes I, Kreikemeyer B. The Gut Microbiome of an Indigenous Agropastoralist Population in a Remote Area of Colombia with High Rates of Gastrointestinal Infections and Dysbiosis. Microorganisms 2023; 11:625. [PMID: 36985199 PMCID: PMC10052337 DOI: 10.3390/microorganisms11030625] [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] [Received: 01/25/2023] [Revised: 02/20/2023] [Accepted: 02/21/2023] [Indexed: 03/05/2023] Open
Abstract
An Indigenous agropastoralist population called the Wiwa from the Sierra Nevada de Santa Marta, in North-East Colombia, shows high rates of gastrointestinal infections. Chronic gut inflammatory processes and dysbiosis could be a reason, suggesting an influence or predisposing potential of the gut microbiome composition. The latter was analyzed by 16S rRNA gene amplicon next generation sequencing from stool samples. Results of the Wiwa population microbiomes were associated with available epidemiological and morphometric data and compared to control samples from a local urban population. Indeed, locational-, age-, and gender-specific differences in the Firmicutes/Bacteriodetes ratio, core microbiome, and overall genera-level microbiome composition were shown. Alpha- and ß-diversity separated the urban site from the Indigenous locations. Urban microbiomes were dominated by Bacteriodetes, whereas Indigenous samples revealed a four times higher abundance of Proteobacteria. Even differences among the two Indigenous villages were noted. PICRUSt analysis identified several enriched location-specific bacterial pathways. Moreover, on a general comparative scale and with a high predictive accuracy, we found Sutterella associated with the abundance of enterohemorrhagic Escherichia coli (EHEC), Faecalibacteria associated with enteropathogenic Escherichia coli (EPEC) and helminth species Hymenolepsis nana and Enterobius vermicularis. Parabacteroides, Prevotella, and Butyrivibrio are enriched in cases of salmonellosis, EPEC, and helminth infections. Presence of Dialister was associated with gastrointestinal symptoms, whereas Clostridia were exclusively found in children under the age of 5 years. Odoribacter and Parabacteroides were exclusively identified in the microbiomes of the urban population of Valledupar. In summary, dysbiotic alterations in the gut microbiome in the Indigenous population with frequent episodes of self-reported gastrointestinal infections were confirmed with epidemiological and pathogen-specific associations. Our data provide strong hints of microbiome alterations associated with the clinical conditions of the Indigenous population.
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Affiliation(s)
- Simone Kann
- Department for Research and Development, Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany
| | - Kirsten Eberhardt
- Department of Tropical Medicine, Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
- Division of Hygiene and Infectious Diseases, Institute of Hygiene and Environment, 20539 Hamburg, Germany
| | - Rebecca Hinz
- SYNLAB Medizinisches Versorgungszentrum Hamburg GmbH, 22083 Hamburg, Germany
| | | | - Juan Carlos Dib
- Department of Medicine, Fundación Universidad de Norte, Baranquilla 080001, Colombia
| | | | | | - Ralf Matthias Hagen
- Department of Microbiology and Hospital Hygiene, Bundeswehr Central Hospital Koblenz, 56070 Koblenz, Germany
| | - Hagen Frickmann
- Department of Microbiology and Hospital Hygiene, Bundeswehr Hospital Hamburg, 20359 Hamburg, Germany
- Institute for Medical Microbiology, Virology and Hygiene, University Medicine Rostock, 18057 Rostock, Germany
| | - Israel Barrantes
- Research Group Translational Bioinformatics, Institute for Biostatistics and Informatics in Medicine und Aging Research, University Medicine Rostock, 18057 Rostock, Germany
| | - Bernd Kreikemeyer
- Institute for Medical Microbiology, Virology and Hygiene, University Medicine Rostock, 18057 Rostock, Germany
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12
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Al‐Emran HM, Rahman S, Hasan MS, Ul Alam R, Islam OK, Anwar A, Jahid MIK, Hossain A. Microbiome analysis revealing microbial interactions and secondary bacterial infections in COVID-19 patients comorbidly affected by Type 2 diabetes. J Med Virol 2023; 95:e28234. [PMID: 36258280 PMCID: PMC9874868 DOI: 10.1002/jmv.28234] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/03/2022] [Accepted: 10/13/2022] [Indexed: 01/27/2023]
Abstract
The mortality of coronavirus disease 2019 (COVID-19) disease is very high among the elderly or individuals having comorbidities such as obesity, cardiovascular diseases, lung infections, hypertension, and/or diabetes. Our study characterizes the metagenomic features in severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)-infected patients with or without type 2 diabetes, to identify the microbial interactions associated with its fatal consequences.This study compared the baseline nasopharyngeal microbiome of SARS-CoV-2-infected diabetic and nondiabetic patients with controls adjusted for age and gender. The metagenomics based on next-generation sequencing was performed using Ion GeneStudio S5 Series and the data were analyzed by the Vegan-package in R. All three groups possessed significant bacterial diversity and dissimilarity indexes (p < 0.05). Spearman's correlation coefficient network analysis illustrated 183 significant positive correlations and 13 negative correlations of pathogenic bacteria (r = 0.6-1.0, p < 0.05), and 109 positive correlations between normal flora and probiotic bacteria (r > 0.6, p < 0.05). The SARS-CoV-2 diabetic group exhibited a significant increase in pathogens and secondary infection-causing bacteria (p < 0.05) with a simultaneous decrease of normal flora (p < 0.05). The dysbiosis of the bacterial community might be linked with severe consequences of COVID-19-infected diabetic patients, although a few probiotic strains inhibited numerous pathogens in the same pathological niches. This study suggested that the promotion of normal flora and probiotics through dietary supplementation and excessive inflammation reduction by preventing secondary infections might lead to a better outcome for those comorbid patients.
