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Du W, Lu L, Liu Y, Yan Y, La R, Wu Q, Xu J, Zhou X. The association between dietary vitamin B1 intake and constipation: a population-based study. BMC Gastroenterol 2024; 24:171. [PMID: 38760704 PMCID: PMC11100033 DOI: 10.1186/s12876-024-03255-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 05/03/2024] [Indexed: 05/19/2024] Open
Abstract
BACKGROUND Numerous researches have indicated a correlation between the intake of dietary micronutrients and the occurrence of constipation. Nevertheless, the correlation between constipation and vitamin B1 remains uninvestigated. The main aim of this research was to examine the association between chronic constipation and the consumption of vitamin B1 in the diet among adult participants of the National Health and Nutrition Examination Survey (NHANES). METHODS This study used data from the NHANES, a survey on health and nutrition conducted between 2005 and 2010. The respondents' dietary information was gathered by utilizing the 24-hour dietary records. Various statistical analyses, such as multiple logistic regression, subgroup analysis, and curve-fitting analysis, were employed to investigate the correlation between dietary intake of vitamin B1 and chronic constipation. RESULTS In the trial, there were 10,371 participants, out of which 1,123 individuals (10.8%) were identified as having chronic constipation. Fully adjusted multiple logistic regression analyses showed that increasing dietary intake of vitamin B1 (OR = 0.87, 95% CI: 0.77-0.99) was significantly associated with a reduced risk of constipation. Following adjustment for multiple variables in Model 3, the odds ratio (OR) and 95% confidence interval (CI) for the third tertile, in comparison to the first tertile (reference group), was 0.80 (0.65, 0.99). In addition, subgroup analyses and interaction tests showed a significant inverse association between vitamin B1 intake and the prevalence of constipation, especially among men, non-hypertensive, and non-diabetic individuals (all P-values less than 0.05). CONCLUSION This research uncovered an inverse correlation between the consumption of vitamin B1 in the diet and the occurrence of chronic constipation. One potential explanation for this phenomenon is that the consumption of vitamin B1 in one's diet is linked to the softening of stools and an augmented occurrence of colonic peristalsis. Additional extensive prospective research is required to thoroughly examine the significance of thiamine in long-term constipation.
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Affiliation(s)
- Wenyi Du
- The Affiliated Stomatological Hospital of Soochow University, Suzhou Stomatological Hospital, Suzhou, Jiangsu, China
- Department of General Surgery, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi Medical Center, Wuxi, Jiangsu, China
| | - Lingchen Lu
- Department of Pediatric Surgery, Maternal and Child Health Care Hospital of Kunshan, Suzhou, Jiangsu, China
| | - Yuxuan Liu
- The Affiliated Stomatological Hospital of Soochow University, Suzhou Stomatological Hospital, Suzhou, Jiangsu, China
| | - Yuxin Yan
- Department of Orthopedic Surgery, The First Affiliated Hospital of Soochow University, Institute of Orthopedics at Soochow University, Suzhou, Jiangsu, China
| | - Rui La
- Department of Orthopedic Surgery, The First Affiliated Hospital of Soochow University, Institute of Orthopedics at Soochow University, Suzhou, Jiangsu, China
| | - Qian Wu
- Department of Orthopedic Surgery, The First Affiliated Hospital of Soochow University, Institute of Orthopedics at Soochow University, Suzhou, Jiangsu, China.
- Research Institute of Clinical Medicine, Jeonbuk National University Medical School, Jeonju, Korea.
| | - Jie Xu
- The Affiliated Stomatological Hospital of Soochow University, Suzhou Stomatological Hospital, Suzhou, Jiangsu, China.
| | - Xiaojun Zhou
- The Affiliated Stomatological Hospital of Soochow University, Suzhou Stomatological Hospital, Suzhou, Jiangsu, China.
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2
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Odriozola A, González A, Odriozola I, Álvarez-Herms J, Corbi F. Microbiome-based precision nutrition: Prebiotics, probiotics and postbiotics. ADVANCES IN GENETICS 2024; 111:237-310. [PMID: 38908901 DOI: 10.1016/bs.adgen.2024.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/24/2024]
Abstract
Microorganisms have been used in nutrition and medicine for thousands of years worldwide, long before humanity knew of their existence. It is now known that the gut microbiota plays a key role in regulating inflammatory, metabolic, immune and neurobiological processes. This text discusses the importance of microbiota-based precision nutrition in gut permeability, as well as the main advances and current limitations of traditional probiotics, new-generation probiotics, psychobiotic probiotics with an effect on emotional health, probiotic foods, prebiotics, and postbiotics such as short-chain fatty acids, neurotransmitters and vitamins. The aim is to provide a theoretical context built on current scientific evidence for the practical application of microbiota-based precision nutrition in specific health fields and in improving health, quality of life and physiological performance.
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Affiliation(s)
- Adrián Odriozola
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain.
| | - Adriana González
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Iñaki Odriozola
- Health Department of Basque Government, Donostia-San Sebastián, Spain
| | - Jesús Álvarez-Herms
- Phymo® Lab, Physiology, and Molecular Laboratory, Collado Hermoso, Segovia, Spain
| | - Francesc Corbi
- Institut Nacional d'Educació Física de Catalunya (INEFC), Centre de Lleida, Universitat de Lleida (UdL), Lleida, Spain
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3
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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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4
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Jotshi A, Sukla KK, Haque MM, Bose C, Varma B, Koppiker CB, Joshi S, Mishra R. Exploring the human microbiome - A step forward for precision medicine in breast cancer. Cancer Rep (Hoboken) 2023; 6:e1877. [PMID: 37539732 PMCID: PMC10644338 DOI: 10.1002/cnr2.1877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 06/24/2023] [Accepted: 07/22/2023] [Indexed: 08/05/2023] Open
Abstract
BACKGROUND The second most frequent cancer in the world and the most common malignancy in women is breast cancer. Breast cancer is a significant health concern in India with a high mortality-to-incidence ratio and presentation at a younger age. RECENT FINDINGS Recent studies have identified gut microbiota as a significant factor that can have an influence on the development, treatment, and prognosis of breast cancer. This review article aims to describe the influence of microbial dysbiosis on breast cancer occurrence and the possible interactions between oncobiome and specific breast cancer molecular subtypes. The review further also discusses the role of epigenetics and diet/nutrition in the regulation of the gut and breast microbiome and its association with breast cancer prevention, therapy, and recurrence. Additionally, the recent technological advances in microbiome research, including next-generation sequencing (NGS) technologies, genome sequencing, single-cell sequencing, and microbial metabolomics along with recent advances in artificial intelligence (AI) have also been reviewed. This is an attempt to present a comprehensive status of the microbiome as a key cancer biomarker. CONCLUSION We believe that correlating microbiome and carcinogenesis is important as it can provide insights into the mechanisms by which microbial dysbiosis can influence cancer development and progression, leading to the potential use of the microbiome as a tool for prognostication and personalized therapy.
