1
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Lu S, Zhao Q, Guan Y, Sun Z, Li W, Guo S, Zhang A. The communication mechanism of the gut-brain axis and its effect on central nervous system diseases: A systematic review. Biomed Pharmacother 2024; 178:117207. [PMID: 39067168 DOI: 10.1016/j.biopha.2024.117207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 07/15/2024] [Accepted: 07/23/2024] [Indexed: 07/30/2024] Open
Abstract
Gut microbiota is involved in intricate and active metabolic processes the host's brain function, especially its role in immune responses, secondary metabolism, and symbiotic connections with the host. Gut microbiota can promote the production of essential metabolites, neurotransmitters, and other neuroactive chemicals that affect the development and treatment of central nervous system diseases. This article introduces the relevant pathways and manners of the communication between the brain and gut, summarizes a comprehensive overview of the current research status of key gut microbiota metabolites that affect the functions of the nervous system, revealing those adverse factors that affect typical communication between the brain-gut axis, and outlining the efforts made by researchers to alleviate these neurological diseases through targeted microbial interventions. The relevant pathways and manners of communication between the brain and gut contribute to the experimental design of new treatment plans and drug development. The factors that may cause changes in gut microbiota and affect metabolites, as well as current intervention methods are summarized, which helps improve gut microbiota brain dialogue, prevent adverse triggering factors from interfering with the gut microbiota system, and minimize neuropathological changes.
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Affiliation(s)
- Shengwen Lu
- Department of Pharmaceutical Analysis, GAP Center, Heilongjiang University of Chinese Medicine, Heping Road 24, Harbin 150040, China
| | - Qiqi Zhao
- Department of Pharmaceutical Analysis, GAP Center, Heilongjiang University of Chinese Medicine, Heping Road 24, Harbin 150040, China
| | - Yu Guan
- Department of Pharmaceutical Analysis, GAP Center, Heilongjiang University of Chinese Medicine, Heping Road 24, Harbin 150040, China
| | - Zhiwen Sun
- Department of Gastroenterology, The First Affiliated Hospital of Heilongjiang University of Chinese Medicine, Heping Road 24, Harbin 150040, China
| | - Wenhao Li
- School of Basic Medical Science of Heilongjiang University of Chinese Medicine, Heping Road 24, Harbin 150040, China
| | - Sifan Guo
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan Medical University, Xueyuan Road 3, Haikou 571199, China
| | - Aihua Zhang
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan Medical University, Xueyuan Road 3, Haikou 571199, China; Graduate School, Heilongjiang University of Chinese Medicine, Harbin 150040, China; INTI International University, Nilai 71800, Malaysia.
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2
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Arzamasov AA, Rodionov DA, Hibberd MC, Guruge JL, Kazanov MD, Leyn SA, Kent JE, Sejane K, Bode L, Barratt MJ, Gordon JI, Osterman AL. Integrative genomic reconstruction of carbohydrate utilization networks in bifidobacteria: global trends, local variability, and dietary adaptation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.06.602360. [PMID: 39005317 PMCID: PMC11245093 DOI: 10.1101/2024.07.06.602360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Bifidobacteria are among the earliest colonizers of the human gut, conferring numerous health benefits. While multiple Bifidobacterium strains are used as probiotics, accumulating evidence suggests that the individual responses to probiotic supplementation may vary, likely due to a variety of factors, including strain type(s), gut community composition, dietary habits of the consumer, and other health/lifestyle conditions. Given the saccharolytic nature of bifidobacteria, the carbohydrate composition of the diet is one of the primary factors dictating the colonization efficiency of Bifidobacterium strains. Therefore, a comprehensive understanding of bifidobacterial glycan metabolism at the strain level is necessary to rationally design probiotic or synbiotic formulations that combine bacterial strains with glycans that match their nutrient preferences. In this study, we systematically reconstructed 66 pathways involved in the utilization of mono-, di-, oligo-, and polysaccharides by analyzing the representation of 565 curated metabolic functional roles (catabolic enzymes, transporters, transcriptional regulators) in 2973 non-redundant cultured Bifidobacterium isolates and metagenome-assembled genomes (MAGs). Our analysis uncovered substantial heterogeneity in the predicted glycan utilization capabilities at the species and strain level and revealed the presence of a yet undescribed phenotypically distinct subspecies-level clade within the Bifidobacterium longum species. We also identified Bangladeshi isolates harboring unique gene clusters tentatively implicated in the breakdown of xyloglucan and human milk oligosaccharides. Predicted carbohydrate utilization phenotypes were experimentally characterized and validated. Our large-scale genomic analysis considerably expands the knowledge of carbohydrate metabolism in bifidobacteria and provides a foundation for rationally designing single- or multi-strain probiotic formulations of a given bifidobacterial species as well as synbiotic combinations of bifidobacterial strains matched with their preferred carbohydrate substrates.
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Affiliation(s)
- Aleksandr A Arzamasov
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Dmitry A Rodionov
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Matthew C Hibberd
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Janaki L Guruge
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Marat D Kazanov
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey, 34956
| | - Semen A Leyn
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Rd, La Jolla, CA 92037, USA
| | - James E Kent
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Kristija Sejane
- Department of Pediatrics, Larsson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence (MOMI CORE), and the Human Milk Institute (HMI), University of California San Diego, La Jolla, CA 92093, USA
| | - Lars Bode
- Department of Pediatrics, Larsson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence (MOMI CORE), and the Human Milk Institute (HMI), University of California San Diego, La Jolla, CA 92093, USA
| | - Michael J Barratt
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jeffrey I Gordon
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Andrei L Osterman
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Rd, La Jolla, CA 92037, USA
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3
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Oliveira-Filho ER, Rodionov DA, Hanson AD. Comparative Genomic and Genetic Evidence on a Role for the OarX Protein in Thiamin Salvage. ACS OMEGA 2024; 9:28888-28894. [PMID: 38973919 PMCID: PMC11223231 DOI: 10.1021/acsomega.4c03514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 05/30/2024] [Accepted: 06/10/2024] [Indexed: 07/09/2024]
Abstract
Salvage pathways for thiamin and its thiazole and pyrimidine moieties are poorly characterized compared to synthesis pathways. A candidate salvage gene is oarX, which encodes a short-chain dehydrogenase/reductase. In diverse bacteria, oarX clusters on the chromosome with genes of thiamin synthesis, salvage, or transport and is preceded by a thiamin pyrophosphate riboswitch. Thiamin and its moieties can undergo oxidations that convert a side-chain hydroxymethyl group to a carboxyl group, or the thiazole ring to a thiazolone, causing a loss of biological activity. To test if OarX participates in salvage of the carboxyl or thiazolone products, we used a genetic approach in Corynebacterium glutamicum ATCC 14067, which is auxotrophic for thiamin's pyrimidine moiety. This strain could not utilize the pyrimidine carboxyl derivative. This excluded a role in salvaging this product and narrowed the function search to metabolism of the carboxyl or thiazolone derivatives of thiamin or its thiazole moiety. However, a ΔthiG (thiazole auxotroph) strain was not rescued by any of these derivatives. Nor did deleting oarX affect rescue by the physiological pyrimidine and thiazole precursors of thiamin. These findings reinforce the genomic evidence that OarX has a function in thiamin metabolism and rule out five logical possibilities for what this function is.
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Affiliation(s)
- Edmar R. Oliveira-Filho
- Horticultural
Sciences Department, University of Florida, Gainesville, Florida 32611, United States
| | - Dmitry A. Rodionov
- Infectious
and Inflammatory Diseases Center, Sanford
Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
| | - Andrew D. Hanson
- Horticultural
Sciences Department, University of Florida, Gainesville, Florida 32611, United States
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4
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Hallberg ZF, Nicolas AM, Alvarez-Aponte ZI, Mok KC, Sieradzki ET, Pett-Ridge J, Banfield JF, Carlson HK, Firestone MK, Taga ME. Soil microbial community response to corrinoids is shaped by a natural reservoir of vitamin B 12. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.12.580003. [PMID: 38405713 PMCID: PMC10888822 DOI: 10.1101/2024.02.12.580003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Soil microbial communities perform critical ecosystem services through the collective metabolic activities of numerous individual organisms. Most microbes use corrinoids, a structurally diverse family of cofactors related to vitamin B12. Corrinoid structure influences the growth of individual microbes, yet how these growth responses scale to the community level remains unknown. Analysis of metagenome-assembled genomes suggests corrinoids are supplied to the community by members of the archaeal and bacterial phyla Thermoproteota, Actinobacteria, and Proteobacteria. Corrinoids were found largely adhered to the soil matrix in a grassland soil, at levels exceeding those required by cultured bacteria. Enrichment cultures and soil microcosms seeded with different corrinoids showed distinct shifts in bacterial community composition, supporting the hypothesis that corrinoid structure can shape communities. Environmental context influenced both community and taxon-specific responses to specific corrinoids. These results implicate corrinoids as key determinants of soil microbiome structure and suggest that environmental micronutrient reservoirs promote community stability.
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Affiliation(s)
- Zachary F. Hallberg
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, 94720 USA
| | - Alexa M. Nicolas
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, 94720 USA
| | - Zoila I. Alvarez-Aponte
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, 94720 USA
| | - Kenny C. Mok
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, 94720 USA
| | - Ella T. Sieradzki
- Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA, 94720 USA
| | - Jennifer Pett-Ridge
- Lawrence Livermore National Laboratory, Livermore, CA, 94550 USA
- Innovative Genomics Institute, Berkeley, CA, 94720 USA
| | - Jillian F. Banfield
- Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA, 94720 USA
- Innovative Genomics Institute, Berkeley, CA, 94720 USA
- Lawrence Berkeley National Laboratory, Berkeley, CA, 94720 USA
- Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, 94720 USA
| | - Hans K. Carlson
- Lawrence Berkeley National Laboratory, Berkeley, CA, 94720 USA
| | - Mary K. Firestone
- Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA, 94720 USA
- Lawrence Berkeley National Laboratory, Berkeley, CA, 94720 USA
| | - Michiko E. Taga
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, 94720 USA
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5
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Simonenko SY, Bogdanova DA, Kuldyushev NA. Emerging Roles of Vitamin B 12 in Aging and Inflammation. Int J Mol Sci 2024; 25:5044. [PMID: 38732262 PMCID: PMC11084641 DOI: 10.3390/ijms25095044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 04/28/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024] Open
Abstract
Vitamin B12 (cobalamin) is an essential nutrient for humans and animals. Metabolically active forms of B12-methylcobalamin and 5-deoxyadenosylcobalamin are cofactors for the enzymes methionine synthase and mitochondrial methylmalonyl-CoA mutase. Malfunction of these enzymes due to a scarcity of vitamin B12 leads to disturbance of one-carbon metabolism and impaired mitochondrial function. A significant fraction of the population (up to 20%) is deficient in vitamin B12, with a higher rate of deficiency among elderly people. B12 deficiency is associated with numerous hallmarks of aging at the cellular and organismal levels. Cellular senescence is characterized by high levels of DNA damage by metabolic abnormalities, increased mitochondrial dysfunction, and disturbance of epigenetic regulation. B12 deficiency could be responsible for or play a crucial part in these disorders. In this review, we focus on a comprehensive analysis of molecular mechanisms through which vitamin B12 influences aging. We review new data about how deficiency in vitamin B12 may accelerate cellular aging. Despite indications that vitamin B12 has an important role in health and healthy aging, knowledge of the influence of vitamin B12 on aging is still limited and requires further research.
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Affiliation(s)
- Sergey Yu. Simonenko
- Research Center for Translational Medicine, Sirius University of Science and Technology, 354340 Sochi, Russia;
| | - Daria A. Bogdanova
- Division of Immunobiology and Biomedicine, Center for Genetics and Life Sciences, Sirius University of Science and Technology, 354340 Sochi, Russia
| | - Nikita A. Kuldyushev
- Research Center for Translational Medicine, Sirius University of Science and Technology, 354340 Sochi, Russia;
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6
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Swaney MH, Henriquez N, Campbell T, Handelsman J, Kalan LR. Skin-associated Corynebacterium amycolatum shares cobamides. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.28.591522. [PMID: 38712214 PMCID: PMC11071462 DOI: 10.1101/2024.04.28.591522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
The underlying interactions that occur to maintain skin microbiome composition, function, and overall skin health are largely unknown. Often, these types of interactions are mediated by microbial metabolites. Cobamides, the vitamin B12 family of cofactors, are essential for metabolism in many bacteria, but are only synthesized by a small fraction of prokaryotes, including certain skin-associated species. Therefore, we hypothesize that cobamide sharing mediates skin community dynamics. Preliminary work predicts that several skin-associated Corynebacterium species encode de novo cobamide biosynthesis and that their abundance is associated with skin microbiome diversity. Here, we show that commensal Corynebacterium amycolatum produces cobamides and that this synthesis can be tuned by cobalt limitation. To demonstrate cobamide sharing by C. amycolatum, we employed a co-culture assay using an E. coli cobamide auxotroph and show that C. amycolatum produces sufficient cobamides to support E. coli growth, both in liquid co-culture and when separated spatially on solid medium. We also generated a C. amycolatum non-cobamide-producing strain (cob-) using UV mutagenesis that contains mutated cobamide biosynthesis genes cobK and cobO and confirm that disruption of cobamide biosynthesis abolishes support of E. coli growth through cobamide sharing. Our study provides a unique model to study metabolite sharing by microorganisms, which will be critical for understanding the fundamental interactions that occur within complex microbiomes and for developing approaches to target the human microbiota for health advances.
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Affiliation(s)
- M H Swaney
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA
- Microbiology Doctoral Training Program, University of Wisconsin, Madison, WI, USA
| | - N Henriquez
- Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON, CAN
| | - T Campbell
- Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON, CAN
| | - J Handelsman
- Wisconsin Institute for Discovery, Madison, WI, USA
- Department of Plant Pathology, University of Wisconsin, Madison, WI, USA
| | - L R Kalan
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA
- Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON, CAN
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, CAN
- David Braley Centre for Antibiotic Discovery, Hamilton, ON, CAN
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7
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Quaiyum S, Yuan Y, Kuipers PJ, Martinelli M, Jaroch M, de Crécy-Lagard V. Deciphering the Diversity in Bacterial Transporters That Salvage Queuosine Precursors. EPIGENOMES 2024; 8:16. [PMID: 38804365 PMCID: PMC11130926 DOI: 10.3390/epigenomes8020016] [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: 03/05/2024] [Revised: 04/04/2024] [Accepted: 04/18/2024] [Indexed: 05/29/2024] Open
Abstract
Queuosine (Q) is a modification of the wobble base of tRNA harboring GUN anticodons with roles in decoding accuracy and efficiency. Its synthesis is complex with multiple enzymatic steps, and several pathway intermediates can be salvaged. The only two transporter families known to salvage Q precursors are QPTR/COG1738 and QrtT/QueT. Analyses of the distribution of known Q synthesis and salvage genes in human gut and oral microbiota genomes have suggested that more transporter families remain to be found and that Q precursor exchanges must occur within the structured microenvironments of the mammalian host. Using physical clustering and fusion-based association with Q salvage genes, candidate genes for missing transporters were identified and five were tested experimentally by complementation assays in Escherichia coli. Three genes encoding transporters from three different Pfam families, a ureide permease (PF07168) from Acidobacteriota bacterium, a hemolysin III family protein (PF03006) from Bifidobacterium breve, and a Major Facilitator Superfamily protein (PF07690) from Bartonella henselae, were found to allow the transport of both preQ0 and preQ1 in this heterologous system. This work suggests that many transporter families can evolve to transport Q precursors, reinforcing the concept of transporter plasticity.
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Affiliation(s)
- Samia Quaiyum
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA; (S.Q.); (Y.Y.); (P.J.K.)
| | - Yifeng Yuan
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA; (S.Q.); (Y.Y.); (P.J.K.)
| | - Paul J. Kuipers
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA; (S.Q.); (Y.Y.); (P.J.K.)
| | - Maria Martinelli
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA; (S.Q.); (Y.Y.); (P.J.K.)
- eSTEAMed Learning Inc., Maitland, FL 32751, USA
| | - Marshall Jaroch
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA; (S.Q.); (Y.Y.); (P.J.K.)
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL 32610, USA
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA; (S.Q.); (Y.Y.); (P.J.K.)