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Affiliation(s)
- Hassan M. Al‐Emran
- Department of Biomedical EngineeringJashore University of Science and TechnologyJashoreBangladesh
| | - Shaminur Rahman
- Department of MicrobiologyJashore University of Science and TechnologyJashoreBangladesh
| | - Md. Shazid Hasan
- Department of MicrobiologyJashore University of Science and TechnologyJashoreBangladesh
| | - Rubayet Ul Alam
- Department of MicrobiologyJashore University of Science and TechnologyJashoreBangladesh
| | - Ovinu Kibria Islam
- Department of MicrobiologyJashore University of Science and TechnologyJashoreBangladesh
| | - Ajwad Anwar
- Department of MicrobiologyUniversity of DhakaDhakaBangladesh
| | - Md. Iqbal K. Jahid
- Department of MicrobiologyJashore University of Science and TechnologyJashoreBangladesh
- Genome CenterJashore University of Science and TechnologyJashoreBangladesh
| | - Anwar Hossain
- Genome CenterJashore University of Science and TechnologyJashoreBangladesh
- Department of MicrobiologyUniversity of DhakaDhakaBangladesh
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13
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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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14
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Mangola SM, Lund JR, Schnorr SL, Crittenden AN. Ethical microbiome research with Indigenous communities. Nat Microbiol 2022; 7:749-756. [PMID: 35577973 DOI: 10.1038/s41564-022-01116-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 03/31/2022] [Indexed: 11/10/2022]
Abstract
Human-microbiome interactions have been associated with evolutionary, cultural and environmental processes. With clinical applications of microbiome research now feasible, it is crucial that the science conducted, particularly among Indigenous communities, adheres to principles of inclusion. This necessitates a transdisciplinary dialogue to decide how biological samples are collected and who benefits from the research and any derived products. As a group of scholars working at the interface of biological and social science, we offer a candid discussion of the lessons learned from our own research and introduce one approach to carry out ethical microbiome research with Indigenous communities.
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Affiliation(s)
- Shani Msafiri Mangola
- Indigenous Peoples Law and Policy Program, James E. Rogers College of Law, University of Arizona, Tucson, AZ, USA.,Olanakwe Community Fund (USA), Boulder City, NV, USA.,Olanakwe Community Fund (TZ), Mang'ola Ward, Karatu, Tanzania
| | - Justin R Lund
- Center for the Ethics of Indigenous Genomics Research, University of Oklahoma, Norman, OK, USA.,Laboratories of Molecular Anthropology and Microbiome Research, Department of Anthropology, University of Oklahoma, Norman, OK, USA
| | - Stephanie L Schnorr
- Konrad Lorenz Institute for Evolution and Cognition Research, Klosterneuburg, Austria.,Center for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Alyssa N Crittenden
- Olanakwe Community Fund (USA), Boulder City, NV, USA. .,Laboratory of Nutrition and Reproduction, Department of Anthropology, University of Nevada, Las Vegas, NV, USA.
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15
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Mundula T, Russo E, Curini L, Giudici F, Piccioni A, Franceschi F, Amedei A. Chronic systemic low-grade inflammation and modern lifestyle: the dark role of gut microbiota on related diseases with a focus on pandemic COVID-19. Curr Med Chem 2022; 29:5370-5396. [PMID: 35524667 DOI: 10.2174/0929867329666220430131018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 02/01/2022] [Accepted: 02/23/2022] [Indexed: 12/12/2022]
Abstract
Inflammation is a physiological, beneficial and auto-limiting response of the host to alarming stimuli. Conversely, a chronic systemic low-grade inflammation (CSLGI), known as a long-time persisting condition, causes organs and host tissues' damage, representing a major risk for chronic diseases. Currently, a worldwide a high incidence of inflammatory chronic diseases is observed, often linked to the lifestyle-related changes occurred in the last decade's society. The mains lifestyle-related factors are a proinflammatory diet, psychological stress, tobacco smoking, alcohol abuse, physical inactivity, and finally indoor living and working with its related consequences such as indoor pollution, artificial light exposure and low vitamin D production. Recent scientific evidences found that gut microbiota (GM) has a main role in shaping the host's health, particularly as CSLGI mediator. As a matter of facts, based on the last discoveries regarding the remarkable GM activity, in this manuscript we focused on the elements of actual lifestyle that influence the composition and function of intestinal microbial community, in order to elicit the CSLGI and its correlated pathologies. In this scenario, we provide a broad review of the interplay between modern lifestyle, GM and CSLGI with a special focus on the COVID symptoms and emerging long-COVID syndrome.