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Affiliation(s)
- Asmita Jotshi
- Centre for Translational Cancer Research: A Joint Initiative of Indian Institute of Science Education and Research (IISER) Pune and Prashanti Cancer Care Mission (PCCM)PuneIndia
| | | | | | - Chandrani Bose
- Life Sciences R&D, TCS Research, Tata Consultancy Services LimitedPuneIndia
| | - Binuja Varma
- TCS Genomics Lab, Tata Consultancy Services LimitedNew DelhiIndia
| | - C. B. Koppiker
- Centre for Translational Cancer Research: A Joint Initiative of Indian Institute of Science Education and Research (IISER) Pune and Prashanti Cancer Care Mission (PCCM)PuneIndia
- Prashanti Cancer Care Mission, Pune, India and Orchids Breast Health Centre, a PCCM initiativePuneIndia
| | - Sneha Joshi
- Centre for Translational Cancer Research: A Joint Initiative of Indian Institute of Science Education and Research (IISER) Pune and Prashanti Cancer Care Mission (PCCM)PuneIndia
| | - Rupa Mishra
- Centre for Translational Cancer Research: A Joint Initiative of Indian Institute of Science Education and Research (IISER) Pune and Prashanti Cancer Care Mission (PCCM)PuneIndia
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5
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Zhang Y, Gan Y, Bao H, Wang R. Perturbations of gut microbiome and metabolome of pigs infected with Mycoplasma hyorhinis. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2023; 103:6219-6232. [PMID: 37145100 DOI: 10.1002/jsfa.12690] [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: 09/01/2022] [Revised: 04/25/2023] [Accepted: 05/02/2023] [Indexed: 05/06/2023]
Abstract
BACKGROUND Mycoplasma hyorhinis is a prevalent respiratory pathogen in swine, causing significant economic loss to pig producers. There is growing evidence that respiratory pathogen infections have a large impact on intestinal microecology. To study the effect of M. hyorhinis infection on gut microbial composition and metabolome profile, pigs were infected with M. hyorhinis. Metagenomic sequencing analysis was performed of fecal samples and a liquid chromatography/tandem mass spectrometry (LC-MS/MS) analysis of gut digesta was made. RESULTS Pigs infected with M. hyorhinis had enriched Sutterella and Mailhella, and depleted Dechloromonas, Succinatimonas, Campylobacter, Blastocystis, Treponema, and Megasphaera. The pigs infected with M. hyorhinis also had greater abundances of bacterium_0_1xD8_71, Ruminococcus_sp__CAG_353, Firmicutes_bacterium_CAG_194, Firmicutes_bacterium_CAG_534, bacterium_1xD42_87, and lower abundances of Chlamydia_suis, Megasphaera_elsdenii, Treponema_porcinum, Bacteroides_sp__CAG_1060, Faecalibacterium_prausnitzii. Metabolomic analysis revealed that some lipids and lipid-like molecules increased in the small intestine, whereas most lipids and lipid-like molecule metabolites decreased in the large intestine. These altered metabolites induce changes in intestinal sphingolipid metabolism, amino acid metabolism, and thiamine metabolism. CONCLUSION These findings demonstrate that infection with M. hyorhinis can alter the gut microbial composition and metabolite structure in pigs, which may further affect amino acid metabolism and lipid metabolism in the intestine. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Yingying Zhang
- Institute of Food Safety and Nutrition, Key Lab of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Yuan Gan
- Key Laboratory for Veterinary Bio-Product Engineering, Ministry of Agriculture and Rural Affairs, Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Hongduo Bao
- Institute of Food Safety and Nutrition, Key Lab of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Ran Wang
- Institute of Food Safety and Nutrition, Key Lab of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, Jiangsu Academy of Agricultural Sciences, Nanjing, China
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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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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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Abstract
Microbial communities are shaped by positive and negative interactions ranging from competition to mutualism. In the context of the mammalian gut and its microbial inhabitants, the integrated output of the community has important impacts on host health. Cross-feeding, the sharing of metabolites between different microbes, has emergent roles in establishing communities of gut commensals that are stable, resistant to invasion, and resilient to external perturbation. In this review, we first explore the ecological and evolutionary implications of cross-feeding as a cooperative interaction. We then survey mechanisms of cross-feeding across trophic levels, from primary fermenters to H2 consumers that scavenge the final metabolic outputs of the trophic network. We extend this analysis to also include amino acid, vitamin, and cofactor cross-feeding. Throughout, we highlight evidence for the impact of these interactions on each species' fitness as well as host health. Understanding cross-feeding illuminates an important aspect of microbe-microbe and host-microbe interactions that establishes and shapes our gut communities.
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Affiliation(s)
- Elizabeth J Culp
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT, USA
| | - Andrew L Goodman
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT, USA.