- Genetic Institute, University of Florida, Gainesville, FL 32611, USA
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8
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Nguélé AT, Carrara C, Mozzicafreddo M, Chen H, Piersanti A, Salum SS, Ali SM, Miceli C. Association between Food or Nutrients and Gut Microbiota in Healthy and Helminth-Infected Women of Reproductive Age from Zanzibar, Tanzania. Nutrients 2024; 16:1266. [PMID: 38732513 PMCID: PMC11085056 DOI: 10.3390/nu16091266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 04/19/2024] [Accepted: 04/20/2024] [Indexed: 05/13/2024] Open
Abstract
Modulating the gut microbiota is recognised as one strategy for preventing and fighting diseases. While the significant impact of diet on the gut microbiota's composition and function has been extensively researched, there is a notable lack of studies on the interactions between diet, microbiota, and helminth infections. Here, we used a combination of self-reported food intake and a 16S rDNA sequencing approach to analyse the composition of the gut microbiota in women of reproductive age from the two main islands of the Zanzibar archipelago, where helminth infections are endemic. We also applied a Spearman correlation analysis to food/nutrients and gut microbiota. Our results reveal that, despite close ethnic and cultural ties, the participants' gut microbiota differs depending on their location. A nutrient intake analysis revealed deficiencies in minerals and vitamins, indicating an imbalanced diet. A correlation analysis identified bacterial taxa consistently correlated with specific food or nutrients in healthy women from both locations, and in two types of helminth infections. Escherichia/Shigella abundances, usually associated with Trichuris trichiura infection, consistently correlated with insufficient levels of vitamins B2 and B12. In conclusion, our findings suggest that the increased consumption of specific food like cassava and fish, as well as essential nutrients such as calcium, B vitamins, and vitamin A, may modulate the gut microbiota of populations residing in regions where helminth infections are endemic.
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Affiliation(s)
- Aristide Toussaint Nguélé
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032 Camerino, Italy; (A.T.N.); (C.C.); (H.C.); (A.P.)
| | - Chiara Carrara
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032 Camerino, Italy; (A.T.N.); (C.C.); (H.C.); (A.P.)
| | - Matteo Mozzicafreddo
- Department of Clinical and Molecular Sciences, Marche Polytechnic University, 60126 Ancona, Italy;
| | - Hongliang Chen
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032 Camerino, Italy; (A.T.N.); (C.C.); (H.C.); (A.P.)
- College of Veterinary Medicine, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun 130118, China
| | - Angela Piersanti
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032 Camerino, Italy; (A.T.N.); (C.C.); (H.C.); (A.P.)
| | - Salum Seif Salum
- School of Health and Medical Sciences, State University of Zanzibar, Zanzibar 146, Tanzania;
| | - Said M. Ali
- Public Health Laboratory Ivo de Carneri, Chake Chake 122, Tanzania;
| | - Cristina Miceli
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032 Camerino, Italy; (A.T.N.); (C.C.); (H.C.); (A.P.)
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9
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Chang HW, Lee EM, Wang Y, Zhou C, Pruss KM, Henrissat S, Chen RY, Kao C, Hibberd MC, Lynn HM, Webber DM, Crane M, Cheng J, Rodionov DA, Arzamasov AA, Castillo JJ, Couture G, Chen Y, Balcazo NP, Lebrilla CB, Terrapon N, Henrissat B, Ilkayeva O, Muehlbauer MJ, Newgard CB, Mostafa I, Das S, Mahfuz M, Osterman AL, Barratt MJ, Ahmed T, Gordon JI. Prevotella copri and microbiota members mediate the beneficial effects of a therapeutic food for malnutrition. Nat Microbiol 2024; 9:922-937. [PMID: 38503977 PMCID: PMC10994852 DOI: 10.1038/s41564-024-01628-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 01/31/2024] [Indexed: 03/21/2024]
Abstract
Microbiota-directed complementary food (MDCF) formulations have been designed to repair the gut communities of malnourished children. A randomized controlled trial demonstrated that one formulation, MDCF-2, improved weight gain in malnourished Bangladeshi children compared to a more calorically dense standard nutritional intervention. Metagenome-assembled genomes from study participants revealed a correlation between ponderal growth and expression of MDCF-2 glycan utilization pathways by Prevotella copri strains. To test this correlation, here we use gnotobiotic mice colonized with defined consortia of age- and ponderal growth-associated gut bacterial strains, with or without P. copri isolates closely matching the metagenome-assembled genomes. Combining gut metagenomics and metatranscriptomics with host single-nucleus RNA sequencing and gut metabolomic analyses, we identify a key role of P. copri in metabolizing MDCF-2 glycans and uncover its interactions with other microbes including Bifidobacterium infantis. P. copri-containing consortia mediated weight gain and modulated energy metabolism within intestinal epithelial cells. Our results reveal structure-function relationships between MDCF-2 and members of the gut microbiota of malnourished children with potential implications for future therapies.
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Affiliation(s)
- Hao-Wei Chang
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Evan M Lee
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Yi Wang
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Cyrus Zhou
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Kali M Pruss
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Suzanne Henrissat
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, Marseille, France
| | - Robert Y Chen
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Clara Kao
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Matthew C Hibberd
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Hannah M Lynn
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Daniel M Webber
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Marie Crane
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Jiye Cheng
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Dmitry A Rodionov
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Aleksandr A Arzamasov
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Juan J Castillo
- Department of Chemistry, University of California, Davis, CA, USA
| | - Garret Couture
- Department of Chemistry, University of California, Davis, CA, USA
| | - Ye Chen
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
- Department of Chemistry, University of California, Davis, CA, USA
| | - Nikita P Balcazo
- Department of Chemistry, University of California, Davis, CA, USA
| | | | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, Marseille, France
| | - Bernard Henrissat
- Department of Biotechnology and Biomedicine (DTU Bioengineering), Technical University of Denmark, Lyngby, Denmark
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Olga Ilkayeva
- Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC, USA
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Michael J Muehlbauer
- Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC, USA
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
| | - Christopher B Newgard
- Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC, USA
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, USA
| | - Ishita Mostafa
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Subhasish Das
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Mustafa Mahfuz
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Andrei L Osterman
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Michael J Barratt
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Tahmeed Ahmed
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Jeffrey I Gordon
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA.
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
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10
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de Crécy-Lagard V, Hutinet G, Cediel-Becerra JDD, Yuan Y, Zallot R, Chevrette MG, Ratnayake RMMN, Jaroch M, Quaiyum S, Bruner S. Biosynthesis and function of 7-deazaguanine derivatives in bacteria and phages. Microbiol Mol Biol Rev 2024; 88:e0019923. [PMID: 38421302 PMCID: PMC10966956 DOI: 10.1128/mmbr.00199-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024] Open
Abstract
SUMMARYDeazaguanine modifications play multifaceted roles in the molecular biology of DNA and tRNA, shaping diverse yet essential biological processes, including the nuanced fine-tuning of translation efficiency and the intricate modulation of codon-anticodon interactions. Beyond their roles in translation, deazaguanine modifications contribute to cellular stress resistance, self-nonself discrimination mechanisms, and host evasion defenses, directly modulating the adaptability of living organisms. Deazaguanine moieties extend beyond nucleic acid modifications, manifesting in the structural diversity of biologically active natural products. Their roles in fundamental cellular processes and their presence in biologically active natural products underscore their versatility and pivotal contributions to the intricate web of molecular interactions within living organisms. Here, we discuss the current understanding of the biosynthesis and multifaceted functions of deazaguanines, shedding light on their diverse and dynamic roles in the molecular landscape of life.
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Affiliation(s)
- Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
- University of Florida Genetics Institute, Gainesville, Florida, USA
| | - Geoffrey Hutinet
- Department of Biology, Haverford College, Haverford, Pennsylvania, USA
| | | | - Yifeng Yuan
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
| | - Rémi Zallot
- Department of Life Sciences, Manchester Metropolitan University, Manchester, United Kingdom
| | - Marc G. Chevrette
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
| | | | - Marshall Jaroch
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
| | - Samia Quaiyum
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
| | - Steven Bruner
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
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11
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Song P, Jiang F, Liu D, Cai Z, Gao H, Gu H, Zhang J, Li B, Xu B, Zhang T. Gut microbiota non-convergence and adaptations in sympatric Tibetan and Przewalski's gazelles. iScience 2024; 27:109117. [PMID: 38384851 PMCID: PMC10879710 DOI: 10.1016/j.isci.2024.109117] [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: 09/06/2023] [Revised: 11/17/2023] [Accepted: 01/31/2024] [Indexed: 02/23/2024] Open
Abstract
Unraveling the connection between gut microbiota and adaptability in wild species in natural habitats is imperative yet challenging. We studied the gut microbiota of sympatric and allopatric populations of two closely related species, the Procapra picticaudata and P. przewalskii, with the latter showing lower adaptability and adaptive potential than the former. Despite shared habitat, sympatric populations showed no convergence in gut microbiota, revealing distinct microbiota-environment relationships between the two gazelle species. Furthermore, the gut microbiota assembly process of the P. przewalskii was shifted toward homogeneous selection processes relative to that of the P. picticaudata. Those taxa which contributed to the shift were mainly from the phyla Firmicutes and Verrucomicrobiota, with functions highly related to micronutrient and macronutrient metabolism. Our study provides new insights into the complex dynamics between gut microbiota, host adaptability, and environment in wildlife adaptation and highlights the need to consider host adaptability when examining wildlife host-microbiome interplay.
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Affiliation(s)
- Pengfei Song
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, Qinghai 810008, China
| | - Feng Jiang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810008, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, Qinghai 810008, China
| | - Daoxin Liu
- Qinghai University, Xining, Qinghai 810016, China
| | - Zhenyuan Cai
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810008, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, Qinghai 810008, China
| | - Hongmei Gao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810008, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, Qinghai 810008, China
| | - Haifeng Gu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810008, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, Qinghai 810008, China
| | - Jingjie Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, Qinghai 810008, China
| | - Bin Li
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, Qinghai 810008, China
| | - Bo Xu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, Qinghai 810008, China
| | - Tongzuo Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810008, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, Qinghai 810008, China
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12
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Law SR, Mathes F, Paten AM, Alexandre PA, Regmi R, Reid C, Safarchi A, Shaktivesh S, Wang Y, Wilson A, Rice SA, Gupta VVSR. Life at the borderlands: microbiomes of interfaces critical to One Health. FEMS Microbiol Rev 2024; 48:fuae008. [PMID: 38425054 PMCID: PMC10977922 DOI: 10.1093/femsre/fuae008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 02/12/2024] [Accepted: 02/27/2024] [Indexed: 03/02/2024] Open
Abstract
Microbiomes are foundational components of the environment that provide essential services relating to food security, carbon sequestration, human health, and the overall well-being of ecosystems. Microbiota exert their effects primarily through complex interactions at interfaces with their plant, animal, and human hosts, as well as within the soil environment. This review aims to explore the ecological, evolutionary, and molecular processes governing the establishment and function of microbiome-host relationships, specifically at interfaces critical to One Health-a transdisciplinary framework that recognizes that the health outcomes of people, animals, plants, and the environment are tightly interconnected. Within the context of One Health, the core principles underpinning microbiome assembly will be discussed in detail, including biofilm formation, microbial recruitment strategies, mechanisms of microbial attachment, community succession, and the effect these processes have on host function and health. Finally, this review will catalogue recent advances in microbiology and microbial ecology methods that can be used to profile microbial interfaces, with particular attention to multi-omic, advanced imaging, and modelling approaches. These technologies are essential for delineating the general and specific principles governing microbiome assembly and functions, mapping microbial interconnectivity across varying spatial and temporal scales, and for the establishment of predictive frameworks that will guide the development of targeted microbiome-interventions to deliver One Health outcomes.
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Affiliation(s)
- Simon R Law
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia
| | - Falko Mathes
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Environment, Floreat, WA 6014, Australia
| | - Amy M Paten
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Environment, Canberra, ACT 2601, Australia
| | - Pamela A Alexandre
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Agriculture and Food, St Lucia, Qld 4072, Australia
| | - Roshan Regmi
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Agriculture and Food, Urrbrae, SA 5064, Australia
| | - Cameron Reid
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Environment, Urrbrae, SA 5064, Australia
| | - Azadeh Safarchi
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Health and Biosecurity, Westmead, NSW 2145, Australia
| | - Shaktivesh Shaktivesh
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Data 61, Clayton, Vic 3168, Australia
| | - Yanan Wang
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Health and Biosecurity, Adelaide SA 5000, Australia
| | - Annaleise Wilson
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Health and Biosecurity, Geelong, Vic 3220, Australia
| | - Scott A Rice
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Agriculture, and Food, Westmead, NSW 2145, Australia
| | - Vadakattu V S R Gupta
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Agriculture and Food, Urrbrae, SA 5064, Australia
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13
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Kundra P, Greppi A, Duppenthaler M, Plüss S, Pugin B, Lacroix C, Geirnaert A. Vitamin B12 analogues from gut microbes and diet differentially impact commensal propionate producers of the human gut. Front Nutr 2024; 11:1360199. [PMID: 38389799 PMCID: PMC10881866 DOI: 10.3389/fnut.2024.1360199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 01/29/2024] [Indexed: 02/24/2024] Open
Abstract
To produce the health-associated metabolite propionate, gut microbes require vitamin B12 as a cofactor to convert succinate to propionate. B12 is sourced in the human gut from the unabsorbed dietary fraction and in situ microbial production. However, experimental data for B12 production by gut microbes is scarce, especially on their produced B12-analogues. Further, the promotion of propionate production by microbially-produced and dietary B12 is not yet fully understood. Here, we demonstrated B12 production in 6 out of 8 in silico predicted B12-producing bacteria from the human gut. Next, we showed in vitro that B12 produced by Blautia hydrogenotrophica, Marvinbryantia formatexigens, and Blautia producta promoted succinate to propionate conversion of two prevalent B12-auxotrophic gut bacteria, Akkermansia muciniphila and Bacteroides thetaiotaomicron. Finally, we examined the propiogenic effect of commercially available B12-analogues present in the human diet (cyano-B12, adenosyl-B12 and hydroxy-B12) at two doses. The low dose resulted in partial conversion of succinate to propionate for A. muciniphila when grown with adenosyl-B12 (14.6 ± 2.4 mM succinate and 18.7 ± 0.6 mM propionate) and hydroxy-B12 (13.0 ± 1.1 mM and 21.9 ± 1.2 mM), in comparison to cyano-B12 (0.7 ± 0.1 mM and 34.1 ± 0.1 mM). Higher doses of adenosyl-B12 and hydroxy-B12 resulted in significantly more conversion of succinate to propionate in both propionate-producing species, compared to the low dose. B12 analogues have different potential to impact the propionate metabolism of prevalent propionate producers in the gut. These results could contribute to strategies for managing gut disorders associated with decreased propionate production.
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Affiliation(s)
- Palni Kundra
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, Zurich, Switzerland
| | - Anna Greppi
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, Zurich, Switzerland
| | - Monica Duppenthaler
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, Zurich, Switzerland
| | - Serafina Plüss
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, Zurich, Switzerland
| | - Benoit Pugin
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, Zurich, Switzerland
| | - Christophe Lacroix
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, Zurich, Switzerland
| | - Annelies Geirnaert
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, Zurich, Switzerland
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14
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Bedani R, Cucick ACC, Albuquerque MACD, LeBlanc JG, Saad SMI. B-Group Vitamins as Potential Prebiotic Candidates: Their Effects on the Human Gut Microbiome. J Nutr 2024; 154:341-353. [PMID: 38176457 DOI: 10.1016/j.tjnut.2023.12.038] [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: 05/16/2023] [Revised: 12/18/2023] [Accepted: 12/22/2023] [Indexed: 01/06/2024] Open
Abstract
In recent years, thousands of studies have demonstrated the importance of the gut microbiome for human health and its relationship with certain diseases. The search for new gut microbiome modulators has thus become an objective to beneficially alter the gut microbiome composition and/or metabolic activity, which may modify intestinal physiology. Growing evidence has shown that B-group vitamins might be considered as potential candidates as gut microbiome modulators. However, the relationship between the B-group vitamins and the gut microbiome remains largely unexplored. Studies have suggested that non-absorbed B-group vitamins administered orally can reach the distal intestine or even the colon where these vitamins may have potential health benefits for the host. Clinical trials supporting this effect are still limited. In this review, we discuss evidence regarding the modulatory effects of B-group vitamins on the gut microbiome with a focus on their potential role as prebiotic candidates.