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Affiliation(s)
- Tiziana Mundula
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Edda Russo
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Lavinia Curini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Francesco Giudici
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Andrea Piccioni
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Francesco Franceschi
- Emergency Department, Fondazione Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy
| | - Amedeo Amedei
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
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16
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Takenaka IKTM, Bartelli TF, Defelicibus A, Sendoya JM, Golubicki M, Robbio J, Serpa MS, Branco GP, Santos LBC, Claro LCL, Dos Santos GO, Kupper BEC, da Silva IT, Llera AS, de Mello CAL, Riechelmann RP, Dias-Neto E, Iseas S, Aguiar S, Nunes DN. Exome and Tissue-Associated Microbiota as Predictive Markers of Response to Neoadjuvant Treatment in Locally Advanced Rectal Cancer. Front Oncol 2022; 12:809441. [PMID: 35392220 PMCID: PMC8982181 DOI: 10.3389/fonc.2022.809441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 02/17/2022] [Indexed: 11/13/2022] Open
Abstract
The clinical and pathological responses to multimodal neoadjuvant therapy in locally advanced rectal cancers (LARCs) remain unpredictable, and robust biomarkers are still lacking. Recent studies have shown that tumors present somatic molecular alterations related to better treatment response, and it is also clear that tumor-associated bacteria are modulators of chemotherapy and immunotherapy efficacy, therefore having implications for long-term survivorship and a good potential as the biomarkers of outcome. Here, we performed whole exome sequencing and 16S ribosomal RNA (rRNA) amplicon sequencing from 44 pre-treatment LARC biopsies from Argentinian and Brazilian patients, treated with neoadjuvant chemoradiotherapy or total neoadjuvant treatment, searching for predictive biomarkers of response (responders, n = 17; non-responders, n = 27). In general, the somatic landscape of LARC was not capable to predict a response; however, a significant enrichment in mutational signature SBS5 was observed in non-responders (p = 0.0021), as well as the co-occurrence of APC and FAT4 mutations (p < 0.05). Microbiota studies revealed a similar alpha and beta diversity of bacteria between response groups. Yet, the linear discriminant analysis (LDA) of effect size indicated an enrichment of Hungatella, Flavonifractor, and Methanosphaera (LDA score ≥3) in the pre-treatment biopsies of responders, while non-responders had a higher abundance of Enhydrobacter, Paraprevotella (LDA score ≥3) and Finegoldia (LDA score ≥4). Altogether, the evaluation of these biomarkers in pre-treatment biopsies could eventually predict a neoadjuvant treatment response, while in post-treatment samples, it could help in guiding non-operative treatment strategies.
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Affiliation(s)
| | - Thais F Bartelli
- Medical Genomics Laboratory, International Center for Research, A.C.Camargo Cancer Center, São Paulo, Brazil
| | - Alexandre Defelicibus
- Laboratory of Bioinformatics and Computational Biology, International Center for Research, A.C. Camargo Cancer Center, São Paulo, Brazil
| | - Juan M Sendoya
- Laboratorio de Terapia Molecular y Celular - Genomics Unit, Fundación Instituto Leloir, Buenos Aires, Argentina.,Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Mariano Golubicki
- Oncology Unit, Hospital de Gastroenterología Carlos Bonorino Udaondo, Buenos Aires, Argentina.,Clinical Oncology, Intergrupo Argentino para el Tratamiento de los Tumores Gastrointestinales (IATTGI), Buenos Aires, Argentina
| | - Juan Robbio
- Clinical Oncology, Intergrupo Argentino para el Tratamiento de los Tumores Gastrointestinales (IATTGI), Buenos Aires, Argentina
| | - Marianna S Serpa
- Medical Genomics Laboratory, International Center for Research, A.C.Camargo Cancer Center, São Paulo, Brazil
| | - Gabriela P Branco
- Medical Genomics Laboratory, International Center for Research, A.C.Camargo Cancer Center, São Paulo, Brazil
| | - Luana B C Santos
- Medical Genomics Laboratory, International Center for Research, A.C.Camargo Cancer Center, São Paulo, Brazil
| | - Laura C L Claro
- Department of Pathology, A.C.Camargo Cancer Center, São Paulo, Brazil
| | | | - Bruna E C Kupper
- Colorectal Cancer Department, A.C.Camargo Cancer Center, São Paulo, Brazil
| | - Israel T da Silva
- Laboratory of Bioinformatics and Computational Biology, International Center for Research, A.C. Camargo Cancer Center, São Paulo, Brazil
| | - Andrea S Llera
- Laboratorio de Terapia Molecular y Celular - Genomics Unit, Fundación Instituto Leloir, Buenos Aires, Argentina.,Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Celso A L de Mello
- Department of Clinical Oncology, A.C.Camargo Cancer Center, São Paulo, Brazil
| | | | - Emmanuel Dias-Neto
- Medical Genomics Laboratory, International Center for Research, A.C.Camargo Cancer Center, São Paulo, Brazil.,Laboratory of Neurosciences (LIM-27) Alzira Denise Hertzog Silva, Institute of Psychiatry, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Soledad Iseas
- Oncology Unit, Hospital de Gastroenterología Carlos Bonorino Udaondo, Buenos Aires, Argentina
| | - Samuel Aguiar
- Colorectal Cancer Department, A.C.Camargo Cancer Center, São Paulo, Brazil
| | - Diana Noronha Nunes
- Medical Genomics Laboratory, International Center for Research, A.C.Camargo Cancer Center, São Paulo, Brazil.,National Institute of Science and Technology in Oncogenomics and Therapeutic Innovation (INCITO), São Paulo, Brazil
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17
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Ostrowski MP, La Rosa SL, Kunath BJ, Robertson A, Pereira G, Hagen LH, Varghese NJ, Qiu L, Yao T, Flint G, Li J, McDonald SP, Buttner D, Pudlo NA, Schnizlein MK, Young VB, Brumer H, Schmidt TM, Terrapon N, Lombard V, Henrissat B, Hamaker B, Eloe-Fadrosh EA, Tripathi A, Pope PB, Martens EC. Mechanistic insights into consumption of the food additive xanthan gum by the human gut microbiota. Nat Microbiol 2022; 7:556-569. [PMID: 35365790 DOI: 10.1038/s41564-022-01093-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 02/24/2022] [Indexed: 12/13/2022]
Abstract
Processed foods often include food additives such as xanthan gum, a complex polysaccharide with unique rheological properties, that has established widespread use as a stabilizer and thickening agent. Xanthan gum's chemical structure is distinct from those of host and dietary polysaccharides that are more commonly expected to transit the gastrointestinal tract, and little is known about its direct interaction with the gut microbiota, which plays a central role in digestion of other dietary fibre polysaccharides. Here we show that the ability to digest xanthan gum is common in human gut microbiomes from industrialized countries and appears contingent on a single uncultured bacterium in the family Ruminococcaceae. Our data reveal that this primary degrader cleaves the xanthan gum backbone before processing the released oligosaccharides using additional enzymes. Some individuals harbour Bacteroides intestinalis that is incapable of consuming polymeric xanthan gum but grows on oligosaccharide products generated by the Ruminococcaceae. Feeding xanthan gum to germfree mice colonized with a human microbiota containing the uncultured Ruminococcaceae supports the idea that the additive xanthan gum can drive expansion of the primary degrader Ruminococcaceae, along with exogenously introduced B. intestinalis. Our work demonstrates the existence of a potential xanthan gum food chain involving at least two members of different phyla of gut bacteria and provides an initial framework for understanding how widespread consumption of a recently introduced food additive influences human microbiomes.