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9
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Lin L, Lai Z, Yang H, Zhang J, Qi W, Xie F, Mao S. Genome-centric investigation of bile acid metabolizing microbiota of dairy cows and associated diet-induced functional implications. THE ISME JOURNAL 2023; 17:172-184. [PMID: 36261508 PMCID: PMC9750977 DOI: 10.1038/s41396-022-01333-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 10/03/2022] [Accepted: 10/07/2022] [Indexed: 11/05/2022]
Abstract
Although the importance of bile acid (BA)-related microbial strains and enzymes is increasingly recognized for monogastric animals, a lack of knowledge about BA metabolism in dairy cows limits functional applications aimed at the targeted modulation of microbe-host interactions for animal production and health. In the present study, 108 content samples from six intestinal regions of dairy cows were used for shotgun metagenomic sequencing. Overall, 372 high-quality metagenome-assembled genomes (MAGs) were involved in BA deconjugation, oxidation, and dehydroxylation pathways. Furthermore, the BA-metabolizing microbiome predominately occurred in the large intestine, resulting in the accumulation of secondary unconjugated BAs. Comparative genomic analysis revealed that the bile salt hydrolase (BSH)-carrying microbial populations managed with the selective environment of the dairy cow intestine by adopting numerous host mucin glycan-degrading abilities. A sequence similarity network analysis classified 439 BSH homologs into 12 clusters and identified different clusters with diverse evolution, taxonomy, signal peptides, and ecological niches. Our omics data further revealed that the strains of Firmicutes bacterium CAG-110 processed the increased abundance of BSHs from Cluster 1, coinciding with the changes in the colon cholic acid concentration after grain introduction, and were intricately related to intestinal inflammation. This study is the first to use a genome-centric approach and whole intestine-targeted metabolomics to reveal microbial BA metabolism and its diet-induced functional implications in dairy cows. These findings provide insight into the manipulation of intestinal microorganisms for improving host health.
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Affiliation(s)
- Limei Lin
- grid.27871.3b0000 0000 9750 7019Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China ,grid.27871.3b0000 0000 9750 7019Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China
| | - Zheng Lai
- grid.27871.3b0000 0000 9750 7019Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China ,grid.27871.3b0000 0000 9750 7019Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China
| | - Huisheng Yang
- grid.27871.3b0000 0000 9750 7019Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China ,grid.27871.3b0000 0000 9750 7019Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China
| | - Jiyou Zhang
- grid.27871.3b0000 0000 9750 7019Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China ,grid.27871.3b0000 0000 9750 7019Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China
| | - Weibiao Qi
- grid.27871.3b0000 0000 9750 7019Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China ,grid.27871.3b0000 0000 9750 7019Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China
| | - Fei Xie
- grid.27871.3b0000 0000 9750 7019Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China ,grid.27871.3b0000 0000 9750 7019Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China
| | - Shengyong Mao
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China. .,Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
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Pearce VH, Groisman EA, Townsend GE. Dietary sugars silence the master regulator of carbohydrate utilization in human gut Bacteroides species. Gut Microbes 2023; 15:2221484. [PMID: 37358144 PMCID: PMC10294740 DOI: 10.1080/19490976.2023.2221484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 05/08/2023] [Indexed: 06/27/2023] Open
Abstract
The mammalian gut microbiota is a critical human health determinant with therapeutic potential for remediation of many diseases. The host diet is a key factor governing the gut microbiota composition by altering nutrient availability and supporting the expansion of distinct microbial populations. Diets rich in simple sugars modify the abundance of microbial subsets, enriching for microbiotas that elicit pathogenic outcomes. We previously demonstrated that diets rich in fructose and glucose can reduce the fitness and abundance of a human gut symbiont, Bacteroides thetaiotaomicron, by silencing the production of a critical intestinal colonization protein, called Roc, via its mRNA leader through an unknown mechanism. We have now determined that dietary sugars silence Roc by reducing the activity of BT4338, a master regulator of carbohydrate utilization. Here, we demonstrate that BT4338 is required for Roc synthesis, and that BT4338 activity is silenced by glucose or fructose. We show that the consequences of glucose and fructose on orthologous transcription factors are conserved across human intestinal Bacteroides species. This work identifies a molecular pathway by which a common dietary additive alters microbial gene expression in the gut that could be harnessed to modulate targeted microbial populations for future therapeutic interventions.
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Affiliation(s)
- Victoria H. Pearce
- Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA, USA
- Penn State Microbiome Center, Pennsylvania State University, State College, PA, USA
- Center for Molecular Carcinogenesis and Toxicology, Pennsylvania State University, State College, PA, USA
| | - Eduardo A. Groisman
- Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Guy E. Townsend
- Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA, USA
- Penn State Microbiome Center, Pennsylvania State University, State College, PA, USA
- Center for Molecular Carcinogenesis and Toxicology, Pennsylvania State University, State College, PA, USA
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11
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Arjes HA, Sun J, Liu H, Nguyen TH, Culver RN, Celis AI, Walton SJ, Vasquez KS, Yu FB, Xue KS, Newton D, Zermeno R, Weglarz M, Deutschbauer A, Huang KC, Shiver AL. Construction and characterization of a genome-scale ordered mutant collection of Bacteroides thetaiotaomicron. BMC Biol 2022; 20:285. [PMID: 36527020 PMCID: PMC9758874 DOI: 10.1186/s12915-022-01481-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 11/24/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Ordered transposon-insertion collections, in which specific transposon-insertion mutants are stored as monocultures in a genome-scale collection, represent a promising tool for genetic dissection of human gut microbiota members. However, publicly available collections are scarce and the construction methodology remains in early stages of development. RESULTS Here, we describe the assembly of a genome-scale ordered collection of transposon-insertion mutants in the model gut anaerobe Bacteroides thetaiotaomicron VPI-5482 that we created as a resource for the research community. We used flow cytometry to sort single cells from a pooled library, located mutants within this initial progenitor collection by applying a pooling strategy with barcode sequencing, and re-arrayed specific mutants to create a condensed collection with single-insertion strains covering >2500 genes. To demonstrate the potential of the condensed collection for phenotypic screening, we analyzed growth dynamics and cell morphology. We identified both growth defects and altered cell shape in mutants disrupting sphingolipid synthesis and thiamine scavenging. Finally, we analyzed the process of assembling the B. theta condensed collection to identify inefficiencies that limited coverage. We demonstrate as part of this analysis that the process of assembling an ordered collection can be accurately modeled using barcode sequencing data. CONCLUSION We expect that utilization of this ordered collection will accelerate research into B. theta physiology and that lessons learned while assembling the collection will inform future efforts to assemble ordered mutant collections for an increasing number of gut microbiota members.