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Affiliation(s)
- Raquel Bedani
- Department of Biochemical and Pharmaceutical Technology, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, São Paulo, Brazil; Food Research Center, University of São Paulo, São Paulo, São Paulo, Brazil.
| | - Ana Clara Candelaria Cucick
- Department of Biochemical and Pharmaceutical Technology, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, São Paulo, Brazil; Food Research Center, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Marcela Albuquerque Cavalcanti de Albuquerque
- Department of Biochemical and Pharmaceutical Technology, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, São Paulo, Brazil; Food Research Center, University of São Paulo, São Paulo, São Paulo, Brazil
| | | | - Susana Marta Isay Saad
- Department of Biochemical and Pharmaceutical Technology, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, São Paulo, Brazil; Food Research Center, University of São Paulo, São Paulo, São Paulo, Brazil
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15
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Alvarez-Aponte ZI, Govindaraju AM, Hallberg ZF, Nicolas AM, Green MA, Mok KC, Fonseca-García C, Coleman-Derr D, Brodie EL, Carlson HK, Taga ME. Phylogenetic distribution and experimental characterization of corrinoid production and dependence in soil bacterial isolates. THE ISME JOURNAL 2024; 18:wrae068. [PMID: 38648288 PMCID: PMC11287214 DOI: 10.1093/ismejo/wrae068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/15/2024] [Accepted: 04/19/2024] [Indexed: 04/25/2024]
Abstract
Soil microbial communities impact carbon sequestration and release, biogeochemical cycling, and agricultural yields. These global effects rely on metabolic interactions that modulate community composition and function. However, the physicochemical and taxonomic complexity of soil and the scarcity of available isolates for phenotypic testing are significant barriers to studying soil microbial interactions. Corrinoids-the vitamin B12 family of cofactors-are critical for microbial metabolism, yet they are synthesized by only a subset of microbiome members. Here, we evaluated corrinoid production and dependence in soil bacteria as a model to investigate the ecological roles of microorganisms involved in metabolic interactions. We isolated and characterized a taxonomically diverse collection of 161 soil bacteria from a single study site. Most corrinoid-dependent bacteria in the collection prefer B12 over other corrinoids, while all tested producers synthesize B12, indicating metabolic compatibility between producers and dependents in the collection. Furthermore, a subset of producers release B12 at levels sufficient to support dependent isolates in laboratory culture at estimated ratios of up to 1000 dependents per producer. Within our isolate collection, we did not find strong phylogenetic patterns in corrinoid production or dependence. Upon investigating trends in the phylogenetic dispersion of corrinoid metabolism categories across sequenced bacteria from various environments, we found that these traits are conserved in 47 out of 85 genera. Together, these phenotypic and genomic results provide evidence for corrinoid-based metabolic interactions among bacteria and provide a framework for the study of nutrient-sharing ecological interactions in microbial communities.
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Affiliation(s)
- Zoila I Alvarez-Aponte
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Alekhya M Govindaraju
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Zachary F Hallberg
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Alexa M Nicolas
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Myka A Green
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Kenny C Mok
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Citlali Fonseca-García
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, United States
- Plant Gene Expression Center, USDA-ARS, Albany, CA 94710, United States
| | - Devin Coleman-Derr
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, United States
- Plant Gene Expression Center, USDA-ARS, Albany, CA 94710, United States
| | - Eoin L Brodie
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Hans K Carlson
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Michiko E Taga
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, United States
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16
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Hallberg ZF, Nicolas AM, Alvarez-Aponte ZI, Mok KC, Sieradzki ET, Pett-Ridge J, Banfield JF, Carlson HK, Firestone MK, Taga ME. Soil microbial community response to corrinoids is shaped by a natural reservoir of vitamin B12. THE ISME JOURNAL 2024; 18:wrae094. [PMID: 38832716 PMCID: PMC11287211 DOI: 10.1093/ismejo/wrae094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/30/2024] [Accepted: 06/03/2024] [Indexed: 06/05/2024]
Abstract
Soil microbial communities perform critical ecosystem services through the collective metabolic activities of numerous individual organisms. Most microbes use corrinoids, a structurally diverse family of cofactors related to vitamin B12. Corrinoid structure influences the growth of individual microbes, yet how these growth responses scale to the community level remains unknown. Analysis of metagenome-assembled genomes suggests that corrinoids are supplied to the community by members of the archaeal and bacterial phyla Thermoproteota, Actinobacteria, and Proteobacteria. Corrinoids were found largely adhered to the soil matrix in a grassland soil, at levels exceeding those required by cultured bacteria. Enrichment cultures and soil microcosms seeded with different corrinoids showed distinct shifts in bacterial community composition, supporting the hypothesis that corrinoid structure can shape communities. Environmental context influenced both community- and taxon-specific responses to specific corrinoids. These results implicate corrinoids as key determinants of soil microbiome structure and suggest that environmental micronutrient reservoirs promote community stability.
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Affiliation(s)
- Zachary F Hallberg
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Alexa M Nicolas
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, United States
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Zoila I Alvarez-Aponte
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Kenny C Mok
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Ella T Sieradzki
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Jennifer Pett-Ridge
- Physical & Life Science Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, United States
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA 94720, United States
| | - Jillian F Banfield
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA 94720, United States
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA 94720, United States
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA 94720, United States
- Earth & Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Hans K Carlson
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Mary K Firestone
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA 94720, United States
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Michiko E Taga
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, United States
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17
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Hibberd MC, Webber DM, Rodionov DA, Henrissat S, Chen RY, Zhou C, Lynn HM, Wang Y, Chang HW, Lee EM, Lelwala-Guruge J, Kazanov MD, Arzamasov AA, Leyn SA, Lombard V, Terrapon N, Henrissat B, Castillo JJ, Couture G, Bacalzo NP, Chen Y, Lebrilla CB, Mostafa I, Das S, Mahfuz M, Barratt MJ, Osterman AL, Ahmed T, Gordon JI. Bioactive glycans in a microbiome-directed food for children with malnutrition. Nature 2024; 625:157-165. [PMID: 38093016 PMCID: PMC10764277 DOI: 10.1038/s41586-023-06838-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 11/06/2023] [Indexed: 12/26/2023]
Abstract
Evidence is accumulating that perturbed postnatal development of the gut microbiome contributes to childhood malnutrition1-4. Here we analyse biospecimens from a randomized, controlled trial of a microbiome-directed complementary food (MDCF-2) that produced superior rates of weight gain compared with a calorically more dense conventional ready-to-use supplementary food in 12-18-month-old Bangladeshi children with moderate acute malnutrition4. We reconstructed 1,000 bacterial genomes (metagenome-assembled genomes (MAGs)) from the faecal microbiomes of trial participants, identified 75 MAGs of which the abundances were positively associated with ponderal growth (change in weight-for-length Z score (WLZ)), characterized changes in MAG gene expression as a function of treatment type and WLZ response, and quantified carbohydrate structures in MDCF-2 and faeces. The results reveal that two Prevotella copri MAGs that are positively associated with WLZ are the principal contributors to MDCF-2-induced expression of metabolic pathways involved in utilizing the component glycans of MDCF-2. The predicted specificities of carbohydrate-active enzymes expressed by their polysaccharide-utilization loci are correlated with (1) the in vitro growth of Bangladeshi P. copri strains, possessing varying degrees of polysaccharide-utilization loci and genomic conservation with these MAGs, in defined medium containing different purified glycans representative of those in MDCF-2, and (2) the levels of faecal carbohydrate structures in the trial participants. These associations suggest that identifying bioactive glycan structures in MDCFs metabolized by growth-associated bacterial taxa will help to guide recommendations about their use in children with acute malnutrition and enable the development of additional formulations.
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Affiliation(s)
- Matthew C Hibberd
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Daniel M Webber
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Dmitry A Rodionov
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Suzanne Henrissat
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, Marseille, France
| | - Robert Y Chen
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
| | - Cyrus Zhou
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
| | - Hannah M Lynn
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
| | - Yi Wang
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
| | - Hao-Wei Chang
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
| | - Evan M Lee
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
| | - Janaki Lelwala-Guruge
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
| | - Marat D Kazanov
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Aleksandr A Arzamasov
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Semen A Leyn
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Vincent Lombard
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, Marseille, France
| | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, Marseille, France
| | - Bernard Henrissat
- Department of Biotechnology and Biomedicine (DTU Bioengineering), Technical University of Denmark, Lyngby, Denmark
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Juan J Castillo
- Department of Chemistry, University of California, Davis, Davis, CA, USA
| | - Garret Couture
- Department of Chemistry, University of California, Davis, Davis, CA, USA
| | - Nikita P Bacalzo
- Department of Chemistry, University of California, Davis, Davis, CA, USA
| | - Ye Chen
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
- Department of Chemistry, University of California, Davis, Davis, CA, USA
| | - Carlito B Lebrilla
- Department of Chemistry, University of California, Davis, Davis, CA, USA
| | - Ishita Mostafa
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Subhasish Das
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Mustafa Mahfuz
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Michael J Barratt
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Andrei L Osterman
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Tahmeed Ahmed
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Jeffrey I Gordon
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA.
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA.
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA.
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18
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Bircher L, Sourabié AM, Paurevic M, Hochuli J, Geirnaert A, Navas C, Drogue B, Lacroix C. Faecalibacterium duncaniae A2-165 growth is strongly promoted by yeast extract and vitamin B5 in cGMP medium. Microb Biotechnol 2024; 17:e14374. [PMID: 38019136 PMCID: PMC10832529 DOI: 10.1111/1751-7915.14374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 10/31/2023] [Accepted: 11/07/2023] [Indexed: 11/30/2023] Open
Abstract
Several gut microbial species within the Faecalibacterium genus have emerged as promising next-generation probiotics (NGP) due to their multifunctional protective effects against gastrointestinal and systemic disorders. To enable clinical studies and further applications, improved methods for cultivating Faecalibacterium must be developed in compliance with current Good Manufacturing Practice regulations, which is complicated by its oxygen sensitivity and complex nutritional requirements. Different yeast-based nutrients (YBNs), including yeast extracts (YEs) and yeast peptones (YPs), are ubiquitously used when cultivating microbes to supply a broad range of macro- and micronutrients. In this study, we evaluated six experimental YBNs, namely three YEs, two YPs and a yeast cell wall product (YCW), and eight B-vitamins in the cultivation of Faecalibacterium duncaniae A2-165, former Faecalibacterium prausnitzii, using growth assays in microtitre plates, dose-effect studies in Hungate tube fermentations and fully controlled bioreactor experiments. We demonstrated that YEs promote F. duncaniae A2-165 growth in a nutritionally limited medium, while YPs and YCW lacked essential growth factors for enabling cell propagation. High cell density was obtained in controlled bioreactors using a medium containing 2-4% of a selected YE and 1% casein peptone (3.4 ± 1.7 × 109 -5.1 ± 1.3 × 109 cells mL-1 ). Among all tested B-vitamins, we identified B5 as a strong growth promoter. Replacing casein peptone with YP and supplementing with vitamin B5 further increased biomass by approximately 50% (6.8 ± 1.7 × 109 cells mL-1 ). Hence, empirical selection of YE, YP and B5 allowed formulation of a high-yielding animal allergen-free nutritive medium to produce F. duncaniae A2-165. Selecting nutritionally suitable YBNs and combining these with other key nutrients are important steps for optimizing production of NGP with high yields and lower cost.
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Affiliation(s)
- Lea Bircher
- Department Health Science and Technology, Laboratory of Food Biotechnology, Institute of Food, Nutrition and HealthETH ZurichZürichSwitzerland
| | - Alain M. Sourabié
- Science Technology and Innovation DepartmentProcelys by LeSaffreMaisons‐AlfortFrance
| | - Marijana Paurevic
- Department Health Science and Technology, Laboratory of Food Biotechnology, Institute of Food, Nutrition and HealthETH ZurichZürichSwitzerland
| | - Janina Hochuli
- Department Health Science and Technology, Laboratory of Food Biotechnology, Institute of Food, Nutrition and HealthETH ZurichZürichSwitzerland
| | - Annelies Geirnaert
- Department Health Science and Technology, Laboratory of Food Biotechnology, Institute of Food, Nutrition and HealthETH ZurichZürichSwitzerland
| | - Chloé Navas
- Science Technology and Innovation DepartmentProcelys by LeSaffreMaisons‐AlfortFrance
| | - Benoît Drogue
- Science Technology and Innovation DepartmentProcelys by LeSaffreMaisons‐AlfortFrance
| | - Christophe Lacroix
- Department Health Science and Technology, Laboratory of Food Biotechnology, Institute of Food, Nutrition and HealthETH ZurichZürichSwitzerland
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19
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Chang HW, Lee EM, Wang Y, Zhou C, Pruss KM, Henrissat S, Chen RY, Kao C, Hibberd MC, Lynn HM, Webber DM, Crane M, Cheng J, Rodionov DA, Arzamasov AA, Castillo JJ, Couture G, Chen Y, Balcazo NP, Lebrilla CB, Terrapon N, Henrissat B, Ilkayeva O, Muehlbauer MJ, Newgard CB, Mostafa I, Das S, Mahfuz M, Osterman AL, Barratt MJ, Ahmed T, Gordon JI. Prevotella copri-related effects of a therapeutic food for malnutrition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.11.553030. [PMID: 37645712 PMCID: PMC10461977 DOI: 10.1101/2023.08.11.553030] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Preclinical and clinical studies are providing evidence that the healthy growth of infants and children reflects, in part, healthy development of their gut microbiomes1-5. This process of microbial community assembly and functional maturation is perturbed in children with acute malnutrition. Gnotobiotic animals, colonized with microbial communities from children with severe and moderate acute malnutrition, have been used to develop microbiome-directed complementary food (MDCF) formulations for repairing the microbiomes of these children during the weaning period5. Bangladeshi children with moderate acute malnutrition (MAM) participating in a previously reported 3-month-long randomized controlled clinical study of one such formulation, MDCF-2, exhibited significantly improved weight gain compared to a commonly used nutritional intervention despite the lower caloric density of the MDCF6. Characterizing the 'metagenome assembled genomes' (MAGs) of bacterial strains present in the microbiomes of study participants revealed a significant correlation between accelerated ponderal growth and the expression by two Prevotella copri MAGs of metabolic pathways involved in processing of MDCF-2 glycans1. To provide a direct test of these relationships, we have now performed 'reverse translation' experiments using a gnotobiotic mouse model of mother-to-offspring microbiome transmission. Mice were colonized with defined consortia of age- and ponderal growth-associated gut bacterial strains cultured from Bangladeshi infants/children in the study population, with or without P. copri isolates resembling the MAGs. By combining analyses of microbial community assembly, gene expression and processing of glycan constituents of MDCF-2 with single nucleus RNA-Seq and mass spectrometric analyses of the intestine, we establish a principal role for P. copri in mediating metabolism of MDCF-2 glycans, characterize its interactions with other consortium members including Bifidobacterium longum subsp. infantis, and demonstrate the effects of P. copri-containing consortia in mediating weight gain and modulating the activities of metabolic pathways involved in lipid, amino acid, carbohydrate plus other facets of energy metabolism within epithelial cells positioned at different locations in intestinal crypts and villi. Together, the results provide insights into structure/function relationships between MDCF-2 and members of the gut communities of malnourished children; they also have implications for developing future prebiotic, probiotic and/or synbiotic therapeutics for microbiome restoration in children with already manifest malnutrition, or who are at risk for this pervasive health challenge.
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Affiliation(s)
- Hao-Wei Chang
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Evan M. Lee
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Yi Wang
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Cyrus Zhou
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Kali M. Pruss
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Suzanne Henrissat
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, F-13288, Marseille, France
| | - Robert Y. Chen
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Clara Kao
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Matthew C. Hibberd
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Hannah M. Lynn
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Daniel M. Webber
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Marie Crane
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Jiye Cheng
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Dmitry A. Rodionov
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037 USA
| | - Aleksandr A. Arzamasov
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037 USA
| | - Juan J. Castillo
- Department of Chemistry, University of California, Davis, CA 95616 USA
| | - Garret Couture
- Department of Chemistry, University of California, Davis, CA 95616 USA
| | - Ye Chen
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
- Department of Chemistry, University of California, Davis, CA 95616 USA
| | - Nikita P. Balcazo
- Department of Chemistry, University of California, Davis, CA 95616 USA
| | | | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, F-13288, Marseille, France
| | - Bernard Henrissat
- Department of Biotechnology and Biomedicine (DTU Bioengineering), Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Olga Ilkayeva
- Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27710 USA
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27710 USA
- Department of Medicine, Duke University Medical Center, Durham, NC, 27710 USA
| | - Michael J. Muehlbauer
- Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27710 USA
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27710 USA
| | - Christopher B. Newgard
- Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27710 USA
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27710 USA
- Department of Medicine, Duke University Medical Center, Durham, NC, 27710 USA
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710 USA
| | - Ishita Mostafa
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Subhasish Das
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Mustafa Mahfuz
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Andrei L. Osterman
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037 USA
| | - Michael J. Barratt
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Tahmeed Ahmed
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Jeffrey I. Gordon
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110 USA
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20
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Beller ZW, Wesener DA, Seebeck TR, Guruge JL, Byrne AE, Henrissat S, Terrapon N, Henrissat B, Rodionov DA, Osterman AL, Suarez C, Bacalzo NP, Chen Y, Couture G, Lebrilla CB, Zhang Z, Eastlund ER, McCann CH, Davis GD, Gordon JI. Inducible CRISPR-targeted "knockdown" of human gut Bacteroides in gnotobiotic mice discloses glycan utilization strategies. Proc Natl Acad Sci U S A 2023; 120:e2311422120. [PMID: 37733741 PMCID: PMC10523453 DOI: 10.1073/pnas.2311422120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 08/08/2023] [Indexed: 09/23/2023] Open
Abstract
Understanding how members of the human gut microbiota prioritize nutrient resources is one component of a larger effort to decipher the mechanisms defining microbial community robustness and resiliency in health and disease. This knowledge is foundational for development of microbiota-directed therapeutics. To model how bacteria prioritize glycans in the gut, germfree mice were colonized with 13 human gut bacterial strains, including seven saccharolytic Bacteroidaceae species. Animals were fed a Western diet supplemented with pea fiber. After community assembly, an inducible CRISPR-based system was used to selectively and temporarily reduce the absolute abundance of Bacteroides thetaiotaomicron or B. cellulosilyticus by 10- to 60-fold. Each knockdown resulted in specific, reproducible increases in the abundances of other Bacteroidaceae and dynamic alterations in their expression of genes involved in glycan utilization. Emergence of these "alternate consumers" was associated with preservation of community saccharolytic activity. Using an inducible system for CRISPR base editing in vitro, we disrupted translation of transporters critical for utilizing dietary polysaccharides in Phocaeicola vulgatus, a B. cellulosilyticus knockdown-responsive taxon. In vitro and in vivo tests of the resulting P. vulgatus mutants allowed us to further characterize mechanisms associated with its increased fitness after knockdown. In principle, the approach described can be applied to study utilization of a range of nutrients and to preclinical efforts designed to develop therapeutic strategies for precision manipulation of microbial communities.