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Affiliation(s)
- Matthew P Ostrowski
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Sabina Leanti La Rosa
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.,Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Benoit J Kunath
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Andrew Robertson
- Life Sciences Institute: Natural Products Discovery Core, University of Michigan, Ann Arbor, MI, USA
| | - Gabriel Pereira
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Live H Hagen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | | | - Ling Qiu
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Tianming Yao
- Department of Food Science and Whistler Center for Carbohydrate Research, Purdue University, West Lafayette, IN, USA
| | - Gabrielle Flint
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - James Li
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sean P McDonald
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Duna Buttner
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Nicholas A Pudlo
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Matthew K Schnizlein
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Vincent B Young
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA.,Department of Internal Medicine, Infectious Diseases Division, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Thomas M Schmidt
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Nicolas Terrapon
- Centre National de la Recherche Scientifique, Aix-Marseille Univ, Marseille, France.,Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Marseille, France
| | - Vincent Lombard
- Centre National de la Recherche Scientifique, Aix-Marseille Univ, Marseille, France.,Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Marseille, France
| | - Bernard Henrissat
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.,Technical University of Denmark, DTU Bioengineering, Lyngby, Denmark
| | - Bruce Hamaker
- Department of Food Science and Whistler Center for Carbohydrate Research, Purdue University, West Lafayette, IN, USA
| | | | - Ashootosh Tripathi
- Life Sciences Institute: Natural Products Discovery Core, University of Michigan, Ann Arbor, MI, USA
| | - Phillip B Pope
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway. .,Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway.
| | - Eric C Martens
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA.
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18
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Merrill BD, Carter MM, Olm MR, Dahan D, Tripathi S, Spencer SP, Yu B, Jain S, Neff N, Jha AR, Sonnenburg ED, Sonnenburg JL. Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Microbes.. [PMID: 36238714 PMCID: PMC9558438 DOI: 10.1101/2022.03.30.486478] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The gut microbiome is a key modulator of immune and metabolic health. Human microbiome data is biased towards industrialized populations, providing limited understanding of the distinct and diverse non-industrialized microbiomes. Here, we performed ultra-deep metagenomic sequencing and strain cultivation on 351 fecal samples from the Hadza, hunter-gatherers in Tanzania, and comparative populations in Nepal and California. We recover 94,971 total genomes of bacteria, archaea, bacteriophages, and eukaryotes, 43% of which are absent from existing unified datasets. Analysis of in situ growth rates, genetic pN/pS signatures, high-resolution strain tracking, and 124 gut-resident species vanishing in industrialized populations reveals differentiating dynamics of the Hadza gut microbiome. Industrialized gut microbes are enriched in genes associated with oxidative stress, possibly a result of microbiome adaptation to inflammatory processes. This unparalleled view of the Hadza gut microbiome provides a valuable resource that expands our understanding of microbes capable of colonizing the human gut and clarifies the extensive perturbation brought on by the industrialized lifestyle.
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19
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Pudlo NA, Pereira GV, Parnami J, Cid M, Markert S, Tingley JP, Unfried F, Ali A, Varghese NJ, Kim KS, Campbell A, Urs K, Xiao Y, Adams R, Martin D, Bolam DN, Becher D, Eloe-Fadrosh EA, Schmidt TM, Abbott DW, Schweder T, Hehemann JH, Martens EC. Diverse events have transferred genes for edible seaweed digestion from marine to human gut bacteria. Cell Host Microbe 2022; 30:314-328.e11. [PMID: 35240043 PMCID: PMC9096808 DOI: 10.1016/j.chom.2022.02.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 11/03/2021] [Accepted: 02/02/2022] [Indexed: 12/16/2022]
Abstract
Humans harbor numerous species of colonic bacteria that digest fiber polysaccharides in commonly consumed terrestrial plants. More recently in history, regional populations have consumed edible macroalgae seaweeds containing unique polysaccharides. It remains unclear how extensively gut bacteria have adapted to digest these nutrients. Here, we show that the ability of gut bacteria to digest seaweed polysaccharides is more pervasive than previously appreciated. Enrichment-cultured Bacteroides harbor previously discovered genes for seaweed degradation, which have mobilized into several members of this genus. Additionally, other examples of marine bacteria-derived genes, and their mobile DNA elements, are involved in gut microbial degradation of seaweed polysaccharides, including genes in gut-resident Firmicutes. Collectively, these results uncover multiple separate events that have mobilized the genes encoding seaweed-degrading-enzymes into gut bacteria. This work further underscores the metabolic plasticity of the human gut microbiome and global exchange of genes in the context of dietary selective pressures.