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Affiliation(s)
- Heidi A Arjes
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Jiawei Sun
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Hualan Liu
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Taylor H Nguyen
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Rebecca N Culver
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Arianna I Celis
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Sophie Jean Walton
- Biophysics Training Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Kimberly S Vasquez
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | | | - Katherine S Xue
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Daniel Newton
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Ricardo Zermeno
- Stanford Shared FACS Facility, Center for Molecular and Genetic Medicine, Stanford University, Stanford, CA, USA
| | - Meredith Weglarz
- Stanford Shared FACS Facility, Center for Molecular and Genetic Medicine, Stanford University, Stanford, CA, USA
| | - Adam Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
- Biophysics Training Program, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
| | - Anthony L Shiver
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
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12
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Wan Z, Zheng J, Zhu Z, Sang L, Zhu J, Luo S, Zhao Y, Wang R, Zhang Y, Hao K, Chen L, Du J, Kan J, He H. Intermediate role of gut microbiota in vitamin B nutrition and its influences on human health. Front Nutr 2022; 9:1031502. [PMID: 36583209 PMCID: PMC9792504 DOI: 10.3389/fnut.2022.1031502] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 11/28/2022] [Indexed: 12/14/2022] Open
Abstract
Vitamin B consists of a group of water-soluble micronutrients that are mainly derived from the daily diet. They serve as cofactors, mediating multiple metabolic pathways in humans. As an integrated part of human health, gut microbiota could produce, consume, and even compete for vitamin B with the host. The interplay between gut microbiota and the host might be a crucial factor affecting the absorbing processes of vitamin B. On the other hand, vitamin B supplementation or deficiency might impact the growth of specific bacteria, resulting in changes in the composition and function of gut microbiota. Together, the interplay between vitamin B and gut microbiota might systemically contribute to human health. In this review, we summarized the interactions between vitamin B and gut microbiota and tried to reveal the underlying mechanism so that we can have a better understanding of its role in human health.
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Affiliation(s)
- Zhijie Wan
- Center of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Nanjing, China
| | | | | | - Lan Sang
- Center of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Nanjing, China
| | - Jinwei Zhu
- Center of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Nanjing, China
| | - Shizheng Luo
- Center of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Nanjing, China
| | - Yixin Zhao
- Center of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Nanjing, China
| | - Ruirui Wang
- Center of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Nanjing, China
| | - Yicui Zhang
- Center of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Nanjing, China
| | - Kun Hao
- Center of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Nanjing, China
| | - Liang Chen
- Nutrilite Health Institute, Shanghai, China
| | - Jun Du
- Nutrilite Health Institute, Shanghai, China
| | - Juntao Kan
- Nutrilite Health Institute, Shanghai, China,*Correspondence: Juntao Kan,
| | - Hua He
- Center of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Nanjing, China,Hua He,
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13
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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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14
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de Moraes RCM, Lima GCA, Cardinali CAEF, Gonçalves AC, Portari GV, Guerra-Shinohara EM, Leboucher A, Júnior JD, Kleinridders A, da Silva Torrão A. Benfotiamine protects against hypothalamic dysfunction in a STZ-induced model of neurodegeneration in rats. Life Sci 2022; 306:120841. [PMID: 35907494 DOI: 10.1016/j.lfs.2022.120841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 07/13/2022] [Accepted: 07/22/2022] [Indexed: 10/16/2022]
Abstract
The neurodegeneration of Alzheimer's disease (AD) affects not only brain structures associate with cognition early in the progression of the disease, but other areas such as the hypothalamus, a region involved in the control of metabolism and appetite. In this context, we evaluated the effects of benfotiamine (BFT), a vitamin B1 analog that is being proposed as a therapeutical approach for AD-related cognitive alterations, which were induced by intracerebroventricular injection of streptozotocin (STZ). In addition to the already described effect of STZ on cognition, we show that this drug also causes metabolic changes which are linked to changes in hypothalamic insulin signaling and orexigenic and anorexigenic circuitries, as well as a decreased cellular integrated stress response. As expected, the supplementation with 150 mg/kg of BFT for 30 days increased blood concentrations of thiamine and its phosphate esters. This led to the prevention of body weight and fat loss in STZ-ICV-treated animals. In addition, we also found an improvement in food consumption, despite hypothalamic gene expression linked to anorexia after STZ exposure. Additionally, decreased apoptosis signaling was observed in the hypothalamus. In in vitro experiments, we noticed a high ability of BFT to increase insulin sensitivity in hypothalamic neurons. Furthermore, we also observed that BFT decreases the mitochondrial unfolded stress response damage by preventing the loss of HSP60 and reversed the mitochondria dysfunction caused by STZ. Taken together, these results suggest that benfotiamine treatment is a potential therapeutic approach in the treatment of hypothalamic dysfunction and metabolic disturbances associated with sporadic AD.
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Affiliation(s)
- Ruan Carlos Macêdo de Moraes
- Department of Physiology and Biophysics, Institute of Biomedical Sciences, University of São Paulo, Brazil; Central Regulation of Metabolism, German Institute of Human Nutrition Potsdam-Rehbruecke, Germany.
| | | | | | - Alisson Carvalho Gonçalves
- Federal Institute of Education, Science and Technology Goiano, Urutaí, GO, Brazil; Laboratory of Experimental Nutrition, Institute of Health Sciences, Federal University of Triângulo Mineiro, Brazil
| | - Guilherme Vannucchi Portari
- Laboratory of Experimental Nutrition, Institute of Health Sciences, Federal University of Triângulo Mineiro, Brazil
| | - Elvira Maria Guerra-Shinohara
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Brazil; Faculty of Pharmaceutical Sciences, Food and Nutrition, Federal University of Mato Grosso do Sul, Brazil
| | - Antoine Leboucher
- Central Regulation of Metabolism, German Institute of Human Nutrition Potsdam-Rehbruecke, Germany
| | - José Donato Júnior
- Department of Physiology and Biophysics, Institute of Biomedical Sciences, University of São Paulo, Brazil
| | - André Kleinridders
- Central Regulation of Metabolism, German Institute of Human Nutrition Potsdam-Rehbruecke, Germany; Institute of Nutritional Science, Department of Molecular and Experimental Nutritional Medicine, University of Potsdam, Germany
| | - Andréa da Silva Torrão
- Department of Physiology and Biophysics, Institute of Biomedical Sciences, University of São Paulo, Brazil
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15
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B Vitamins and Their Roles in Gut Health. Microorganisms 2022; 10:microorganisms10061168. [PMID: 35744686 PMCID: PMC9227236 DOI: 10.3390/microorganisms10061168] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/02/2022] [Accepted: 06/04/2022] [Indexed: 02/04/2023] Open
Abstract
B vitamins act as coenzymes in a myriad of cellular reactions. These include energy production, methyl donor generation, neurotransmitter synthesis, and immune functions. Due to the ubiquitous roles of these vitamins, their deficiencies significantly affect the host’s metabolism. Recently, novel roles of B vitamins in the homeostasis of gut microbial ecology and intestinal health continue to be unravelled. This review focuses on the functional roles and biosynthesis of B vitamins and how these vitamins influence the growth and proliferation of the gut microbiota. We have identified the gut bacteria that can produce vitamins, and their biosynthetic mechanisms are presented. The effects of B vitamin deficiencies on intestinal morphology, inflammation, and its effects on intestinal disorders are also discussed.