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Affiliation(s)
- Zachary W. Beller
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO63110
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO63110
| | - Darryl A. Wesener
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO63110
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO63110
| | - Timothy R. Seebeck
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO63110
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO63110
- Genome Engineering R&D, MilliporeSigma, the Life Science business Merck KGaA, Darmstadt, Germany, St. Louis, MO63103
| | - Janaki L. Guruge
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO63110
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO63110
| | - Alexandra E. Byrne
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO63110
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO63110
| | - Suzanne Henrissat
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO63110
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO63110
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique and Aix-Marseille University, 13288Marseille, France
| | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique and Aix-Marseille University, 13288Marseille, France
| | - Bernard Henrissat
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. LyngbyDK-2800, Denmark
- Department of Biological Sciences, King Abdulaziz University, Jeddah21589, Saudi Arabia
| | - Dmitry A. Rodionov
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA92037
| | - Andrei L. Osterman
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA92037
| | - Chris Suarez
- Department of Chemistry, University of California, Davis, CA95616
| | | | - Ye Chen
- Department of Chemistry, University of California, Davis, CA95616
| | - Garret Couture
- Department of Chemistry, University of California, Davis, CA95616
| | | | - Zhigang Zhang
- Genome Engineering R&D, MilliporeSigma, the Life Science business Merck KGaA, Darmstadt, Germany, St. Louis, MO63103
| | - Erik R. Eastlund
- Genome Engineering R&D, MilliporeSigma, the Life Science business Merck KGaA, Darmstadt, Germany, St. Louis, MO63103
| | - Caitlin H. McCann
- Genome Engineering R&D, MilliporeSigma, the Life Science business Merck KGaA, Darmstadt, Germany, St. Louis, MO63103
| | - Gregory D. Davis
- Genome Engineering R&D, MilliporeSigma, the Life Science business Merck KGaA, Darmstadt, Germany, St. Louis, MO63103
| | - Jeffrey I. Gordon
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO63110
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO63110
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21
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Chanin RB, West PT, Park RM, Wirbel J, Green GZM, Miklos AM, Gill MO, Hickey AS, Brooks EF, Bhatt AS. Intragenic DNA inversions expand bacterial coding capacity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.11.532203. [PMID: 36945655 PMCID: PMC10028968 DOI: 10.1101/2023.03.11.532203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2023]
Abstract
Bacterial populations that originate from a single bacterium are not strictly clonal. Often, they contain subgroups with distinct phenotypes. Bacteria can generate heterogeneity through phase variation: a preprogrammed, reversible mechanism that alters gene expression levels across a population. One well studied type of phase variation involves enzyme-mediated inversion of specific intergenic regions of genomic DNA. Frequently, these DNA inversions flip the orientation of promoters, turning ON or OFF adjacent coding regions within otherwise isogenic populations. Through this mechanism, inversion can affect fitness, survival, or group dynamics. Here, we develop and apply bioinformatic approaches to discover thousands of previously undescribed phase-variable regions in prokaryotes using long-read datasets. We identify 'intragenic invertons', a surprising new class of invertible elements found entirely within genes, in bacteria and archaea. To date, inversions within single genes have not been described. Intragenic invertons allow a gene to encode two or more versions of a protein by flipping a DNA sequence within the coding region, thereby increasing coding capacity without increasing genome size. We experimentally characterize specific intragenic invertons in the gut commensal Bacteroides thetaiotaomicron, presenting a 'roadmap' for investigating this new gene-diversifying phenomenon.
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Affiliation(s)
- Rachael B. Chanin
- Department of Medicine (Hematology, Blood and Marrow Transplantation); Stanford, USA
| | - Patrick T. West
- Department of Medicine (Hematology, Blood and Marrow Transplantation); Stanford, USA
| | - Ryan M. Park
- Department of Medicine (Hematology, Blood and Marrow Transplantation); Stanford, USA
| | - Jakob Wirbel
- Department of Medicine (Hematology, Blood and Marrow Transplantation); Stanford, USA
| | - Gabriella Z. M. Green
- Department of Medicine (Hematology, Blood and Marrow Transplantation); Stanford, USA
| | - Arjun M. Miklos
- Department of Medicine (Hematology, Blood and Marrow Transplantation); Stanford, USA
| | | | | | - Erin F. Brooks
- Department of Medicine (Hematology, Blood and Marrow Transplantation); Stanford, USA
| | - Ami S. Bhatt
- Department of Medicine (Hematology, Blood and Marrow Transplantation); Stanford, USA
- Department of Genetics, Stanford University; Stanford, USA
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22
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Hibberd MC, Webber DM, Rodionov DA, Henrissat S, Chen RY, Zhou C, Lynn HM, Wang Y, Chang HW, Lee EM, Lelwala-Guruge J, Kazanov MD, Arzamasov AA, Leyn SA, Lombard V, Terrapon N, Henrissat B, Castillo JJ, Couture G, Bacalzo NP, Chen Y, Lebrilla CB, Mostafa I, Das S, Mahfuz M, Barratt MJ, Osterman AL, Ahmed T, Gordon JI. Bioactive glycans in a microbiome-directed food for malnourished children. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.08.14.23293998. [PMID: 37645824 PMCID: PMC10462212 DOI: 10.1101/2023.08.14.23293998] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Evidence is accumulating that perturbed postnatal development of the gut microbiome contributes to childhood malnutrition1-4. Designing effective microbiome-directed therapeutic foods to repair these perturbations requires knowledge about how food components interact with the microbiome to alter its expressed functions. Here we use biospecimens from a randomized, controlled trial of a microbiome-directed complementary food prototype (MDCF-2) that produced superior rates of weight gain compared to a conventional ready-to-use supplementary food (RUSF) in 12-18-month-old Bangladeshi children with moderate acute malnutrition (MAM)4. We reconstructed 1000 bacterial genomes (metagenome-assembled genomes, MAGs) present in their fecal microbiomes, identified 75 whose abundances were positively associated with weight gain (change in weight-for-length Z score, WLZ), characterized gene expression changes in these MAGs as a function of treatment type and WLZ response, and used mass spectrometry to quantify carbohydrate structures in MDCF-2 and feces. The results reveal treatment-induced changes in expression of carbohydrate metabolic pathways in WLZ-associated MAGs. Comparing participants consuming MDCF-2 versus RUSF, and MDCF-2-treated children in the upper versus lower quartiles of WLZ responses revealed that two Prevotella copri MAGs positively associated with WLZ were principal contributors to MDCF-2-induced expression of metabolic pathways involved in utilization of its component glycans. Moreover, the predicted specificities of carbohydrate active enzymes expressed by polysaccharide utilization loci (PULs) in these two MAGs correlate with the (i) in vitro growth of Bangladeshi P. copri strains, possessing differing degrees of PUL and overall genomic content similarity to these MAGs, cultured in defined medium containing different purified glycans representative of those in MDCF-2, and (ii) levels of carbohydrate structures identified in feces from clinical trial participants. In the accompanying paper5, we use a gnotobiotic mouse model colonized with age- and WLZ-associated bacterial taxa cultured from this study population, and fed diets resembling those consumed by study participants, to directly test the relationship between P. copri, MDCF-2 glycan metabolism, host ponderal growth responses, and intestinal gene expression and metabolism. The ability to identify bioactive glycan structures in MDCFs that are metabolized by growth-associated bacterial taxa will help guide recommendations about use of this MDCF for children with acute malnutrition representing different geographic locales and ages, as well as enable development of bioequivalent, or more efficacious, formulations composed of culturally acceptable and affordable ingredients.
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Affiliation(s)
- Matthew C. Hibberd
- Edison Family Center for Genome Sciences and Systems Biology,
Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington
University School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University
School of Medicine, St. Louis, MO 63110 USA
| | - Daniel M. Webber
- Edison Family Center for Genome Sciences and Systems Biology,
Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington
University School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University
School of Medicine, St. Louis, MO 63110 USA
| | - Dmitry A. Rodionov
- Infectious and Inflammatory Disease Center, Sanford Burnham
Prebys Medical Discovery Institute, La Jolla, CA 92037 USA
| | - Suzanne Henrissat
- Edison Family Center for Genome Sciences and Systems Biology,
Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington
University School of Medicine, St. Louis, MO 63110 USA
- Architecture et Fonction des Macromolécules Biologiques,
CNRS, Aix-Marseille University, F-13288, Marseille, France
| | - Robert Y. Chen
- Edison Family Center for Genome Sciences and Systems Biology,
Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington
University School of Medicine, St. Louis, MO 63110 USA
| | - Cyrus Zhou
- Edison Family Center for Genome Sciences and Systems Biology,
Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington
University School of Medicine, St. Louis, MO 63110 USA
| | - Hannah M. Lynn
- Edison Family Center for Genome Sciences and Systems Biology,
Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington
University School of Medicine, St. Louis, MO 63110 USA
| | - Yi Wang
- Edison Family Center for Genome Sciences and Systems Biology,
Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington
University School of Medicine, St. Louis, MO 63110 USA
| | - Hao-Wei Chang
- Edison Family Center for Genome Sciences and Systems Biology,
Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington
University School of Medicine, St. Louis, MO 63110 USA
| | - Evan M. Lee
- Edison Family Center for Genome Sciences and Systems Biology,
Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington
University School of Medicine, St. Louis, MO 63110 USA
| | - Janaki Lelwala-Guruge
- Edison Family Center for Genome Sciences and Systems Biology,
Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington
University School of Medicine, St. Louis, MO 63110 USA
| | - Marat D. Kazanov
- Faculty of Engineering and Natural Sciences, Sabanci University,
Istanbul, Turkey, 34956
| | - Aleksandr A. Arzamasov
- Infectious and Inflammatory Disease Center, Sanford Burnham
Prebys Medical Discovery Institute, La Jolla, CA 92037 USA
| | - Semen A. Leyn
- Infectious and Inflammatory Disease Center, Sanford Burnham
Prebys Medical Discovery Institute, La Jolla, CA 92037 USA
| | - Vincent Lombard
- Architecture et Fonction des Macromolécules Biologiques,
CNRS, Aix-Marseille University, F-13288, Marseille, France
| | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques,
CNRS, Aix-Marseille University, F-13288, Marseille, France
| | - Bernard Henrissat
- Department of Biotechnology and Biomedicine (DTU Bioengineering),
Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
- Department of Biological Sciences, King Abdulaziz University,
Jeddah, Saudi Arabia
| | - Juan J. Castillo
- Department of Chemistry, University of California, Davis, CA
95616, USA
| | - Garret Couture
- Department of Chemistry, University of California, Davis, CA
95616, USA
| | - Nikita P. Bacalzo
- Department of Chemistry, University of California, Davis, CA
95616, USA
| | - Ye Chen
- Edison Family Center for Genome Sciences and Systems Biology,
Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington
University School of Medicine, St. Louis, MO 63110 USA
- Department of Chemistry, University of California, Davis, CA
95616, USA
| | | | - Ishita Mostafa
- International Centre for Diarrhoeal Disease Research,
Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Subhasish Das
- International Centre for Diarrhoeal Disease Research,
Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Mustafa Mahfuz
- International Centre for Diarrhoeal Disease Research,
Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Michael J. Barratt
- Edison Family Center for Genome Sciences and Systems Biology,
Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington
University School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University
School of Medicine, St. Louis, MO 63110 USA
| | - Andrei L. Osterman
- Infectious and Inflammatory Disease Center, Sanford Burnham
Prebys Medical Discovery Institute, La Jolla, CA 92037 USA
| | - Tahmeed Ahmed
- International Centre for Diarrhoeal Disease Research,
Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Jeffrey I. Gordon
- Edison Family Center for Genome Sciences and Systems Biology,
Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington
University School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University
School of Medicine, St. Louis, MO 63110 USA
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23
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Kawasaki S, Ozawa K, Mori T, Yamamoto A, Ito M, Ohkuma M, Sakamoto M, Matsutani M. Symbiosis of Carpenter Bees with Uncharacterized Lactic Acid Bacteria Showing NAD Auxotrophy. Microbiol Spectr 2023; 11:e0078223. [PMID: 37347191 PMCID: PMC10433979 DOI: 10.1128/spectrum.00782-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 05/30/2023] [Indexed: 06/23/2023] Open
Abstract
Eusocial bees (such as honey bees and bumble bees) harbor core gut microbiomes that are transmitted through social interaction between nestmates. Carpenter bees are not eusocial; however, recent microbiome analyses found that Xylocopa species harbor distinctive core gut microbiomes. In this study, we analyzed the gut microbiomes of three Xylocopa species in Japan between 2016 and 2021 by V1 to V2 region-based 16S rDNA amplicon sequencing, and 14 candidate novel species were detected based on the full-length 16S rRNA gene sequences. All Xylocopa species harbor core gut microbiomes consisting of primarily lactic acid bacteria (LAB) that were phylogenetically distant from known species. Although they were difficult to cultivate, two LAB species from two different Xylocopa species were isolated by supplementing bacterial culture supernatants. Both genomes exhibited an average LAB genome size with a large set of genes for carbohydrate utilization but lacked genes to synthesize an essential coenzyme NAD, which is unique among known insect symbionts. Our findings of phylogenetically distinct core LAB of NAD auxotrophy reflected the evolution of Xylocopa-restricted bacteria retention and maintenance through vertical transmission of microbes during solitary life. We propose five candidate novel species belonging to the families Lactobacillaceae and Bifidobacteriaceae, including a novel genus, and their potential functions in carbohydrate utilization. IMPORTANCE Recent investigations found unique microbiomes in carpenter bees, but the description of individual microbes, including isolation and genomics, remains largely unknown. Here, we found that the Japanese Xylocopa species also harbor core gut microbiomes. Although most of them were difficult to isolate a pure colony, we successfully isolated several strains. We performed whole-genome sequencing of the isolated candidate novel species and found that the two Lactobacillaceae strains belonging to the Xylocopa-specific novel LAB clade lack the genes for synthesizing NAD, a coenzyme central to metabolism in all living organisms. Here, we propose a novel genus for the two LAB species based on very low 16S rRNA gene sequence similarities and genotypic characters.
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Affiliation(s)
- Shinji Kawasaki
- Department of Molecular Microbiology, Tokyo University of Agriculture, Tokyo, Japan
| | - Kaori Ozawa
- Department of Molecular Microbiology, Tokyo University of Agriculture, Tokyo, Japan
| | - Tatsunori Mori
- Department of Molecular Microbiology, Tokyo University of Agriculture, Tokyo, Japan
| | - Arisa Yamamoto
- Department of Molecular Microbiology, Tokyo University of Agriculture, Tokyo, Japan
| | - Midoriko Ito
- Department of Molecular Microbiology, Tokyo University of Agriculture, Tokyo, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Japan
| | - Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Japan
| | - Minenosuke Matsutani
- NODAI Genome Research Center, Research Institute, Tokyo University of Agriculture, Tokyo, Japan
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24
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Cui W, Nagano Y, Morita S, Tanoue T, Yamane H, Ishikawa K, Sato T, Kubo M, Hori S, Taniguchi T, Hatakeyama M, Atarashi K, Honda K. Diet-mediated constitutive induction of novel IL-4+ ILC2 cells maintains intestinal homeostasis in mice. J Exp Med 2023; 220:214103. [PMID: 37163450 PMCID: PMC10174189 DOI: 10.1084/jem.20221773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 03/06/2023] [Accepted: 04/26/2023] [Indexed: 05/12/2023] Open
Abstract
Group 2 innate lymphoid cells (ILC2s) expressing IL-5 and IL-13 are localized at various mucosal tissues and play critical roles in the induction of type 2 inflammation, response to helminth infection, and tissue repair. Here, we reveal a unique ILC2 subset in the mouse intestine that constitutively expresses IL-4 together with GATA3, ST2, KLRG1, IL-17RB, and IL-5. In this subset, IL-4 expression is regulated by mechanisms similar to but distinct from those observed in T cells and is partly affected by IL-25 signaling. Although the absence of the microbiota had marginal effects, feeding mice with a vitamin B1-deficient diet compromised the number of intestinal IL-4+ ILC2s. The decrease in the number of IL-4+ ILC2s caused by the vitamin B1 deficiency was accompanied by a reduction in IL-25-producing tuft cells. Our findings reveal that dietary vitamin B1 plays a critical role in maintaining interaction between tuft cells and IL-4+ ILC2s, a previously uncharacterized immune cell population that may contribute to maintaining intestinal homeostasis.