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Affiliation(s)
- Nicholas A Pudlo
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Jaagni Parnami
- Max Planck Institute for Marine Biology, Bremen, Germany
| | - Melissa Cid
- Max Planck Institute for Marine Biology, Bremen, Germany
| | - Stephanie Markert
- Pharmaceutical Biotechnology, University of Greifswald, 17487 Greifswald, Germany; Institute of Marine Biotechnology, 17489 Greifswald, Germany
| | - Jeffrey P Tingley
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB, Canada
| | - Frank Unfried
- Institute of Marine Biotechnology, 17489 Greifswald, Germany
| | - Ahmed Ali
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Kwi S Kim
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Austin Campbell
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Karthik Urs
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yao Xiao
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ryan Adams
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Duña Martin
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - David N Bolam
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
| | | | | | - Thomas M Schmidt
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - D Wade Abbott
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB, Canada
| | - Thomas Schweder
- Pharmaceutical Biotechnology, University of Greifswald, 17487 Greifswald, Germany; Institute of Marine Biotechnology, 17489 Greifswald, Germany
| | - Jan Hendrik Hehemann
- Max Planck Institute for Marine Biology, Bremen, Germany; University of Bremen, Center for Marine Environmental Sciences (MARUM), 28359 Bremen, Germany.
| | - Eric C Martens
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA.
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20
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Chelliah R, Banan-MwineDaliri E, Khan I, Wei S, Elahi F, Yeon SJ, Selvakumar V, Ofosu FK, Rubab M, Ju HH, Rallabandi HR, Madar IH, Sultan G, Oh DH. A review on the application of bioinformatics tools in food microbiome studies. Brief Bioinform 2022; 23:6533500. [PMID: 35189636 DOI: 10.1093/bib/bbac007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/20/2021] [Accepted: 01/05/2022] [Indexed: 12/12/2022] Open
Abstract
There is currently a transformed interest toward understanding the impact of fermentation on functional food development due to growing consumer interest on modified health benefits of sustainable foods. In this review, we attempt to summarize recent findings regarding the impact of Next-generation sequencing and other bioinformatics methods in the food microbiome and use prediction software to understand the critical role of microbes in producing fermented foods. Traditionally, fermentation methods and starter culture development were considered conventional methods needing optimization to eliminate errors in technique and were influenced by technical knowledge of fermentation. Recent advances in high-output omics innovations permit the implementation of additional logical tactics for developing fermentation methods. Further, the review describes the multiple functions of the predictions based on docking studies and the correlation of genomic and metabolomic analysis to develop trends to understand the potential food microbiome interactions and associated products to become a part of a healthy diet.
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Affiliation(s)
- Ramachandran Chelliah
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Gangwon-do 24341, Korea
| | - Eric Banan-MwineDaliri
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Gangwon-do 24341, Korea
| | - Imran Khan
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Gangwon-do 24341, Korea.,Department of Biotechnology, University of Malakand, Khyber Pakhtunkhwa Pakistan
| | - Shuai Wei
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Gangwon-do 24341, Korea.,Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, College of Food Science and Technology, Guangdong Ocean University, Zhanjiang 524088, China
| | - Fazle Elahi
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Gangwon-do 24341, Korea
| | - Su-Jung Yeon
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Gangwon-do 24341, Korea
| | - Vijayalakshmi Selvakumar
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Gangwon-do 24341, Korea
| | - Fred Kwame Ofosu
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Gangwon-do 24341, Korea
| | - Momna Rubab
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Gangwon-do 24341, Korea
| | - Hum Hun Ju
- Department of Biological Environment, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Gangwon-do 24341, Korea
| | - Harikrishna Reddy Rallabandi
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Gangwon-do 24341, Korea
| | - Inamul Hasan Madar
- Department of Biochemistry, School of Life Science, Bharathidasan, University, Thiruchirappalli, Tamilnadu, India
| | - Ghazala Sultan
- Department of Computer Science, Aligarh Muslim University, Aligarh, Uttar Pradesh, 202002, India
| | - Deog Hwan Oh
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Gangwon-do 24341, Korea
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21
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Human Gut Faecalibacterium prausnitzii Deploys a Highly Efficient Conserved System To Cross-Feed on β-Mannan-Derived Oligosaccharides. mBio 2021; 12:e0362820. [PMID: 34061597 PMCID: PMC8262883 DOI: 10.1128/mbio.03628-20] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