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16
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Exchange of Vitamin B 1 and Its Biosynthesis Intermediates Shapes the Composition of Synthetic Microbial Cocultures and Reveals Complexities of Nutrient Sharing. J Bacteriol 2022; 204:e0050321. [PMID: 35357164 DOI: 10.1128/jb.00503-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Microbial communities occupy diverse niches in nature, and community members routinely exchange a variety of nutrients among themselves. While large-scale metagenomic and metabolomic studies shed some light on these exchanges, the contribution of individual species and the molecular details of specific interactions are difficult to track. In this study, we follow the exchange of vitamin B1 (thiamin) and its intermediates between microbes within synthetic cocultures of Escherichia coli and Vibrio anguillarum. Thiamin contains two moieties, 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP) and 4-methyl-5-(2-hydroxyethyl)thiazole (THZ), which are synthesized by distinct pathways using enzymes ThiC and ThiG, respectively, and then coupled by ThiE to form thiamin. Even though E. coli ΔthiC, ΔthiE, and ΔthiG mutants are thiamin auxotrophs, we observed that cocultures of ΔthiC-ΔthiE and ΔthiC-ΔthiG mutants are able to grow in a thiamin-deficient medium, whereas the ΔthiE-ΔthiG coculture does not. Further, the exchange of thiamin and its intermediates in V. anguillarum cocultures and in mixed cocultures of V. anguillarum and E. coli revealed that there exist specific patterns for thiamin metabolism and exchange among these microbes. Our findings show that HMP is shared more frequently than THZ, concurrent with previous observations that free HMP and HMP auxotrophy is commonly found in various environments. Furthermore, we observe that the availability of exogenous thiamin in the media affects whether these strains interact with each other or grow independently. These findings collectively underscore the importance of the exchange of essential metabolites as a defining factor in building and modulating synthetic or natural microbial communities. IMPORTANCE Vitamin B1 (thiamin) is an essential nutrient for cellular metabolism. Microorganisms that are unable to synthesize thiamin either fully or in part exogenously obtain it from their environment or via exchanges with other microbial members in their community. In this study, we created synthetic microbial cocultures that rely on sharing thiamin and its biosynthesis intermediates and observed that some of them are preferentially exchanged. We also observed that the coculture composition is dictated by the production and/or availability of thiamin and its intermediates. Our studies with synthetic cocultures provide the molecular basis for understanding thiamin sharing among microorganisms and lay out broad guidelines for setting up synthetic microbial cocultures by using the exchange of an essential metabolite as their foundation.
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17
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Oh S, Hosseindoust A, Ha S, Moturi J, Mun J, Tajudeen H, Kim J. Metabolic Responses of Dietary Fiber during Heat Stress: Effects on Reproductive Performance and Stress Level of Gestating Sows. Metabolites 2022; 12:metabo12040280. [PMID: 35448467 PMCID: PMC9028640 DOI: 10.3390/metabo12040280] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/10/2022] [Accepted: 03/19/2022] [Indexed: 02/07/2023] Open
Abstract
Heat stress is an important issue, and the addition of fiber to the diet is an option in modifying intestinal health. This study evaluated the effect of acid detergent fiber (ADF) levels on reproductive performance, intestinal integrity, and metabolism of gestating sows, and its carry-over effect on the lactation period during heat stress. The diets included 4.3% (Low fiber; LF), 5.4% (Medium fiber; MF), and 6.5% (High fiber; HF) ADF. Sows fed the HF diet showed a lower respiratory rate, hair cortisol concentration, and farrowing duration compared with the LF treatment. The HF diet increased the pyruvate, citrate cycle, glyoxylate, dicarboxylate, and thiamine metabolism compared with the MF. The concentration of acetate and total short-chain fatty acids were increased in the sows fed the HF diet. The gene expression of glucose transporter 3 and glucose transporter 4 was increased in the HF treatment. The gene expression of heat shock protein 70 was decreased in the HF treatment. The HF diet during gestation increased feed intake, constipation index, piglet weight, and litter weight compared with the LF. Sows in the LF treatment showed the greatest digestibility of crude protein and the lowest digestibility of ADF. In conclusion, a 6.5% ADF level is recommended for gestating sows during heat stress.
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Affiliation(s)
- SeungMin Oh
- Gyeongbuk Livestock Research Institute, Yeongju 63052, Korea;
| | - Abdolreza Hosseindoust
- Department of Animal Industry Convergence, Kangwon National University, Chuncheon 24341, Korea; (A.H.); (S.H.); (J.M.); (J.M.); (H.T.)
| | - SangHun Ha
- Department of Animal Industry Convergence, Kangwon National University, Chuncheon 24341, Korea; (A.H.); (S.H.); (J.M.); (J.M.); (H.T.)
| | - Joseph Moturi
- Department of Animal Industry Convergence, Kangwon National University, Chuncheon 24341, Korea; (A.H.); (S.H.); (J.M.); (J.M.); (H.T.)
| | - JunYoung Mun
- Department of Animal Industry Convergence, Kangwon National University, Chuncheon 24341, Korea; (A.H.); (S.H.); (J.M.); (J.M.); (H.T.)
| | - Habeeb Tajudeen
- Department of Animal Industry Convergence, Kangwon National University, Chuncheon 24341, Korea; (A.H.); (S.H.); (J.M.); (J.M.); (H.T.)
| | - JinSoo Kim
- Department of Animal Industry Convergence, Kangwon National University, Chuncheon 24341, Korea; (A.H.); (S.H.); (J.M.); (J.M.); (H.T.)