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Affiliation(s)
- Wanlin Cui
- Department of Microbiology and Immunology, School of Medicine, Keio University, Tokyo, Japan
- Department of Pediatrics, The First Hospital of China Medical University, Shenyang, China
| | - Yuji Nagano
- RIKEN Center for Integrative Medical Sciences (IMS) , Yokohama, Japan
- Graduate School of Medicine, The University of Tokyo , Tokyo, Japan
| | - Satoru Morita
- Department of Microbiology and Immunology, School of Medicine, Keio University, Tokyo, Japan
| | - Takeshi Tanoue
- Department of Microbiology and Immunology, School of Medicine, Keio University, Tokyo, Japan
| | - Hidehiro Yamane
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Keiko Ishikawa
- Department of Organoid Medicine, Sakaguchi Laboratory, School of Medicine, Keio University, Tokyo, Japan
| | - Toshiro Sato
- Department of Organoid Medicine, Sakaguchi Laboratory, School of Medicine, Keio University, Tokyo, Japan
| | - Masato Kubo
- RIKEN Center for Integrative Medical Sciences (IMS) , Yokohama, Japan
- Division of Molecular Pathology, Research Institute for Biomedical Science, Tokyo University of Science, Noda, Japan
| | - Shohei Hori
- Graduate School of Pharmaceutical Sciences, The University of Tokyo , Tokyo, Japan
| | - Tadatsugu Taniguchi
- Graduate School of Medicine, The University of Tokyo , Tokyo, Japan
- Institute of Industrial Science, The University of Tokyo , Tokyo, Japan
| | - Masanori Hatakeyama
- Graduate School of Medicine, The University of Tokyo , Tokyo, Japan
- Institute of Microbial Chemistry (BIKAKEN), Microbial Chemistry Research Foundation, Tokyo, Japan
- Center of infection-associated cancer, Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
| | - Koji Atarashi
- Department of Microbiology and Immunology, School of Medicine, Keio University, Tokyo, Japan
- RIKEN Center for Integrative Medical Sciences (IMS) , Yokohama, Japan
- Human Biology-Microbiome-Quantum Research Center (WPI-Bio2Q), Keio University, Tokyo, Japan
| | - Kenya Honda
- Department of Microbiology and Immunology, School of Medicine, Keio University, Tokyo, Japan
- RIKEN Center for Integrative Medical Sciences (IMS) , Yokohama, Japan
- Human Biology-Microbiome-Quantum Research Center (WPI-Bio2Q), Keio University, Tokyo, Japan
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25
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Peterson CT, Iablokov SN, Rodionov DA, Peterson SN. Personalized Response of Parkinson's Disease Gut Microbiota to Nootropic Medicinal Herbs In Vitro: A Proof of Concept. Microorganisms 2023; 11:1979. [PMID: 37630539 PMCID: PMC10457923 DOI: 10.3390/microorganisms11081979] [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: 06/30/2023] [Revised: 07/25/2023] [Accepted: 07/28/2023] [Indexed: 08/27/2023] Open
Abstract
Parkinson's disease (PD) is a neurodegenerative disease characterized by the loss of dopaminergic neurons. Although the etiology of PD remains elusive, it has been hypothesized that initial dysregulation may occur in the gastrointestinal tract and may be accompanied by gut barrier defects. A strong clinical interest in developing therapeutics exists, including for the treatment of gut microbiota and physiology. We previously reported the impact of healthy fecal microbiota anaerobic cultures supplemented with nootropic herbs. Here, we evaluated the effect of nootropic Ayurvedic herbs on fecal microbiota derived from subjects with PD in vitro using 16S rRNA sequencing. The microbiota underwent substantial change in response to each treatment, comparable in magnitude to that observed from healthy subjects. However, the fecal samples derived from each participant displayed unique changes, consistent with a personalized response. We used genome-wide metabolic reconstruction to predict the community's metabolic potential to produce products relevant to PD pathology, including SCFAs, vitamins and amino acid degradation products. These results suggest the potential value of conducting in vitro cultivation and analyses of PD stool samples as a means of prescreening patients to select the medicinal herbs for which that individual is most likely to respond and derive benefit.
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Affiliation(s)
- Christine Tara Peterson
- Center of Excellence for Research and Training in Integrative Health, Department of Family Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92023, USA
| | | | - Dmitry A. Rodionov
- Bioinformatics and Structural Biology Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA;
| | - Scott N. Peterson
- Tumor Microenvironment and Cancer Immunology Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA;
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26
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Dje Kouadio DK, Wieringa F, Greffeuille V, Humblot C. Bacteria from the gut influence the host micronutrient status. Crit Rev Food Sci Nutr 2023:1-16. [PMID: 37366286 DOI: 10.1080/10408398.2023.2227888] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
Micronutrient deficiencies or "hidden hunger" remains a serious public health problem in most low- and middle-income countries, with severe consequences for child development. Traditional methods of treatment and prevention, such as supplementation and fortification, have not always proven to be effective and may have undesirable side-effects (i.e., digestive troubles with iron supplementation). Commensal bacteria in the gut may increase bioavailability of specific micronutrients (i.e., minerals), notably by removing anti-nutritional compounds, such as phytates and polyphenols, or by the synthesis of vitamins. Together with the gastrointestinal mucosa, gut microbiota is also the first line of protection against pathogens. It contributes to the reinforcement of the integrity of the intestinal epithelium and to a better absorption of micronutrients. However, its role in micronutrient malnutrition is still poorly understood. Moreover, the bacterial metabolism is also dependent of micronutrients acquired from the gut environment and resident bacteria may compete or collaborate to maintain micronutrient homeostasis. Gut microbiota composition can therefore be modulated by micronutrient availability. This review brings together current knowledge on this two-way relationship between micronutrients and gut microbiota bacteria, with a focus on iron, zinc, vitamin A and folate (vitamin B9), as these deficiencies are public health concerns in a global context.
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Affiliation(s)
- Dorgeles Kouakou Dje Kouadio
- QualiSud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, Montpellier, France
- French National Research Institute for Sustainable Development (IRD), Montpellier, France, France
| | - Frank Wieringa
- QualiSud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, Montpellier, France
- French National Research Institute for Sustainable Development (IRD), Montpellier, France, France
| | - Valérie Greffeuille
- QualiSud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, Montpellier, France
- French National Research Institute for Sustainable Development (IRD), Montpellier, France, France
| | - Christèle Humblot
- QualiSud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, Montpellier, France
- French National Research Institute for Sustainable Development (IRD), Montpellier, France, France
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27
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Torres-Morales J, Mark Welch JL, Dewhirst FE, Borisy GG. Site-specialization of human oral Gemella species. J Oral Microbiol 2023; 15:2225261. [PMID: 37361319 PMCID: PMC10288933 DOI: 10.1080/20002297.2023.2225261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/07/2023] [Accepted: 06/08/2023] [Indexed: 06/28/2023] Open
Abstract
Gemella species are core members of the human oral microbiome in healthy subjects and are regarded as commensals, although they can cause opportunistic infections. Our objective was to evaluate the site-specialization of Gemella species among various habitats within the mouth by combining pangenomics and metagenomics. With pangenomics, we identified genome relationships and categorized genes as core and accessory to each species. With metagenomics, we identified the primary oral habitat of individual genomes. Our results establish that the genomes of three species, G. haemolysans, G. sanguinis and G. morbillorum, are abundant and prevalent in human mouths at different oral sites: G. haemolysans on buccal mucosa and keratinized gingiva; G. sanguinis on tongue dorsum, throat, and tonsils; and G. morbillorum in dental plaque. The gene-level basis of site-specificity was investigated by identifying genes that were core to Gemella genomes at a specific oral site but absent from other Gemella genomes. The riboflavin biosynthesis pathway was present in G. haemolysans genomes associated with buccal mucosa but absent from the rest of the genomes. Overall, metapangenomics show that Gemella species have clear ecological preferences in the oral cavity of healthy humans and provides an approach to identifying gene-level drivers of site specificity.
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Affiliation(s)
| | - Jessica L. Mark Welch
- The Forsyth Institute, Cambridge, MA, USA
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA
| | - Floyd E. Dewhirst
- The Forsyth Institute, Cambridge, MA, USA
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
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28
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Huang H, Wu H, Qi M, Wang H, Lu Z. Thiamine-Mediated Microbial Interaction between Auxotrophic Rhodococcus ruber ZM07 and Prototrophic Cooperators in the Tetrahydrofuran-Degrading Microbial Community H-1. Microbiol Spectr 2023; 11:e0454122. [PMID: 37125924 PMCID: PMC10269752 DOI: 10.1128/spectrum.04541-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 04/10/2023] [Indexed: 05/02/2023] Open
Abstract
As a crucial growth factor, thiamine can regulate functional microbial communities; however, our current understanding of its effect on bioremediation is lacking. Using metatranscriptome and 16S rRNA gene sequencing, we explored the mechanism of response of an efficient tetrahydrofuran (THF)-degrading microbial culture, designated H-1, to exogenous thiamine. Rhodococcus ruber ZM07, a strain performing the THF degradation function in H-1, is a thiamine-auxotrophic bacterium. Furthermore, thiamine affected the microbial community structure of H-1 by altering resource and niche distributions. A microbial co-occurrence network was constructed to help us identify and isolate the cooperators of strain ZM07 in the microbial community. Based on the prediction of the network, two non-THF-degrading bacteria, Hydrogenophaga intermedia ZM11 and Pigmentiphaga daeguensis ZM12, were isolated. Our results suggest that strain ZM11 is a good cooperator of ZM07, and it might be more competitive than other cooperators (e.g., ZM12) in cocultured systems. Additionally, two dominant strains in our microbial culture displayed a "seesaw" pattern, and they showed completely different responses to exogenous thiamine. The growth of the THF degrader ZM07 was spurred by additional thiamine (with an increased relative abundance and significant upregulation of most metabolic pathways), while the growth of the cooperator ZM11 was obviously suppressed under the same circumstances. This relationship was the opposite without thiamine addition. Our study reveals that exogenous thiamine can affect the interaction patterns between THF- and non-THF-degrading microorganisms and provides new insight into the effects of micronutrients on the environmental microbial community. IMPORTANCE Auxotrophic microorganisms play important roles in the biodegradation of pollutants in nature. Exploring the interspecies relationship between auxotrophic THF-degrading bacteria and other microbes is helpful for the efficient utilization of auxotrophic functional microorganisms. Herein, the thiamine-auxotrophic THF-degrading bacterium ZM07 was isolated from the microbial culture H-1, and the effect of thiamine on the structure of H-1 during THF bioremediation was studied. Thiamine may help ZM07 occupy more niches and utilize more resources, thus improving THF degradation efficiency. This research provides a new strategy to improve the THF or other xenobiotic compound biodegradation performance of auxotrophic functional microorganisms/microbial communities by artificially adding special micronutrients. Additionally, the "seesaw" relationship between the thiamine-auxotrophic strain ZM07 and its prototrophic cooperator ZM11 during THF bioremediation could be changed by exogenous thiamine. This study reveals the effect of micronutrients on microbial interactions and provides an effective way to regulate the pollutant biodegradation efficiency of microbial communities.
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Affiliation(s)
- Hui Huang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
- Institute of Translational Medicine, Zhejiang University, Hangzhou, China
| | - Hao Wu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Minbo Qi
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Haixia Wang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Zhenmei Lu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
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29
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McCully AL, Loop Yao M, Brower KK, Fordyce PM, Spormann AM. Double emulsions as a high-throughput enrichment and isolation platform for slower-growing microbes. ISME COMMUNICATIONS 2023; 3:47. [PMID: 37160952 PMCID: PMC10169782 DOI: 10.1038/s43705-023-00241-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 03/27/2023] [Accepted: 04/12/2023] [Indexed: 05/11/2023]
Abstract
Our understanding of in situ microbial physiology is primarily based on physiological characterization of fast-growing and readily-isolatable microbes. Microbial enrichments to obtain novel isolates with slower growth rates or physiologies adapted to low nutrient environments are plagued by intrinsic biases for fastest-growing species when using standard laboratory isolation protocols. New cultivation tools to minimize these biases and enrich for less well-studied taxa are needed. In this study, we developed a high-throughput bacterial enrichment platform based on single cell encapsulation and growth within double emulsions (GrowMiDE). We showed that GrowMiDE can cultivate many different microorganisms and enrich for underrepresented taxa that are never observed in traditional batch enrichments. For example, preventing dominance of the enrichment by fast-growing microbes due to nutrient privatization within the double emulsion droplets allowed cultivation of slower-growing Negativicutes and Methanobacteria from stool samples in rich media enrichment cultures. In competition experiments between growth rate and growth yield specialist strains, GrowMiDE enrichments prevented competition for shared nutrient pools and enriched for slower-growing but more efficient strains. Finally, we demonstrated the compatibility of GrowMiDE with commercial fluorescence-activated cell sorting (FACS) to obtain isolates from GrowMiDE enrichments. Together, GrowMiDE + DE-FACS is a promising new high-throughput enrichment platform that can be easily applied to diverse microbial enrichments or screens.
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Affiliation(s)
- Alexandra L McCully
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA
| | - McKenna Loop Yao
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - Kara K Brower
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Polly M Fordyce
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- ChEM-H Institute, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Alfred M Spormann
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA.
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA.
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Noecker C, Sanchez J, Bisanz JE, Escalante V, Alexander M, Trepka K, Heinken A, Liu Y, Dodd D, Thiele I, DeFelice BC, Turnbaugh PJ. Systems biology elucidates the distinctive metabolic niche filled by the human gut microbe Eggerthella lenta. PLoS Biol 2023; 21:e3002125. [PMID: 37205710 PMCID: PMC10234575 DOI: 10.1371/journal.pbio.3002125] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 06/01/2023] [Accepted: 04/14/2023] [Indexed: 05/21/2023] Open
Abstract
Human gut bacteria perform diverse metabolic functions with consequences for host health. The prevalent and disease-linked Actinobacterium Eggerthella lenta performs several unusual chemical transformations, but it does not metabolize sugars and its core growth strategy remains unclear. To obtain a comprehensive view of the metabolic network of E. lenta, we generated several complementary resources: defined culture media, metabolomics profiles of strain isolates, and a curated genome-scale metabolic reconstruction. Stable isotope-resolved metabolomics revealed that E. lenta uses acetate as a key carbon source while catabolizing arginine to generate ATP, traits which could be recapitulated in silico by our updated metabolic model. We compared these in vitro findings with metabolite shifts observed in E. lenta-colonized gnotobiotic mice, identifying shared signatures across environments and highlighting catabolism of the host signaling metabolite agmatine as an alternative energy pathway. Together, our results elucidate a distinctive metabolic niche filled by E. lenta in the gut ecosystem. Our culture media formulations, atlas of metabolomics data, and genome-scale metabolic reconstructions form a freely available collection of resources to support further study of the biology of this prevalent gut bacterium.