β-Mannans are hemicelluloses that are abundant in modern diets as components in seed endosperms and common additives in processed food. Currently, the collective understanding of β-mannan saccharification in the human colon is limited to a few keystone species, which presumably liberate low-molecular-weight mannooligosaccharide fragments that become directly available to the surrounding microbial community. Here, we show that a dominant butyrate producer in the human gut, Faecalibacterium prausnitzii, is able to acquire and degrade various β-mannooligosaccharides (β-MOS), which are derived by the primary mannanolytic activity of neighboring gut microbiota. Detailed biochemical analyses of selected protein components from their two β-MOS utilization loci (F. prausnitzii β-MOS utilization loci [FpMULs]) supported a concerted model whereby the imported β-MOS are stepwise disassembled intracellularly by highly adapted enzymes. Coculturing experiments of F. prausnitzii with the primary degraders Bacteroides ovatus and Roseburia intestinalis on polymeric β-mannan resulted in syntrophic growth, thus confirming the high efficiency of the FpMULs' uptake system. Genomic comparison with human F. prausnitzii strains and analyses of 2,441 public human metagenomes revealed that FpMULs are highly conserved and distributed worldwide. Together, our results provide a significant advance in the knowledge of β-mannan metabolism and the degree to which its degradation is mediated by cross-feeding interactions between prominent beneficial microbes in the human gut. IMPORTANCE Commensal butyrate-producing bacteria belonging to the Firmicutes phylum are abundant in the human gut and are crucial for maintaining health. Currently, insight is lacking into how they target otherwise indigestible dietary fibers and into the trophic interactions they establish with other glycan degraders in the competitive gut environment. By combining cultivation, genomic, and detailed biochemical analyses, this work reveals the mechanism enabling F. prausnitzii, as a model Ruminococcaceae within Firmicutes, to cross-feed and access β-mannan-derived oligosaccharides released in the gut ecosystem by the action of primary degraders. A comprehensive survey of human gut metagenomes shows that FpMULs are ubiquitous in human populations globally, highlighting the importance of microbial metabolism of β-mannans/β-MOS as a common dietary component. Our findings provide a mechanistic understanding of the β-MOS utilization capability by F. prausnitzii that may be exploited to select dietary formulations specifically boosting this beneficial symbiont, and thus butyrate production, in the gut.
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22
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Sudhakar P, Machiels K, Verstockt B, Korcsmaros T, Vermeire S. Computational Biology and Machine Learning Approaches to Understand Mechanistic Microbiome-Host Interactions. Front Microbiol 2021; 12:618856. [PMID: 34046017 PMCID: PMC8148342 DOI: 10.3389/fmicb.2021.618856] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 03/19/2021] [Indexed: 12/11/2022] Open
Abstract
The microbiome, by virtue of its interactions with the host, is implicated in various host functions including its influence on nutrition and homeostasis. Many chronic diseases such as diabetes, cancer, inflammatory bowel diseases are characterized by a disruption of microbial communities in at least one biological niche/organ system. Various molecular mechanisms between microbial and host components such as proteins, RNAs, metabolites have recently been identified, thus filling many gaps in our understanding of how the microbiome modulates host processes. Concurrently, high-throughput technologies have enabled the profiling of heterogeneous datasets capturing community level changes in the microbiome as well as the host responses. However, due to limitations in parallel sampling and analytical procedures, big gaps still exist in terms of how the microbiome mechanistically influences host functions at a system and community level. In the past decade, computational biology and machine learning methodologies have been developed with the aim of filling the existing gaps. Due to the agnostic nature of the tools, they have been applied in diverse disease contexts to analyze and infer the interactions between the microbiome and host molecular components. Some of these approaches allow the identification and analysis of affected downstream host processes. Most of the tools statistically or mechanistically integrate different types of -omic and meta -omic datasets followed by functional/biological interpretation. In this review, we provide an overview of the landscape of computational approaches for investigating mechanistic interactions between individual microbes/microbiome and the host and the opportunities for basic and clinical research. These could include but are not limited to the development of activity- and mechanism-based biomarkers, uncovering mechanisms for therapeutic interventions and generating integrated signatures to stratify patients.
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Affiliation(s)
- Padhmanand Sudhakar
- Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders (TARGID), KU Leuven, Leuven, Belgium
- Earlham Institute, Norwich, United Kingdom
- Quadram Institute Bioscience, Norwich, United Kingdom
| | - Kathleen Machiels
- Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders (TARGID), KU Leuven, Leuven, Belgium
| | - Bram Verstockt
- Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders (TARGID), KU Leuven, Leuven, Belgium
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Tamas Korcsmaros
- Earlham Institute, Norwich, United Kingdom
- Quadram Institute Bioscience, Norwich, United Kingdom
| | - Séverine Vermeire
- Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders (TARGID), KU Leuven, Leuven, Belgium
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, KU Leuven, Leuven, Belgium
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23
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Pfefferle PI, Keber CU, Cohen RM, Garn H. The Hygiene Hypothesis - Learning From but Not Living in the Past. Front Immunol 2021; 12:635935. [PMID: 33796103 PMCID: PMC8007786 DOI: 10.3389/fimmu.2021.635935] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/17/2021] [Indexed: 12/14/2022] Open
Abstract
Postulated by Strachan more than 30 years ago, the Hygiene Hypothesis has undergone many revisions and adaptations. This review journeys back to the beginnings of the Hygiene Hypothesis and describes the most important landmarks in its development considering the many aspects that have refined and generalized the Hygiene Hypothesis over time. From an epidemiological perspective, the Hygiene Hypothesis advanced to a comprehensive concept expanding beyond the initial focus on allergies. The Hygiene Hypothesis comprise immunological, microbiological and evolutionary aspects. Thus, the original postulate developed into a holistic model that explains the impact of post-modern life-style on humans, who initially evolved in close proximity to a more natural environment. Focusing on diet and the microbiome as the most prominent exogenous influences we describe these discrepancies and the resulting health outcomes and point to potential solutions to reestablish the immunological homeostasis that frequently have been lost in people living in developed societies.