- Correspondence: ; Tel.: +82-33-250-8614
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18
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König RS, Albrich WC, Kahlert CR, Bahr LS, Löber U, Vernazza P, Scheibenbogen C, Forslund SK. The Gut Microbiome in Myalgic Encephalomyelitis (ME)/Chronic Fatigue Syndrome (CFS). Front Immunol 2022; 12:628741. [PMID: 35046929 PMCID: PMC8761622 DOI: 10.3389/fimmu.2021.628741] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 12/09/2021] [Indexed: 12/16/2022] Open
Abstract
Myalgic encephalomyelitis (ME) or Chronic Fatigue Syndrome (CFS) is a neglected, debilitating multi-systemic disease without diagnostic marker or therapy. Despite evidence for neurological, immunological, infectious, muscular and endocrine pathophysiological abnormalities, the etiology and a clear pathophysiology remains unclear. The gut microbiome gained much attention in the last decade with manifold implications in health and disease. Here we review the current state of knowledge on the interplay between ME/CFS and the microbiome, to identify potential diagnostic or interventional approaches, and propose areas where further research is needed. We iteratively selected and elaborated on key theories about a correlation between microbiome state and ME/CFS pathology, developing further hypotheses. Based on the literature we hypothesize that antibiotic use throughout life favours an intestinal microbiota composition which might be a risk factor for ME/CFS. Main proposed pathomechanisms include gut dysbiosis, altered gut-brain axis activity, increased gut permeability with concomitant bacterial translocation and reduced levels of short-chain-fatty acids, D-lactic acidosis, an abnormal tryptophan metabolism and low activity of the kynurenine pathway. We review options for microbiome manipulation in ME/CFS patients including probiotic and dietary interventions as well as fecal microbiota transplantations. Beyond increasing gut permeability and bacterial translocation, specific dysbiosis may modify fermentation products, affecting peripheral mitochondria. Considering the gut-brain axis we strongly suspect that the microbiome may contribute to neurocognitive impairments of ME/CFS patients. Further larger studies are needed, above all to clarify whether D-lactic acidosis and early-life antibiotic use may be part of ME/CFS etiology and what role changes in the tryptophan metabolism might play. An association between the gut microbiome and the disease ME/CFS is plausible. As causality remains unclear, we recommend longitudinal studies. Activity levels, bedridden hours and disease progression should be compared to antibiotic exposure, drug intakes and alterations in the composition of the microbiota. The therapeutic potential of fecal microbiota transfer and of targeted dietary interventions should be systematically evaluated.
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Affiliation(s)
- Rahel S König
- Faculty of Medicine, University of Basel, Basel, Switzerland
| | - Werner C Albrich
- Division of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St. Gallen, St. Gallen, Switzerland
| | - Christian R Kahlert
- Division of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St. Gallen, St. Gallen, Switzerland.,Division of Infectious Diseases and Hospital Epidemiology, Children's Hospital of Eastern Switzerland, St. Gallen, Switzerland
| | - Lina Samira Bahr
- Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.,Experimental and Clinical Research Center, A Joint Cooperation of Max-Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Ulrike Löber
- Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.,Experimental and Clinical Research Center, A Joint Cooperation of Max-Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Berlin, Germany.,Host-Microbiome Factors in Cardiovascular Disease, Max Delbruck Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Pietro Vernazza
- Division of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St. Gallen, St. Gallen, Switzerland
| | - Carmen Scheibenbogen
- Institute for Medical Immunology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Sofia K Forslund
- Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.,Experimental and Clinical Research Center, A Joint Cooperation of Max-Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Berlin, Germany.,Host-Microbiome Factors in Cardiovascular Disease, Max Delbruck Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.,European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
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19
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Zafar H, Saier MH. Comparative Analyses of the Transport Proteins Encoded within the Genomes of nine Bifidobacterium Species. Microb Physiol 2022; 32:30-44. [PMID: 34555832 PMCID: PMC8940750 DOI: 10.1159/000518954] [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: 03/07/2021] [Accepted: 08/02/2021] [Indexed: 01/03/2023]
Abstract
The human microbiome influences human health in both negative and positive ways. Studies on the transportomes of these organisms yield information that may be utilized for various purposes, including the identification of novel drug targets and the manufacture of improved probiotic strains. Moreover, these genomic analyses help to improve our understanding of the physiology and metabolic capabilities of these organisms. The present study is a continuation of our studies on the transport proteins of the major gut microbes. Bifidobacterium species are essential members of the human gut microbiome, and they initiate colonization of the gut at birth, providing health benefits that last a lifetime. In this study we analyze the transportomes of nine bifidobacterial species: B. adolescentis, B. animalis, B. bifidum, B. breve, B. catenulatum, B. dentium, B. longum subsp. infantis, B. longum subsp. longum, and B. pseudocatenulatum. All of these species have proven probiotic characteristics and exert beneficial effects on human health. Surprisingly, we found that all nine of these species have similar pore-forming toxins and drug exporters that may play roles in pathogenesis. These species have transporters for amino acids, carbohydrates, and proteins, essential for their organismal lifestyles and adaption to their respective ecological niches. The strictly probiotic species, B. bifidum, however, contains fewer such transporters, thus indicative of limited interactions with host cells and other gut microbial counterparts. The results of this study were compared with those of our previous studies on the transportomes of multiple species of Bacteroides, Escherichia coli/Salmonella, and Lactobacillus. Overall, bifidobacteria have larger transportomes (based on percentages of total proteins) than the previously examined groups of bacterial species, with a preference for primary active transport systems over secondary carriers. Taken together, these results provide useful information about the physiologies and pathogenic potentials of these probiotic organisms as reflected by their transportomes.