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Affiliation(s)
- Cecilia Noecker
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, California, United States of America
| | - Juan Sanchez
- Chan Zuckerberg Biohub–San Francisco, San Francisco, California, United States of America
| | - Jordan E. Bisanz
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, California, United States of America
| | - Veronica Escalante
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, California, United States of America
| | - Margaret Alexander
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, California, United States of America
| | - Kai Trepka
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, California, United States of America
| | - Almut Heinken
- School of Medicine, National University of Ireland, Galway, Ireland
| | - Yuanyuan Liu
- Department of Pathology, Stanford University, Stanford, California, United States of America
| | - Dylan Dodd
- Department of Pathology, Stanford University, Stanford, California, United States of America
- Department of Microbiology & Immunology, Stanford University, Stanford, California, United States of America
| | - Ines Thiele
- School of Medicine, National University of Ireland, Galway, Ireland
- Ryan Institute, University of Galway, Galway, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Brian C. DeFelice
- Chan Zuckerberg Biohub–San Francisco, San Francisco, California, United States of America
| | - Peter J. Turnbaugh
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, California, United States of America
- Chan Zuckerberg Biohub–San Francisco, San Francisco, California, United States of America
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31
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Gholami H, Chmiel JA, Burton JP, Maleki Vareki S. The Role of Microbiota-Derived Vitamins in Immune Homeostasis and Enhancing Cancer Immunotherapy. Cancers (Basel) 2023; 15:cancers15041300. [PMID: 36831641 PMCID: PMC9954268 DOI: 10.3390/cancers15041300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 02/15/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
Not all cancer patients who receive immunotherapy respond positively and emerging evidence suggests that the gut microbiota may be linked to treatment efficacy. Though mechanisms of microbial contributions to the immune response have been postulated, one likely function is the supply of basic co-factors to the host including selected vitamins. Bacteria, fungi, and plants can produce their own vitamins, whereas humans primarily obtain vitamins from exogenous sources, yet despite the significance of microbial-derived vitamins as crucial immune system modulators, the microbiota is an overlooked source of these nutrients in humans. Microbial-derived vitamins are often shared by gut bacteria, stabilizing bioenergetic pathways amongst microbial communities. Compositional changes in gut microbiota can affect metabolic pathways that alter immune function. Similarly, the immune system plays a pivotal role in maintaining the gut microbiota, which parenthetically affects vitamin biosynthesis. Here we elucidate the immune-interactive mechanisms underlying the effects of these microbially derived vitamins and how they can potentially enhance the activity of immunotherapies in cancer.
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Affiliation(s)
- Hasti Gholami
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | - John A. Chmiel
- Department of Microbiology and Immunology, Western University, London, ON N6A 3K7, Canada
- Canadian Research and Development Centre for Probiotics, Lawson Research Health Research Institute, London, ON N6A 5W9, Canada
| | - Jeremy P. Burton
- Department of Microbiology and Immunology, Western University, London, ON N6A 3K7, Canada
- Canadian Research and Development Centre for Probiotics, Lawson Research Health Research Institute, London, ON N6A 5W9, Canada
- Division of Urology, Department of Surgery, Western University, London, ON N6A 3K7, Canada
- Correspondence: (J.P.B.); (S.M.V.); Tel.: +1-519-685-8500 (ext. 55769) (S.M.V.)
| | - Saman Maleki Vareki
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
- London Regional Cancer Program, Lawson Health Research Institute, London, ON N6A 5W9, Canada
- Department of Oncology, Western University, London, ON N6A 3K7, Canada
- Department of Medical Biophysics, Western University, London, ON N6A 3K7, Canada
- Correspondence: (J.P.B.); (S.M.V.); Tel.: +1-519-685-8500 (ext. 55769) (S.M.V.)
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32
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Sharma S, Hegde P, Panda S, Orimoloye MO, Aldrich CC. Drugging the microbiome: targeting small microbiome molecules. Curr Opin Microbiol 2023; 71:102234. [PMID: 36399893 DOI: 10.1016/j.mib.2022.102234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 10/12/2022] [Accepted: 10/17/2022] [Indexed: 11/17/2022]
Abstract
The human microbiome represents a large and diverse collection of microbes that plays an integral role in human physiology and pathophysiology through interactions with the host and within the microbial community. While early work exploring links between microbiome signatures and diseases states has been associative, emerging evidence demonstrates the metabolic products of the human microbiome have more proximal causal effects on disease phenotypes. The therapeutic implications of this shift are profound as manipulation of the microbiome by the administration of live biotherapeutics, ongoing, can now be pursued alongside research efforts toward describing inhibitors of key microbiome enzymes involved in the biosynthesis of metabolites implicated in various disease states and processing of host-derived metabolites. With growing interest in 'drugging the microbiome', we review few notable microbial metabolites for which traditional drug-development campaigns have yielded compounds with therapeutic promise.
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Affiliation(s)
- Sachin Sharma
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, USA
| | - Pooja Hegde
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, USA
| | - Subhankar Panda
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, USA
| | - Moyosore O Orimoloye
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, USA
| | - Courtney C Aldrich
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, USA.
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33
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Denise R, Babor J, Gerlt JA, de Crécy-Lagard V. Pyridoxal 5'-phosphate synthesis and salvage in Bacteria and Archaea: predicting pathway variant distributions and holes. Microb Genom 2023; 9:mgen000926. [PMID: 36729913 PMCID: PMC9997740 DOI: 10.1099/mgen.0.000926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Pyridoxal 5’-phosphate or PLP is a cofactor derived from B6 vitamers and essential for growth in all known organisms. PLP synthesis and salvage pathways are well characterized in a few model species even though key components, such as the vitamin B6 transporters, are still to be identified in many organisms including the model bacteria Escherichia coli or Bacillus subtilis. Using a comparative genomic approach, PLP synthesis and salvage pathways were predicted in 5840 bacterial and archaeal species with complete genomes. The distribution of the two known de novo biosynthesis pathways and previously identified cases of non-orthologous displacements were surveyed in the process. This analysis revealed that several PLP de novo pathway genes remain to be identified in many organisms, either because sequence similarity alone cannot be used to discriminate among several homologous candidates or due to non-orthologous displacements. Candidates for some of these pathway holes were identified using published TnSeq data, but many remain. We find that ~10 % of the analysed organisms rely on salvage but further analyses will be required to identify potential transporters. This work is a starting point to model the exchanges of B6 vitamers in communities, predict the sensitivity of a given organism to drugs targeting PLP synthesis enzymes, and identify numerous gaps in knowledge that will need to be tackled in the years to come.
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Affiliation(s)
- Rémi Denise
- Department of Microbiology and Cell Sciences, Gainesville, USA.,Present address: APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Jill Babor
- Department of Microbiology and Cell Sciences, Gainesville, USA
| | | | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Sciences, Gainesville, USA.,Genetics Institute, University of Florida, Gainesville, FL 32611, USA
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34
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Isenring J, Bircher L, Geirnaert A, Lacroix C. In vitro human gut microbiota fermentation models: opportunities, challenges, and pitfalls. MICROBIOME RESEARCH REPORTS 2023; 2:2. [PMID: 38045607 PMCID: PMC10688811 DOI: 10.20517/mrr.2022.15] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/12/2022] [Accepted: 01/09/2023] [Indexed: 12/05/2023]
Abstract
The human gut microbiota (HGM) plays a pivotal role in health and disease. Consequently, nutritional and medical research focusing on HGM modulation strategies as a means of improving host health is steadily increasing. In vitro HGM fermentation models offer a valid complement to human and animal studies when it comes to the mechanistic exploration of novel modulation approaches and their direct effects on HGM composition and activity, while excluding interfering host effects. However, in vitro cultivation of HGM can be challenging due to its high oxygen sensitivity and the difficulties of accurately modeling the physio-chemical complexity of the gut environment. Despite the increased use of in vitro HGM models, there is no consensus about appropriate model selection and operation, sometimes leading to major deficiencies in study design and result interpretation. In this review paper, we aim to analyze crucial aspects of the application, setup and operation, data validation and result interpretation of in vitro HGM models. When carefully designed and implemented, in vitro HGM modeling is a powerful strategy for isolating and investigating biotic and abiotic factors in the HGM, as well as evaluating their effects in a controlled environment akin to the gut. Furthermore, complementary approaches combining different in vitro and in vivo models can strengthen the design and interpretation of human studies.
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Affiliation(s)
| | | | | | - Christophe Lacroix
- Department of Health Sciences and Technology, ETH Zurich, Zürich 8092, Switzerland
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35
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Juthi RT, Sazed SA, Sarmin M, Haque R, Alam MS. COVID-19 and diarrhea: putative mechanisms and management. Int J Infect Dis 2023; 126:125-131. [PMID: 36403817 PMCID: PMC9672967 DOI: 10.1016/j.ijid.2022.11.018] [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: 09/16/2022] [Revised: 11/08/2022] [Accepted: 11/13/2022] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the causative agent of the coronavirus disease 2019 (COVID-19), has recently posed a threat to global health by spreading at a high rate and taking millions of lives worldwide. Along with the respiratory symptoms, there are gastrointestinal manifestations and one of the most common gastrointestinal symptoms is diarrhea which is seen in a significant percentage of COVID-19 patients. LITERATURE REVIEW Several studies have shown the plausible correlation between overexpressed angiotensin converting enzyme 2 (ACE2) in enterocytes and SARS-CoV-2, as ACE2 is the only known receptor for the virus entry. Along with the dysregulated ACE2, there are other contributing factors such as gut microbiome dysbiosis, adverse effects of antiviral and antibiotics for treating infections and inflammatory response to SARS-CoV-2 which bring about increased permeability of gut cells and subsequent occurrence of diarrhea. Few studies found that the SARS-CoV-2 is capable of damaging liver cells too. No single effective treatment option is available. LIMITATIONS Confirmed pathophysiology is still unavailable. Studies regarding global population are also insufficient. CONCLUSION In this review, based on the previous works and literature, we summarized the putative molecular pathophysiology of COVID-19 associated diarrhea, concomitant complications and the standard practices of management of diarrhea and hepatic manifestations in international setups.
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Affiliation(s)
- Rifat Tasnim Juthi
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Saiful Arefeen Sazed
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Monira Sarmin
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Rashidul Haque
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Mohammad Shafiul Alam
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh,Corresponding author. Mohammad Shafiul Alam, Scientist, Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka-1212, Bangladesh. Tel: +8801711-469232
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36
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Murugkar P, Dimise E, Stewart E, Viala SN, Clardy J, Dewhirst FE, Lewis K. Identification of a growth factor required for culturing specific fastidious oral bacteria. J Oral Microbiol 2023; 15:2143651. [DOI: 10.1080/20002297.2022.2143651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
- Pallavi Murugkar
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, 134 Mugar Hall, 360 Huntington Ave 02115, Boston, MA, USA
| | - Eric Dimise
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School 02115, Boston, MA, USA
| | - Eric Stewart
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, 134 Mugar Hall, 360 Huntington Ave 02115, Boston, MA, USA
| | - Stéphane N. Viala
- Department of Microbiology, the Forsyth Institute, Cambridge, MA, USA
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School 02115, Boston, MA, USA
| | - Floyd E. Dewhirst
- Department of Microbiology, the Forsyth Institute, Cambridge, MA, USA
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
| | - Kim Lewis
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, 134 Mugar Hall, 360 Huntington Ave 02115, Boston, MA, USA
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37
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Alterations in Healthy Adult Canine Faecal Microbiome and Selected Metabolites as a Result of Feeding a Commercial Complete Synbiotic Diet with Enterococcus faecium NCIMB 10415. Animals (Basel) 2022; 13:ani13010144. [PMID: 36611752 PMCID: PMC9817848 DOI: 10.3390/ani13010144] [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: 12/06/2022] [Revised: 12/22/2022] [Accepted: 12/28/2022] [Indexed: 01/01/2023] Open
Abstract
In dogs, the use of probiotics for preventive or therapeutic purposes has become increasingly common, however the evidence for beneficial effects are often limited. The aim of this study was to investigate the effects of feeding a diet containing Enterococcus faecium NCIMB 10415 on faecal quality, faecal short-chain fatty acid concentrations, serum concentrations of cholesterol, triglycerides, cobalamin and folate as well as faecal microbiome in adult dogs. Eleven healthy client owned dogs were enrolled in a randomized, double-blinded crossover study. All dogs were fed the same balanced diet with or without incorporation of Enterococcus faecium NCIMB 10415 for 16 days each. Blood and faecal samples were collected at baseline and during the feeding trial and owners recorded daily faecal scores. An Enterococcus spp. ASV, likely representing E. faecium NCIMB 10415 was detected in the faecal microbiome of some dogs 18-19 days after withdrawal of oral supplementation. Inclusion of E. faecium decreased circulating cholesterol (p = 0.008) compared to baseline. There were no differences in cholesterol concentrations between diets. Owners reported 0.6 ± 0.3) days less of loose stools compared to the control diet. Comparing to baseline, both diets significantly increased faecal concentration of acetate and butyrate, decreased serum cobalamin and increased faecal microbial diversity. Decreased serum cobalamin, and increased faecal acetate correlated with decreases in the Fusobacterium, Streptococcus, Blautia, and Peptoclostridium. Except for effects on circulating cholesterol and faecal score, effects were observed regardless of the addition of E. faecium. It is therefore likely that these effects can be contributed to dietary prebiotic effects on the faecal microbiome.
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38
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Haas EA, Saad MJA, Santos A, Vitulo N, Lemos WJF, Martins AMA, Picossi CRC, Favarato D, Gaspar RS, Magro DO, Libby P, Laurindo FRM, Da Luz PL. A red wine intervention does not modify plasma trimethylamine N-oxide but is associated with broad shifts in the plasma metabolome and gut microbiota composition. Am J Clin Nutr 2022; 116:1515-1529. [PMID: 36205549 PMCID: PMC9761755 DOI: 10.1093/ajcn/nqac286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 03/16/2022] [Accepted: 09/30/2022] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Gut microbiota profiles are closely related to cardiovascular diseases through mechanisms that include the reported deleterious effects of metabolites, such as trimethylamine N-oxide (TMAO), which have been studied as diagnostic and therapeutic targets. Moderate red wine (RW) consumption is reportedly cardioprotective, possibly by affecting the gut microbiota. OBJECTIVES To investigate the effects of RW consumption on the gut microbiota, plasma TMAO, and the plasma metabolome in men with documented coronary artery disease (CAD) using a multiomics assessment in a crossover trial. METHODS We conducted a randomized, crossover, controlled trial involving 42 men (average age, 60 y) with documented CAD comparing 3-wk RW consumption (250 mL/d, 5 d/wk) with an equal period of alcohol abstention, both preceded by a 2-wk washout period. The gut microbiota was analyzed via 16S rRNA high-throughput sequencing. Plasma TMAO was evaluated by LC-MS/MS. The plasma metabolome of 20 randomly selected participants was evaluated by ultra-high-performance LC-MS/MS. The effect of RW consumption was assessed by individual comparisons using paired tests during the abstention and RW periods. RESULTS Plasma TMAO did not differ between RW intervention and alcohol abstention, and TMAO concentrations showed low intraindividual concordance over time, with an intraclass correlation coefficient of 0.049 during the control period. After RW consumption, there was significant remodeling of the gut microbiota, with a difference in β diversity and predominance of Parasutterella, Ruminococcaceae, several Bacteroides species, and Prevotella. Plasma metabolomic analysis revealed significant changes in metabolites after RW consumption, consistent with improved redox homeostasis. CONCLUSIONS Modulation of the gut microbiota may contribute to the putative cardiovascular benefits of moderate RW consumption. The low intraindividual concordance of TMAO presents challenges regarding its role as a cardiovascular risk biomarker at the individual level. This study was registered at clinical trials.gov as NCT03232099.
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Affiliation(s)
- Elisa A Haas
- Instituto do Coracao (InCor), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Mario J A Saad
- Department of Internal Medicine, State University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Andrey Santos
- Department of Internal Medicine, State University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Nicola Vitulo
- Department of Biotechnology, Verona University, Verona, Italy
| | - Wilson J F Lemos
- Bioresources Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Aline M A Martins
- Department of Medical Science, University of Brasília (UnB), Brasília, Brazil
| | | | - Desidério Favarato
- Instituto do Coracao (InCor), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Renato S Gaspar
- Instituto do Coracao (InCor), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Daniéla O Magro
- Department of Internal Medicine, State University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Peter Libby
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Francisco R M Laurindo
- Instituto do Coracao (InCor), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Protasio L Da Luz
- Instituto do Coracao (InCor), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brazil
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Munteanu C, Schwartz B. The relationship between nutrition and the immune system. Front Nutr 2022; 9:1082500. [PMID: 36570149 PMCID: PMC9772031 DOI: 10.3389/fnut.2022.1082500] [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: 10/28/2022] [Accepted: 11/22/2022] [Indexed: 12/12/2022] Open
Abstract
Nutrition plays an essential role in the regulation of optimal immunological response, by providing adequate nutrients in sufficient concentrations to immune cells. There are a large number of micronutrients, such as minerals, and vitamins, as well as some macronutrients such as some amino acids, cholesterol and fatty acids demonstrated to exert a very important and specific impact on appropriate immune activity. This review aims to summarize at some extent the large amount of data accrued to date related to the modulation of immune function by certain micro and macronutrients and to emphasize their importance in maintaining human health. Thus, among many, some relevant case in point examples are brought and discussed: (1) The role of vitamin A/all-trans-retinoic-acids (ATRA) in acute promyelocytic leukemia, being this vitamin utilized as a very efficient therapeutic agent via effective modulation of the immune function (2) The involvement of vitamin C in the fight against tumor cells via the increase of the number of active NK cells. (3) The stimulation of apoptosis, the suppression of cancer cell proliferation, and delayed tumor development mediated by calcitriol/vitamin D by means of immunity regulation (4) The use of selenium as a cofactor to reach more effective immune response to COVID vaccination (5). The crucial role of cholesterol to regulate the immune function, which is demonstrated to be very sensitive to the variations of this macronutrient concentration. Other important examples are reviewed as well.