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Affiliation(s)
- Petra I Pfefferle
- Comprehensive Biobank Marburg, Medical Faculty, Philipps University of Marburg, Comprehensive Biobank Marburg, Marburg, Germany.,German Center for Lung Research (DZL), Marburg, Germany.,German Biobank Alliance, Marburg, Germany
| | - Corinna U Keber
- Comprehensive Biobank Marburg, Medical Faculty, Philipps University of Marburg, Comprehensive Biobank Marburg, Marburg, Germany.,German Biobank Alliance, Marburg, Germany.,Institute for Pathology, Medical Faculty, Institute for Pathology, Philipps University of Marburg, Marburg, Germany
| | - Robert M Cohen
- Comprehensive Biobank Marburg, Medical Faculty, Philipps University of Marburg, Comprehensive Biobank Marburg, Marburg, Germany
| | - Holger Garn
- German Center for Lung Research (DZL), Marburg, Germany.,Translational Inflammation Research Division & Core Facility for Single Cell Multiomics, Medical Faculty, Biochemical Pharmacological Center, Philipps University of Marburg, Marburg, Germany
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24
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Ngowi EE, Wang YZ, Khattak S, Khan NH, Mahmoud SSM, Helmy YASH, Jiang QY, Li T, Duan SF, Ji XY, Wu DD. Impact of the factors shaping gut microbiota on obesity. J Appl Microbiol 2021; 131:2131-2147. [PMID: 33570819 DOI: 10.1111/jam.15036] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 02/01/2021] [Accepted: 02/08/2021] [Indexed: 12/12/2022]
Abstract
Obesity is considered as a risk factor for chronic health diseases such as heart diseases, cancer and diabetes 2. Reduced physical activities, lifestyle, poor nutritional diet and genetics are among the risk factors associated with the development of obesity. In recent years, several studies have explored the link between the gut microbiome and the progression of diseases including obesity, with the shift in microbiome abundance and composition being the main focus. The alteration of gut microbiome composition affects both nutrients metabolism and specific gene expressions, thereby disturbing body physiology. Specifically, the abundance of fibre-metabolizing microbes is associated with weight loss and that of protein and fat-metabolizing bacteria with weight gain. Various internal and external factors such as genetics, maternal obesity, mode of delivery, breastfeeding, nutrition, antibiotic use and the chemical compounds present in the environment are known to interfere with the richness of the gut microbiota (GM), thus influencing weight gain/loss and ultimately the development of obesity. However, the effectiveness of each factor in potentiating the shift in microbes' abundance to result in significant changes that can lead to obesity is not yet clear. In this review, we will highlight the factors involved in shaping GM, their influence on obesity and possible interventions. Understanding the influence of these factors on the diversity of the GM and how to improve their effectiveness on disease conditions could be keys in the treatment of metabolic diseases.
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Affiliation(s)
- Ebenezeri Erasto Ngowi
- Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, Henan, China.,Kaifeng Municipal Key Laboratory of Cell Signal Transduction, Henan Provincial Engineering Centre for Tumor Molecular Medicine, Henan University, Kaifeng, Henan, China.,Department of Biological Sciences, Faculty of Science, Dares Salaam University College of Education, Dares Salaam, Tanzania
| | - Yi-Zhen Wang
- Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, Henan, China.,Kaifeng Municipal Key Laboratory of Cell Signal Transduction, Henan Provincial Engineering Centre for Tumor Molecular Medicine, Henan University, Kaifeng, Henan, China
| | - Saadullah Khattak
- Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, Henan, China.,Kaifeng Municipal Key Laboratory of Cell Signal Transduction, Henan Provincial Engineering Centre for Tumor Molecular Medicine, Henan University, Kaifeng, Henan, China
| | - Nazeer Hussain Khan
- Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, Henan, China.,Kaifeng Municipal Key Laboratory of Cell Signal Transduction, Henan Provincial Engineering Centre for Tumor Molecular Medicine, Henan University, Kaifeng, Henan, China
| | - Salma Sayed Mohamed Mahmoud
- Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, Henan, China.,Kaifeng Municipal Key Laboratory of Cell Signal Transduction, Henan Provincial Engineering Centre for Tumor Molecular Medicine, Henan University, Kaifeng, Henan, China
| | - Yasmeen Ahmed Saleheldin Hassan Helmy
- Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, Henan, China.,Kaifeng Municipal Key Laboratory of Cell Signal Transduction, Henan Provincial Engineering Centre for Tumor Molecular Medicine, Henan University, Kaifeng, Henan, China
| | - Qi-Ying Jiang
- Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, Henan, China.,Kaifeng Municipal Key Laboratory of Cell Signal Transduction, Henan Provincial Engineering Centre for Tumor Molecular Medicine, Henan University, Kaifeng, Henan, China
| | - Tao Li
- Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, Henan, China.,Kaifeng Municipal Key Laboratory of Cell Signal Transduction, Henan Provincial Engineering Centre for Tumor Molecular Medicine, Henan University, Kaifeng, Henan, China
| | - Shao-Feng Duan
- Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, Henan, China.,Institute for Innovative Drug Design and Evaluation, School of Pharmacy, Henan University, Kaifeng, Henan, China
| | - Xin-Ying Ji
- Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, Henan, China.,Kaifeng Key Laboratory of Infection and Biological Safety, School of Basic Medical Sciences, Henan University, Kaifeng, Henan, China
| | - Dong-Dong Wu
- Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, Henan, China.,School of Stomatology, Henan University, Kaifeng, Henan, China
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25
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Abstract
BACKGROUND The gut microbiome has been increasingly acknowledged as playing a pivotal role in human health. Therefore, a number of studies have focused on variables that impact its microbial structure and consequent functionality. A wide range of factors, such as diet, age, sex, life stage, behavior, ethnicity, and diseases have been considered, and strong links were set out. However, some aspects regarding the microbiome determinants are still under-explored. DISCUSSION Recently, Bosman et al. presented evidence that skin exposure to narrowband UVB light modulated the gut microbiome of a specific human cohort. This cohort presented an increase of biodiversity, Firmicutes and Proteobacteria, and a decrease of Bacteroidetes. Based on these findings, we revisited our data on a hunter-gatherer gut microbiome (Yanomami) and identified similarities in the gut microbiome of these two cohorts. Both presented a high abundance of Proteobacteria, which had been observed as a unique feature in the Yanomami gut microbiome, and based on Bosman et al study, could be associated with their natural sunlight exposure. CONCLUSION In this commentary, we would like to point out that the human lifestyle concerning sunlight exposure should be considered as one force modulating the gut microbiome, highlighting, as proposed by Bosman et al, a novel skin-gut axis which is associated with health and disease.