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Affiliation(s)
- Hassan Zafar
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116.,Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic.,Corresponding Authors HZ: Tel: +420773283624, ; MS: Tel: +1 858 534 4084, Fax: +1 858 534 7108,
| | - Milton H. Saier
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116.,Corresponding Authors HZ: Tel: +420773283624, ; MS: Tel: +1 858 534 4084, Fax: +1 858 534 7108,
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20
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Frye KA, Piamthai V, Hsiao A, Degnan PH. Mobilization of vitamin B12 transporters alters competitive dynamics in a human gut microbe. Cell Rep 2021; 37:110164. [PMID: 34965410 PMCID: PMC8759732 DOI: 10.1016/j.celrep.2021.110164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/29/2021] [Accepted: 12/02/2021] [Indexed: 02/07/2023] Open
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21
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Adams AND, Azam MS, Costliow ZA, Ma X, Degnan PH, Vanderpool CK. A Novel Family of RNA-Binding Proteins Regulate Polysaccharide Metabolism in Bacteroides thetaiotaomicron. J Bacteriol 2021; 203:e0021721. [PMID: 34251866 PMCID: PMC8508124 DOI: 10.1128/jb.00217-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/08/2021] [Indexed: 11/20/2022] Open
Abstract
Human gut microbiome composition is constantly changing, and diet is a major driver of these changes. Gut microbial species that persist in mammalian hosts for long periods of time must possess mechanisms for sensing and adapting to nutrient shifts to avoid being outcompeted. Global regulatory mechanisms mediated by RNA-binding proteins (RBPs) that govern responses to nutrient shifts have been characterized in Proteobacteria and Firmicutes but remain undiscovered in the Bacteroidetes. Here, we report the identification of RBPs that are broadly distributed across the Bacteroidetes, with many genomes encoding multiple copies. Genes encoding these RBPs are highly expressed in many Bacteroides species. A purified RBP, RbpB, from Bacteroides thetaiotaomicron binds to single-stranded RNA in vitro with an affinity similar to other characterized regulatory RBPs. B. thetaiotaomicron mutants lacking RBPs show dramatic shifts in expression of polysaccharide utilization and capsular polysaccharide loci, suggesting that these RBPs may act as global regulators of polysaccharide metabolism. A B. thetaiotaomicron ΔrbpB mutant shows a growth defect on dietary sugars belonging to the raffinose family of oligosaccharides (RFOs). The ΔrbpB mutant had reduced expression of BT1871, encoding a predicted RFO-degrading melibiase, compared to the wild-type strain. Mutation of BT1871 confirmed that the enzyme it encodes is essential for growth on melibiose and promotes growth on the RFOs raffinose and stachyose. Our data reveal that RbpB is required for optimal expression of BT1871 and other polysaccharide-related genes, suggesting that we have identified an important new family of global regulatory proteins in the Bacteroidetes. IMPORTANCE The human colon houses hundreds of bacterial species, including many belonging to the genus Bacteroides, that aid in breaking down our food to keep us healthy. Bacteroides have many genes responsible for breaking down different dietary carbohydrates, and complex regulatory mechanisms ensure that specific genes are only expressed when the right carbohydrates are available. In this study, we discovered that Bacteroides use a family of RNA-binding proteins as global regulators to coordinate expression of carbohydrate utilization genes. The ability to turn different carbohydrate utilization genes on and off in response to changing nutrient conditions is critical for Bacteroides to live successfully in the gut, and thus the new regulators we have identified may be important for life in the host.
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Affiliation(s)
- Amanda N. D. Adams
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Muhammad S. Azam
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Zachary A. Costliow
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Xiangqian Ma
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Patrick H. Degnan
- Department of Microbiology and Plant Pathology, University of California-Riverside, Riverside, California, USA
| | - Carin K. Vanderpool
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
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22
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Hiding in Plain Sight: Modern Thiamine Deficiency. Cells 2021; 10:cells10102595. [PMID: 34685573 PMCID: PMC8533683 DOI: 10.3390/cells10102595] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/22/2021] [Accepted: 09/23/2021] [Indexed: 12/13/2022] Open
Abstract
Thiamine or vitamin B1 is an essential, water-soluble vitamin required for mitochondrial energetics—the production of adenosine triphosphate (ATP). It is a critical and rate-limiting cofactor to multiple enzymes involved in this process, including those at the entry points and at critical junctures for the glucose, fatty acid, and amino acid pathways. It has a very short half-life, limited storage capacity, and is susceptible to degradation and depletion by a number of products that epitomize modern life, including environmental and pharmaceutical chemicals. The RDA for thiamine is 1.1–1.2 mg for adult females and males, respectively. With an average diet, even a poor one, it is not difficult to meet that daily requirement, and yet, measurable thiamine deficiency has been observed across multiple patient populations with incidence rates ranging from 20% to over 90% depending upon the study. This suggests that the RDA requirement may be insufficient to meet the demands of modern living. Inasmuch as thiamine deficiency syndromes pose great risk of chronic morbidity, and if left untreated, mortality, a more comprehensive understanding thiamine chemistry, relative to energy production, modern living, and disease, may prove useful.
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23
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Horizontal gene transfer-mediated bacterial strain variation affects host fitness in Drosophila. BMC Biol 2021; 19:187. [PMID: 34565363 PMCID: PMC8474910 DOI: 10.1186/s12915-021-01124-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 08/13/2021] [Indexed: 02/07/2023] Open
Abstract
Background How microbes affect host fitness and environmental adaptation has become a fundamental research question in evolutionary biology. To better understand the role of microbial genomic variation for host fitness, we tested for associations of bacterial genomic variation and Drosophila melanogaster offspring number in a microbial Genome Wide Association Study (GWAS). Results We performed a microbial GWAS, leveraging strain variation in the genus Gluconobacter, a genus of bacteria that are commonly associated with Drosophila under natural conditions. We pinpoint the thiamine biosynthesis pathway (TBP) as contributing to differences in fitness conferred to the fly host. While an effect of thiamine on fly development has been described, we show that strain variation in TBP between bacterial isolates from wild-caught D. melanogaster contributes to variation in offspring production by the host. By tracing the evolutionary history of TBP genes in Gluconobacter, we find that TBP genes were most likely lost and reacquired by horizontal gene transfer (HGT). Conclusion Our study emphasizes the importance of strain variation and highlights that HGT can add to microbiome flexibility and potentially to host adaptation. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01124-y.