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Affiliation(s)
- Camelia Munteanu
- Department of Plant Culture, Faculty of Agriculture, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, Cluj-Napoca, Romania,Camelia Munteanu,
| | - Betty Schwartz
- Robert H. Smith Faculty of Agriculture, Food and Environment, The School of Nutritional Sciences, The Institute of Biochemistry, Food Science and Nutrition, The Hebrew University of Jerusalem, Rehovot, Israel,*Correspondence: Betty Schwartz,
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40
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Belda E, Voland L, Tremaroli V, Falony G, Adriouch S, Assmann KE, Prifti E, Aron-Wisnewsky J, Debédat J, Le Roy T, Nielsen T, Amouyal C, André S, Andreelli F, Blüher M, Chakaroun R, Chilloux J, Coelho LP, Dao MC, Das P, Fellahi S, Forslund S, Galleron N, Hansen TH, Holmes B, Ji B, Krogh Pedersen H, Le P, Le Chatelier E, Lewinter C, Mannerås-Holm L, Marquet F, Myridakis A, Pelloux V, Pons N, Quinquis B, Rouault C, Roume H, Salem JE, Sokolovska N, Søndertoft NB, Touch S, Vieira-Silva S, Galan P, Holst J, Gøtze JP, Køber L, Vestergaard H, Hansen T, Hercberg S, Oppert JM, Nielsen J, Letunic I, Dumas ME, Stumvoll M, Pedersen OB, Bork P, Ehrlich SD, Zucker JD, Bäckhed F, Raes J, Clément K. Impairment of gut microbial biotin metabolism and host biotin status in severe obesity: effect of biotin and prebiotic supplementation on improved metabolism. Gut 2022; 71:2463-2480. [PMID: 35017197 PMCID: PMC9664128 DOI: 10.1136/gutjnl-2021-325753] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 12/15/2021] [Indexed: 01/08/2023]
Abstract
OBJECTIVES Gut microbiota is a key component in obesity and type 2 diabetes, yet mechanisms and metabolites central to this interaction remain unclear. We examined the human gut microbiome's functional composition in healthy metabolic state and the most severe states of obesity and type 2 diabetes within the MetaCardis cohort. We focused on the role of B vitamins and B7/B8 biotin for regulation of host metabolic state, as these vitamins influence both microbial function and host metabolism and inflammation. DESIGN We performed metagenomic analyses in 1545 subjects from the MetaCardis cohorts and different murine experiments, including germ-free and antibiotic treated animals, faecal microbiota transfer, bariatric surgery and supplementation with biotin and prebiotics in mice. RESULTS Severe obesity is associated with an absolute deficiency in bacterial biotin producers and transporters, whose abundances correlate with host metabolic and inflammatory phenotypes. We found suboptimal circulating biotin levels in severe obesity and altered expression of biotin-associated genes in human adipose tissue. In mice, the absence or depletion of gut microbiota by antibiotics confirmed the microbial contribution to host biotin levels. Bariatric surgery, which improves metabolism and inflammation, associates with increased bacterial biotin producers and improved host systemic biotin in humans and mice. Finally, supplementing high-fat diet-fed mice with fructo-oligosaccharides and biotin improves not only the microbiome diversity, but also the potential of bacterial production of biotin and B vitamins, while limiting weight gain and glycaemic deterioration. CONCLUSION Strategies combining biotin and prebiotic supplementation could help prevent the deterioration of metabolic states in severe obesity. TRIAL REGISTRATION NUMBER NCT02059538.
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Affiliation(s)
- Eugeni Belda
- Nutrition and Obesities: Systemic Approaches, NutriOmics, Research Unit, Sorbonne Université, INSERM, Paris, France,Integrative Phenomics, Paris, France
| | - Lise Voland
- Nutrition and Obesities: Systemic Approaches, NutriOmics, Research Unit, Sorbonne Université, INSERM, Paris, France
| | - Valentina Tremaroli
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Sahlgrenska Center for Cardiovascular and Metabolic Research, University of Gothenburg, Goteborg, Sweden
| | - Gwen Falony
- Center for Microbiology, VIB, Leuven, Belgium,Vlaams Instituut voor Biotechnologie, VIB-KU Leuven, Heverlee, Flanders, Belgium
| | - Solia Adriouch
- Nutrition and Obesities: Systemic Approaches, NutriOmics, Research Unit, Sorbonne Université, INSERM, Paris, France
| | - Karen E Assmann
- Nutrition and Obesities: Systemic Approaches, NutriOmics, Research Unit, Sorbonne Université, INSERM, Paris, France
| | - Edi Prifti
- Unité de Modélisation Mathématique et Informatique des Systèmes Complexes, UMMISCO, Sorbonne Université, IRD, Bondy, France
| | - Judith Aron-Wisnewsky
- Nutrition and Obesities: Systemic Approaches, NutriOmics, Research Unit, Sorbonne Université, INSERM, Paris, France,Department of Nutrition, Pitié-Salpêtrière Hospital, Assistance Publique - Hopitaux de Paris, Paris, France
| | - Jean Debédat
- Nutrition and Obesities: Systemic Approaches, NutriOmics, Research Unit, Sorbonne Université, INSERM, Paris, France
| | - Tiphaine Le Roy
- Nutrition and Obesities: Systemic Approaches, NutriOmics, Research Unit, Sorbonne Université, INSERM, Paris, France
| | - Trine Nielsen
- Center for Basic Metabolic Research, Novo Nordisk Foundation, University of Copenhagen, Kobenhavn, Denmark
| | - Chloé Amouyal
- Nutrition and Obesities: Systemic Approaches, NutriOmics, Research Unit, Sorbonne Université, INSERM, Paris, France
| | - Sébastien André
- Nutrition and Obesities: Systemic Approaches, NutriOmics, Research Unit, Sorbonne Université, INSERM, Paris, France
| | - Fabrizio Andreelli
- Nutrition and Obesities: Systemic Approaches, NutriOmics, Research Unit, Sorbonne Université, INSERM, Paris, France
| | - Matthias Blüher
- Medical Department III - Endocrinology, Nephrology, Rheumatology - Medical Center, Faculty of Medicine, University of Leipzig, Leipzig, Germany
| | - Rima Chakaroun
- Medical Department III - Endocrinology, Nephrology, Rheumatology - Medical Center, Faculty of Medicine, University of Leipzig, Leipzig, Germany
| | - Julien Chilloux
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London Faculty of Medicine, London, UK
| | - Luis Pedro Coelho
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Maria Carlota Dao
- Nutrition and Obesities: Systemic Approaches, NutriOmics, Research Unit, Sorbonne Université, INSERM, Paris, France
| | - Promi Das
- Department of Biology, Chalmers University of Technology, Goteborg, Sweden
| | - Soraya Fellahi
- Functional Unit, Biochemistry and Hormonology Department, enon Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France,Saint-Antoine Research Center, Sorbonne Université, INSERM, Paris, France
| | - Sofia Forslund
- Max Delbrück Center for Molecular Medicine, MDC, Berlin-Buch, Germany
| | - Nathalie Galleron
- MetaGenoPolis, Université Paris-Saclay, INRAE, Jouy-en-Josas, France
| | - Tue H Hansen
- Center for Basic Metabolic Research, Novo Nordisk Foundation, University of Copenhagen, Kobenhavn, Denmark
| | - Bridget Holmes
- Centre Daniel Carasso, Global Nutrition Department, Danone Nutricia Research, Palaiseau, France
| | - Boyang Ji
- Department of Biology, Chalmers University of Technology, Goteborg, Sweden
| | - Helle Krogh Pedersen
- Center for Basic Metabolic Research, Novo Nordisk Foundation, University of Copenhagen, Kobenhavn, Denmark
| | - Phuong Le
- Nutrition and Obesities: Systemic Approaches, NutriOmics, Research Unit, Sorbonne Université, INSERM, Paris, France
| | | | | | - Louise Mannerås-Holm
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Sahlgrenska Center for Cardiovascular and Metabolic Research, University of Gothenburg, Goteborg, Sweden
| | - Florian Marquet
- Nutrition and Obesities: Systemic Approaches, NutriOmics, Research Unit, Sorbonne Université, INSERM, Paris, France
| | - Antonis Myridakis
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Veronique Pelloux
- Nutrition and Obesities: Systemic Approaches, NutriOmics, Research Unit, Sorbonne Université, INSERM, Paris, France
| | - Nicolas Pons
- MetaGenoPolis, Université Paris-Saclay, INRAE, Jouy-en-Josas, France
| | - Benoit Quinquis
- MetaGenoPolis, Université Paris-Saclay, INRAE, Jouy-en-Josas, France
| | - Christine Rouault
- Nutrition and Obesities: Systemic Approaches, NutriOmics, Research Unit, Sorbonne Université, INSERM, Paris, France
| | - Hugo Roume
- MetaGenoPolis, Université Paris-Saclay, INRAE, Jouy-en-Josas, France
| | - Joe-Elie Salem
- Department of Pharmacology and CIC-1421, Assistance Publique-Hôpitaux de Paris, AP-HP, Pitié-Salpêtrière Hospital, Paris, France
| | - Nataliya Sokolovska
- Nutrition and Obesities: Systemic Approaches, NutriOmics, Research Unit, Sorbonne Université, INSERM, Paris, France
| | - Nadja B Søndertoft
- Center for Basic Metabolic Research, Novo Nordisk Foundation, University of Copenhagen, Kobenhavn, Denmark
| | - Sothea Touch
- Nutrition and Obesities: Systemic Approaches, NutriOmics, Research Unit, Sorbonne Université, INSERM, Paris, France
| | - Sara Vieira-Silva
- Center for Microbiology, VIB, Leuven, Belgium,Vlaams Instituut voor Biotechnologie, VIB-KU Leuven, Heverlee, Flanders, Belgium
| | | | - Pilar Galan
- Nutritional Epidemiology Unit, INSERM, INRAE, CNAM, Paris 13 University, Bobigny, France
| | - Jens Holst
- Center for Basic Metabolic Research, Novo Nordisk Foundation, University of Copenhagen, Kobenhavn, Denmark
| | - Jens Peter Gøtze
- Department of Clinical Biochemistry, Rigshospitalet, Kobenhavn, Denmark
| | - Lars Køber
- Department of Cardiology, Rigshospitalet, Kobenhavn, Denmark
| | - Henrik Vestergaard
- Center for Basic Metabolic Research, Novo Nordisk Foundation, University of Copenhagen, Kobenhavn, Denmark,Steno Diabetes Center, Copenhagen, Gentofte, Denmark
| | - Torben Hansen
- Center for Basic Metabolic Research, Novo Nordisk Foundation, University of Copenhagen, Kobenhavn, Denmark,Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | - Serge Hercberg
- Nutritional Epidemiology Unit, INSERM, INRAE, CNAM, Paris 13 University, Bobigny, France
| | - Jean-Michel Oppert
- Department of Nutrition, Pitié-Salpêtrière Hospital, Assistance Publique - Hopitaux de Paris, Paris, France
| | - Jens Nielsen
- Department of Biology, Chalmers University of Technology, Goteborg, Sweden
| | | | - Marc-Emmanuel Dumas
- Department of Surgery and Cancer, Section of Computational and Systems Medicine, Imperial College London, London, UK,National Heart & Lung Institute, Section of Genomic & Environmental Medicine, Imperial College London, London, UK
| | - Michael Stumvoll
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München, University of Leipzig Faculty of Medicine, Leipzig, Germany
| | - Oluf Borbye Pedersen
- Center for Basic Metabolic Research, Novo Nordisk Foundation, University of Copenhagen, Kobenhavn, Denmark
| | - Peer Bork
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Stanislav Dusko Ehrlich
- MetaGenoPolis, Université Paris-Saclay, INRAE, Jouy-en-Josas, France,Center for Host Microbiome Interactions, King's College London Dental Institute, London, UK
| | - Jean-Daniel Zucker
- Nutrition and Obesities: Systemic Approaches, NutriOmics, Research Unit, Sorbonne Université, INSERM, Paris, France,Unité de Modélisation Mathématique et Informatique des Systèmes Complexes, UMMISCO, Sorbonne Université, IRD, Bondy, France
| | - Fredrik Bäckhed
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Sahlgrenska Center for Cardiovascular and Metabolic Research, University of Gothenburg, Goteborg, Sweden
| | - Jeroen Raes
- Center for Microbiology, VIB, Leuven, Belgium,Vlaams Instituut voor Biotechnologie, VIB-KU Leuven, Heverlee, Flanders, Belgium
| | - Karine Clément
- Nutrition and Obesities: Systemic Approaches, NutriOmics, Research Unit, Sorbonne Université, INSERM, Paris, France .,Department of Nutrition, Pitié-Salpêtrière Hospital, Assistance Publique - Hopitaux de Paris, Paris, France
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41
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Kundra P, Geirnaert A, Pugin B, Morales Martinez P, Lacroix C, Greppi A. Healthy adult gut microbiota sustains its own vitamin B12 requirement in an in vitro batch fermentation model. Front Nutr 2022; 9:1070155. [PMID: 36532531 PMCID: PMC9751363 DOI: 10.3389/fnut.2022.1070155] [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: 10/14/2022] [Accepted: 11/14/2022] [Indexed: 12/05/2023] Open
Abstract
Vitamin B12 (cobalamin) is present in the human lower gastrointestinal tract either coming from the unabsorbed dietary fraction or from in situ production of the gut microbiota. However, it is unclear whether the gut microbial communities need exogenous B12 for growth and metabolism, or whether B12 in low and high levels could affect gut community composition and metabolite production. Here, we investigated in vitro B12 production of human fecal microbiota and the effects of different levels of B12 (as cyanocobalamin) on composition and activity. Eight fecal communities from healthy human adults distributed over three enterotypes, dominated by Firmicutes (n = 5), Bacteroides (n = 1) or Prevotella (n = 2) were used to perform batch fermentations in Macfarlane medium supplemented with low B12 medium (Control, 5 ng/ml, within the tested fecal range), no B12 addition (NB12), and high B12 addition (ExtraB12, 2500 ng/ml). The microbiota community composition (qPCR, 16S rRNA metabarcoding), metabolic activity (HPLC-RI), and B12 levels (UHPLC-DAD) were measured after 24 h incubation at 37°C under strict anaerobic conditions. All fecal microbial communities produced B12 in the NB12 condition after 24 h, in the range from 152 ± 4 to 564 ± 25 ng/ml. None of the B12 treatments had an impact on total bacterial growth, community richness, diversity and total metabolite production, compared to the low B12 control. However, a significant increase of propionate was measured in ExtraB12 compared to NB12. Most taxonomic and metabolite changes compared to control incubations were donor-dependent, implying donor-microbiota-specific changes upon B12 treatments. Our in vitro data suggest that healthy human adult gut microbial communities have the capacity to produce B12 at levels fulfilling their own requirements, independently of the initial B12 content tested in the donor's feces. Further, supplementation of exogenous dietary B12 may have limited impact on the healthy human gut microbial community composition and function.
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Affiliation(s)
| | | | | | | | | | - Anna Greppi
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zürich, Zurich, Switzerland
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42
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Ryback B, Bortfeld-Miller M, Vorholt JA. Metabolic adaptation to vitamin auxotrophy by leaf-associated bacteria. THE ISME JOURNAL 2022; 16:2712-2724. [PMID: 35987782 PMCID: PMC9666465 DOI: 10.1038/s41396-022-01303-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 07/13/2022] [Accepted: 07/25/2022] [Indexed: 12/15/2022]
Abstract
Auxotrophs are unable to synthesize all the metabolites essential for their metabolism and rely on others to provide them. They have been intensively studied in laboratory-generated and -evolved mutants, but emergent adaptation mechanisms to auxotrophy have not been systematically addressed. Here, we investigated auxotrophies in bacteria isolated from Arabidopsis thaliana leaves and found that up to half of the strains have auxotrophic requirements for biotin, niacin, pantothenate and/or thiamine. We then explored the genetic basis of auxotrophy as well as traits that co-occurred with vitamin auxotrophy. We found that auxotrophic strains generally stored coenzymes with the capacity to grow exponentially for 1-3 doublings without vitamin supplementation; however, the highest observed storage was for biotin, which allowed for 9 doublings in one strain. In co-culture experiments, we demonstrated vitamin supply to auxotrophs, and found that auxotrophic strains maintained higher species richness than prototrophs upon external supplementation with vitamins. Extension of a consumer-resource model predicted that auxotrophs can utilize carbon compounds provided by other organisms, suggesting that auxotrophic strains benefit from metabolic by-products beyond vitamins.