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Affiliation(s)
- Liliane Costa Conteville
- Laboratory of Molecular Genetics of Microorganisms, Oswaldo Cruz Institute, Rio De Janeiro, Brazil,CONTACT Liliane Costa Conteville Laboratory of Molecular Genetics of Microorganisms, Oswaldo Cruz Institute, Avenida Brasil 4365, Manguinhos, Rio De Janeiro 21040-360, Brazil
| | - Ana Carolina P Vicente
- Laboratory of Molecular Genetics of Microorganisms, Oswaldo Cruz Institute, Rio De Janeiro, Brazil
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26
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Déjean G, Tamura K, Cabrera A, Jain N, Pudlo NA, Pereira G, Viborg AH, Van Petegem F, Martens EC, Brumer H. Synergy between Cell Surface Glycosidases and Glycan-Binding Proteins Dictates the Utilization of Specific Beta(1,3)-Glucans by Human Gut Bacteroides. mBio 2020; 11:e00095-20. [PMID: 32265336 PMCID: PMC7157763 DOI: 10.1128/mbio.00095-20] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 03/09/2020] [Indexed: 01/06/2023] Open
Abstract
The human gut microbiota (HGM) has far-reaching impacts on human health and nutrition, which are fueled primarily by the metabolism of otherwise indigestible complex carbohydrates commonly known as dietary fiber. However, the molecular basis of the ability of individual taxa of the HGM to address specific dietary glycan structures remains largely unclear. In particular, the utilization of β(1,3)-glucans, which are widespread in the human diet as yeast, seaweed, and plant cell walls, had not previously been resolved. Through a systems-based approach, here we show that the symbiont Bacteroides uniformis deploys a single, exemplar polysaccharide utilization locus (PUL) to access yeast β(1,3)-glucan, brown seaweed β(1,3)-glucan (laminarin), and cereal mixed-linkage β(1,3)/β(1,4)-glucan. Combined biochemical, enzymatic, and structural analysis of PUL-encoded glycoside hydrolases (GHs) and surface glycan-binding proteins (SGBPs) illuminates a concerted molecular system by which B. uniformis recognizes and saccharifies these distinct β-glucans. Strikingly, the functional characterization of homologous β(1,3)-glucan utilization loci (1,3GUL) in other Bacteroides further demonstrated that the ability of individual taxa to utilize β(1,3)-glucan variants and/or β(1,3)/β(1,4)-glucans arises combinatorially from the individual specificities of SGBPs and GHs at the cell surface, which feed corresponding signals to periplasmic hybrid two-component sensors (HTCSs) via TonB-dependent transporters (TBDTs). These data reveal the importance of cooperativity in the adaptive evolution of GH and SGBP cohorts to address individual polysaccharide structures. We anticipate that this fine-grained knowledge of PUL function will inform metabolic network analysis and proactive manipulation of the HGM. Indeed, a survey of 2,441 public human metagenomes revealed the international, yet individual-specific, distribution of each 1,3GUL.IMPORTANCEBacteroidetes are a dominant phylum of the human gut microbiota (HGM) that target otherwise indigestible dietary fiber with an arsenal of polysaccharide utilization loci (PULs), each of which is dedicated to the utilization of a specific complex carbohydrate. Here, we provide novel insight into this paradigm through functional characterization of homologous PULs from three autochthonous Bacteroides species, which target the family of dietary β(1,3)-glucans. Through detailed biochemical and protein structural analysis, we observed an unexpected diversity in the substrate specificity of PUL glycosidases and glycan-binding proteins with regard to β(1,3)-glucan linkage and branching patterns. In combination, these individual enzyme and protein specificities support taxon-specific growth on individual β(1,3)-glucans. This detailed metabolic insight, together with a comprehensive survey of individual 1,3GULs across human populations, further expands the fundamental roadmap of the HGM, with potential application to the future development of microbial intervention therapies.
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Affiliation(s)
- Guillaume Déjean
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kazune Tamura
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Adriana Cabrera
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Namrata Jain
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nicholas A Pudlo
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Gabriel Pereira
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Alexander Holm Viborg
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Filip Van Petegem
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Eric C Martens
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
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