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Affiliation(s)
- Birgitta Ryback
- grid.5801.c0000 0001 2156 2780Institute of Microbiology, ETH Zurich, 8093 Zurich, Switzerland
| | - Miriam Bortfeld-Miller
- grid.5801.c0000 0001 2156 2780Institute of Microbiology, ETH Zurich, 8093 Zurich, Switzerland
| | - Julia A. Vorholt
- grid.5801.c0000 0001 2156 2780Institute of Microbiology, ETH Zurich, 8093 Zurich, Switzerland
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43
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Larsen PE, Dai Y. Modeling interaction networks between host, diet, and bacteria predicts obesogenesis in a mouse model. Front Mol Biosci 2022; 9:1059094. [DOI: 10.3389/fmolb.2022.1059094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 10/31/2022] [Indexed: 11/17/2022] Open
Abstract
Host-microbiome interactions are known to have substantial effects on human health, but the diversity of the human microbiome makes it difficult to definitively attribute specific microbiome features to a host phenotype. One approach to overcoming this challenge is to use animal models of host-microbiome interaction, but it must be determined that relevant aspects of host-microbiome interactions are reflected in the animal model. One such experimental validation is an experiment by Ridura et al. In that experiment, transplanting a microbiome from a human into a mouse also conferred the human donor’s obesity phenotype. We have aggregated a collection of previously published host-microbiome mouse-model experiments and combined it with thousands of sequenced and annotated bacterial genomes and metametabolomic pathways. Three computational models were generated, each model reflecting an aspect of host-microbiome interactions: 1) Predict the change in microbiome community structure in response to host diet using a community interaction network, 2) Predict metagenomic data from microbiome community structure, and 3) Predict host obesogenesis from modeled microbiome metagenomic data. These computationally validated models were combined into an integrated model of host-microbiome-diet interactions and used to replicate the Ridura experiment in silico. The results of the computational models indicate that network-based models are significantly more predictive than similar but non-network-based models. Network-based models also provide additional insight into the molecular mechanisms of host-microbiome interaction by highlighting metabolites and metabolic pathways proposed to be associated with microbiome-based obesogenesis. While the models generated in this study are likely too specific to the animal models and experimental conditions used to train our models to be of general utility in a broader understanding of obesogenesis, the approach detailed here is expected to be a powerful tool of investigating multiple types of host-microbiome interactions.
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44
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Shift of Choline/Betaine Pathway in Recombinant Pseudomonas for Cobalamin Biosynthesis and Abiotic Stress Protection. Int J Mol Sci 2022; 23:ijms232213934. [PMID: 36430408 PMCID: PMC9699165 DOI: 10.3390/ijms232213934] [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: 10/16/2022] [Revised: 11/04/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
The B12-producing strains Pseudomonas nitroreducens DSM 1650 and Pseudomonas sp. CCUG 2519 (both formerly Pseudomonas denitrificans), with the most distributed pathway among bacteria for exogenous choline/betaine utilization, are promising recombinant hosts for the endogenous production of B12 precursor betaine by direct methylation of bioavailable glycine or non-proteinogenic β-alanine. Two plasmid-based de novo betaine pathways, distinguished by their enzymes, have provided an expression of the genes encoding for N-methyltransferases of the halotolerant cyanobacterium Aphanothece halophytica or plant Limonium latifolium to synthesize the internal glycine betaine or β-alanine betaine, respectively. These betaines equally allowed the recombinant pseudomonads to grow effectively and to synthesize a high level of cobalamin, as well as to increase their protective properties against abiotic stresses to a degree comparable with the supplementation of an exogenous betaine. Both de novo betaine pathways significantly enforced the protection of bacterial cells against lowering temperature to 15 °C and increasing salinity to 400 mM of NaCl. However, the expression of the single plant-derived gene for the β-alanine-specific N-methyltransferase additionally increased the effectiveness of exogenous glycine betaine almost twofold on cobalamin biosynthesis, probably due to the Pseudomonas' ability to use two independent pathways, their own choline/betaine pathway and the plant β-alanine betaine biosynthetic pathway.
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Abstract
The skin microbiome is a key player in human health, with diverse functions ranging from defense against pathogens to education of the immune system. While recent studies have begun to shed light on the valuable role that skin microorganisms have in maintaining the skin barrier, a detailed understanding of the complex interactions that shape healthy skin microbial communities is limited. Cobamides, the vitamin B12 class of cofactor, are essential for organisms across the tree of life. Because this vitamin is only produced by a limited fraction of prokaryotes, cobamide sharing is predicted to mediate community dynamics within microbial communities. Here, we provide the first large-scale metagenomic assessment of cobamide biosynthesis and utilization in the skin microbiome. We show that while numerous and diverse taxa across the major bacterial phyla on the skin encode cobamide-dependent enzymes, relatively few species encode de novo cobamide biosynthesis. We show that cobamide producers and users are integrated into the network structure of microbial communities across the different microenvironments of the skin and that changes in microbiome community structure and diversity are associated with the abundance of cobamide producers in the Corynebacterium genus, for both healthy and diseased skin states. Finally, we find that de novo cobamide biosynthesis is enriched only in Corynebacterium species associated with hosts, including those prevalent on human skin. We confirm that the cofactor is produced in excess through quantification of cobamide production by human skin-associated species isolated in the laboratory. Taken together, our results reveal the potential for cobamide sharing within skin microbial communities, which we hypothesize mediates microbiome community dynamics and host interactions. IMPORTANCE The skin microbiome is essential for maintaining skin health and function. However, the microbial interactions that dictate microbiome structure, stability, and function are not well understood. Here, we investigate the biosynthesis and use of cobamides, a cofactor needed by many organisms but only produced by select prokaryotes, within the human skin microbiome. We found that while a large proportion of skin taxa encode cobamide-dependent enzymes, only a select few encode de novo cobamide biosynthesis. Further, the abundance of cobamide-producing Corynebacterium species is associated with skin microbiome diversity and structure, and within this genus, de novo biosynthesis is enriched in host-associated species compared to environment-associated species. These findings identify cobamides as a potential mediator of skin microbiome dynamics and skin health.
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Zhan Q, Wang R, Thakur K, Feng JY, Zhu YY, Zhang JG, Wei ZJ. Unveiling of dietary and gut-microbiota derived B vitamins: Metabolism patterns and their synergistic functions in gut-brain homeostasis. Crit Rev Food Sci Nutr 2022; 64:4046-4058. [PMID: 36271691 DOI: 10.1080/10408398.2022.2138263] [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] [Indexed: 11/03/2022]
Abstract
Nutrition-gut cross-talk holds a vital position in sustaining intestinal function, and micronutrient metabolism has emerged as the foremost metabolic pathway to preserve gut homeostasis. Among micronutrients, B vitamins have evolved prior to DNA/RNA and are known for their vital roles for major evolutionary transitions in extant organisms. Despite their universal requirement and critical role, not all the three domains of life are endowed with a natural ability for de novo B vitamins synthesis. The human gut microbiome constitutes prototrophs and auxotroph which are entirely dependent on dietary intake and gut microbial production of B vitamins. The syntrophic metabolism involving cross-feeding of B vitamins and community-wide exchange between commensal bacteria elicit important changes in the diversity and composition of the human gut microbiome. Hereto, we discuss the B-vitamins sharing among prototrophic and auxotrophic gut bacteria, their absorption in small intestine and transport in distal gut, functional role in relation to the gut homeostasis and symptoms linked to their deficiency. We also briefly explore their potential involvement as psychobiotics in brain energetic metabolism (kynurenines/tryptophan pathway) for neurological functions and highlight their deficiency related malfunctioning.
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Affiliation(s)
- Qi Zhan
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, People's Republic of China
| | - Rui Wang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, People's Republic of China
| | - Kiran Thakur
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, People's Republic of China
- Ningxia Key Laboratory for the Development and Application of Microbial Resources in Extreme Environments, School of Biological Science and Engineering, North Minzu University, Yinchuan, People's Republic of China
| | - Jing-Yu Feng
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, People's Republic of China
| | - Yun-Yang Zhu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, People's Republic of China
| | - Jian-Guo Zhang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, People's Republic of China
- Ningxia Key Laboratory for the Development and Application of Microbial Resources in Extreme Environments, School of Biological Science and Engineering, North Minzu University, Yinchuan, People's Republic of China
| | - Zhao-Jun Wei
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, People's Republic of China
- Ningxia Key Laboratory for the Development and Application of Microbial Resources in Extreme Environments, School of Biological Science and Engineering, North Minzu University, Yinchuan, People's Republic of China
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Exploring Bacterial Attributes That Underpin Symbiont Life in the Monogastric Gut. Appl Environ Microbiol 2022; 88:e0112822. [PMID: 36036591 PMCID: PMC9499014 DOI: 10.1128/aem.01128-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The large bowel of monogastric animals, such as that of humans, is home to a microbial community (microbiota) composed of a diversity of mostly bacterial species. Interrelationships between the microbiota as an entity and the host are complex and lifelong and are characteristic of a symbiosis. The relationships may be disrupted in association with disease, resulting in dysbiosis. Modifications to the microbiota to correct dysbiosis require knowledge of the fundamental mechanisms by which symbionts inhabit the gut. This review aims to summarize aspects of niche fitness of bacterial species that inhabit the monogastric gut, especially of humans, and to indicate the research path by which progress can be made in exploring bacterial attributes that underpin symbiont life in the gut.
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48
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Wienhausen G, Bruns S, Sultana S, Dlugosch L, Groon LA, Wilkes H, Simon M. The overlooked role of a biotin precursor for marine bacteria - desthiobiotin as an escape route for biotin auxotrophy. THE ISME JOURNAL 2022; 16:2599-2609. [PMID: 35963899 PMCID: PMC9561691 DOI: 10.1038/s41396-022-01304-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 07/19/2022] [Accepted: 07/28/2022] [Indexed: 11/30/2022]
Abstract
Biotin (vitamin B7) is involved in a wide range of essential biochemical reactions and a crucial micronutrient that is vital for many pro- and eukaryotic organisms. The few biotin measurements in the world’s oceans show that availability is subject to strong fluctuations. Numerous marine microorganisms exhibit biotin auxotrophy and therefore rely on supply by other organisms. Desthiobiotin is the primary precursor of biotin and has recently been detected at concentrations similar to biotin in seawater. The last enzymatic reaction in the biotin biosynthetic pathway converts desthiobiotin to biotin via the biotin synthase (BioB). The role of desthiobiotin as a precursor of biotin synthesis in microbial systems, however, is largely unknown. Here we demonstrate experimentally that bacteria can overcome biotin auxotrophy if they retain the bioB gene and desthiobiotin is available. A genomic search of 1068 bacteria predicts that the biotin biosynthetic potential varies greatly among different phylogenetic groups and that 20% encode solely bioB and thus can potentially overcome biotin auxotrophy. Many Actino- and Alphaproteobacteria cannot synthesize biotin de novo, but some possess solely bioB, whereas the vast majority of Gammaproteobacteria and Flavobacteriia exhibit the last four crucial biotin synthesis genes. We detected high intra- and extracellular concentrations of the precursor relative to biotin in the prototrophic bacterium, Vibrio campbellii, with extracellular desthiobiotin reaching up to 1.09 ± 0.15*106 molecules per cell during exponential growth. Our results provide evidence for the ecological role of desthiobiotin as an escape route to overcome biotin auxotrophy for bacteria in the ocean and presumably in other ecosystems.
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49
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Frolova MS, Suvorova IA, Iablokov SN, Petrov SN, Rodionov DA. Genomic reconstruction of short-chain fatty acid production by the human gut microbiota. Front Mol Biosci 2022; 9:949563. [PMID: 36032669 PMCID: PMC9403272 DOI: 10.3389/fmolb.2022.949563] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 07/19/2022] [Indexed: 12/04/2022] Open
Abstract
Short-chain fatty acids (SCFAs) including acetate, formate, propionate, and butyrate are the end products of dietary fiber and host glycan fermentation by the human gut microbiota (HGM). SCFAs produced in the column are of utmost importance for host physiology and health. Butyrate and propionate improve gut health and play a key role in the neuroendocrine and immune systems. Prediction of HGM metabolic potential is important for understanding the influence of diet and HGM-produced metabolites on human health. We conducted a detailed metabolic reconstruction of pathways for the synthesis of SCFAs and L- and D-lactate, as additional fermentation products, in a reference set of 2,856 bacterial genomes representing strains of >800 known HGM species. The reconstructed butyrate and propionate pathways included four and three pathway variants, respectively, that start from different metabolic precursors. Altogether, we identified 48 metabolic enzymes, including five alternative enzymes in propionate pathways, and propagated their occurrences across all studied genomes. We established genomic signatures for reconstructed pathways and classified genomes according to their simplified binary phenotypes encoding the ability (“1”) or inability (“0”) of a given organism to produce SCFAs. The resulting binary phenotypes combined into a binary phenotype matrix were used to assess the SCFA synthesis potential of HGM samples from several public metagenomic studies. We report baseline and variance for Community Phenotype Indices calculated for SCFAs production capabilities in 16S metagenomic samples of intestinal microbiota from two large national cohorts (American Gut Project, UK twins), the Hadza hunter-gatherers, and the young children cohort of infants with high-risk for type 1 diabetes. We further linked the predicted SCFA metabolic capabilities with available SCFA concentrations both for in vivo fecal samples and in vitro fermentation samples from previous studies. Finally, we analyzed differential representation of individual SCFA pathway genes across several WGS metagenomic datasets. The obtained collection of SCFA pathway genes and phenotypes enables the predictive metabolic phenotype profiling of HGM datasets and enhances the in silico methodology to study cross-feeding interactions in the gut microbiomes.
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Affiliation(s)
- Maria S. Frolova
- Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino, Russia
| | - Inna A. Suvorova
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Stanislav N. Iablokov
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Sergei N. Petrov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Dmitry A. Rodionov
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
- *Correspondence: Dmitry A. Rodionov,
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50
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Madigan KE, Bundy R, Weinberg RB. Distinctive Clinical Correlates of Small Intestinal Bacterial Overgrowth with Methanogens. Clin Gastroenterol Hepatol 2022; 20:1598-1605.e2. [PMID: 34597730 DOI: 10.1016/j.cgh.2021.09.035] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/13/2021] [Accepted: 09/22/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND AND AIMS Most patients with small intestinal bacterial overgrowth (SIBO) produce hydrogen by fermentation of dietary carbohydrates; however, ∼30% of patients with SIBO are colonized with Archaea, anaerobic organisms that produce methane. SIBO is associated with a plethora of symptoms and conditions, but their diagnostic significance is unclear. We aimed to determine if specific symptoms and conditions are associated with methanogenic SIBO. METHODS This study received institutional review board approval (IRB00059873). In this retrospective cross-sectional study, we queried a database of glucose breath tests conducted for suspected SIBO at our tertiary care medical center, which included data on the presence or absence of gastrointestinal symptoms and conditions often associated with SIBO. All patients had undergone a standardized breath testing protocol. RESULTS In a cohort of 1461 patients, 33.1% were SIBO positive; of these, 49.8% produced only hydrogen, 38.8% produced only methane, and 11.4% produced both gases. The following factors distinguished patients with hydrogen-producing SIBO, but not methanogenic SIBO, from SIBO-negative patients: vitamin B12 deficiency (odds ratio, 1.44; confidence interval [CI], 1.01-2.06; P = .046), Roux-en-Y gastric bypass (odds ratio, 2.14; CI, 1.09-4.18; P = .027), cholecystectomy (odds ratio, 1.42; CI, 1.06-1.91; P = .020), and diabetes (odds ratio, 1.59; CI, 1.13-2.24; P = .008). The absence of vitamin B12 deficiency was the sole discriminating factor between methanogenic and hydrogenic SIBO (odds ratio, 0.57; CI, 0.34-0.97; P = .038). CONCLUSIONS Patients with SIBO caused by methane-producing Archaea display a different spectrum of associated symptoms and clinical conditions compared with patients with SIBO caused by hydrogen-producing bacteria, particularly a lower incidence of vitamin B12 deficiency.
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Affiliation(s)
- Katelyn E Madigan
- Department of Internal Medicine, Wake Forest School of Medicine, Winston Salem, North Carolina
| | - Richa Bundy
- Department of Internal Medicine, Wake Forest School of Medicine, Winston Salem, North Carolina
| | - Richard B Weinberg
- Department of Internal Medicine-Gastroenterology, Wake Forest School of Medicine, Winston Salem, North Carolina; Department of Physiology & Pharmacology, Wake Forest School of Medicine, Winston Salem, North Carolina.
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