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24
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Zysset-Burri DC, Schlegel I, Lincke JB, Jaggi D, Keller I, Heller M, Lagache SB, Wolf S, Zinkernagel MS. Understanding the Interactions Between the Ocular Surface Microbiome and the Tear Proteome. Invest Ophthalmol Vis Sci 2021; 62:8. [PMID: 34369983 PMCID: PMC8354087 DOI: 10.1167/iovs.62.10.8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Purpose The purpose of this study was to explore the interplay between the ocular surface microbiome and the tear proteome in humans in order to better understand the pathogenesis of ocular surface-associated diseases. Methods Twenty eyes from 20 participants were included in the study. The ocular surface microbiome was sequenced by whole-metagenome shotgun sequencing using lid and conjunctival swabs. Furthermore, the tear proteome was identified using chromatography tandem mass spectrometry. After compositional and functional profiling of the metagenome and functional characterization of the proteome by gene ontology, association studies between the ocular microbiome and tear proteome were assessed. Results Two hundred twenty-nine taxa were identified with Actinobacteria and Proteobacteria being the most abundant phyla with significantly more Propionibacterium acnes and Staphylococcus epidermidis in lid compared to conjunctival swabs. The lid metagenomes were enriched in genes of the glycolysis lll and adenosine nucleotides de novo and L-isoleucine biosynthesis. Correlations between the phylum Firmicutes and fatty acid metabolism, between the genus Agrobacterium as well as vitamin B1 synthesis and antimicrobial activity, and between biosynthesis of heme, L-arginine, as well as L-citrulline and human vision were detected. Conclusions The ocular surface microbiome was found to be associated with the tear proteome with a role in human immune defense. This study has a potential impact on the development of treatment strategies for ocular surface-associated diseases.
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Affiliation(s)
- Denise C Zysset-Burri
- Department of Ophthalmology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.,Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Irina Schlegel
- Department of Ophthalmology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Joel-Benjamin Lincke
- Department of Ophthalmology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Damian Jaggi
- Department of Ophthalmology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Irene Keller
- Department for BioMedical Research, University of Bern, Bern, Switzerland.,Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Manfred Heller
- Proteomics and Mass Spectrometry Core Facility, Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Sophie Braga Lagache
- Proteomics and Mass Spectrometry Core Facility, Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Sebastian Wolf
- Department of Ophthalmology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.,Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Martin S Zinkernagel
- Department of Ophthalmology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.,Department for BioMedical Research, University of Bern, Bern, Switzerland
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25
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Lawal OU, Fraqueza MJ, Bouchami O, Worning P, Bartels MD, Gonçalves ML, Paixão P, Gonçalves E, Toscano C, Empel J, Urbaś M, Domínguez MA, Westh H, de Lencastre H, Miragaia M. Foodborne Origin and Local and Global Spread of Staphylococcus saprophyticus Causing Human Urinary Tract Infections. Emerg Infect Dis 2021; 27:880-893. [PMID: 33622483 PMCID: PMC7920669 DOI: 10.3201/eid2703.200852] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Staphylococcus saprophyticus is a primary cause of community-acquired urinary tract infections (UTIs) in young women. S. saprophyticus colonizes humans and animals but basic features of its molecular epidemiology are undetermined. We conducted a phylogenomic analysis of 321 S. saprophyticus isolates collected from human UTIs worldwide during 1997–2017 and 232 isolates from human UTIs and the pig-processing chain in a confined region during 2016–2017. We found epidemiologic and genomic evidence that the meat-production chain is a major source of S. saprophyticus causing human UTIs; human microbiota is another possible origin. Pathogenic S. saprophyticus belonged to 2 lineages with distinctive genetic features that are globally and locally disseminated. Pangenome-wide approaches identified a strong association between pathogenicity and antimicrobial resistance, phages, platelet binding proteins, and an increased recombination rate. Our study provides insight into the origin, transmission, and population structure of pathogenic S. saprophyticus and identifies putative new virulence factors.
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26
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Johnson RC, Van Nostrand JD, Tisdale M, Swierczewski B, Simons MP, Connor P, Fraser J, Melton-Celsa AR, Tribble DR, Riddle MS. Fecal Microbiota Functional Gene Effects Related to Single-Dose Antibiotic Treatment of Travelers' Diarrhea. Open Forum Infect Dis 2021; 8:ofab271. [PMID: 34189178 DOI: 10.1093/ofid/ofab271] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/25/2021] [Indexed: 11/14/2022] Open
Abstract
Background Travelers' diarrhea (TD) is common among military personnel deployed to tropical and subtropical regions. It remains unclear how TD and subsequent antibiotic treatment impact the resident microflora within the gut, especially given increased prevalence of antibiotic resistance among enteric pathogens and acquisition of multidrug-resistant organisms. We examined functional properties of the fecal microflora in response to TD, along with subsequent antibiotic treatment. Methods Fecal samples from US and UK military service members deployed to Djibouti, Kenya, and Honduras who presented with acute watery diarrhea were collected. A sample was collected at acute presentation to the clinic (day 0, before antibiotics), as well as 7 and/or 21 days following a single dose of antibiotics (azithromycin [500 mg], levofloxacin [500 mg], or rifaximin [1650 mg], all with loperamide). Each stool sample underwent culture and TaqMan reverse transcription polymerase chain reaction analyses for pathogen and antibiotic resistance gene detection. Purified DNA from each sample was analyzed using the HumiChip3.1 functional gene array. Results In total, 108 day 1 samples, 50 day 7 samples, and 94 day 21 samples were available for analysis from 119 subjects. Geographic location and disease severity were associated with distinct functional compositions of fecal samples. There were no overt functional differences between pre- and postantibiotic treatment samples, nor was there increased acquisition of antibiotic resistance determinants for any of the antibiotic regimens. Conclusions These results indicate that single-dose antibiotic regimens may not drastically alter the functional or antibiotic resistance composition of fecal microflora, which should inform clinical practice guidelines and antimicrobial stewardship. Clinical Trials Registration Number NCT01618591.
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Affiliation(s)
- Ryan C Johnson
- Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA.,The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Joy D Van Nostrand
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
| | - Michele Tisdale
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA.,Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA.,Naval Medical Center, Portsmouth, Virginia, USA
| | | | - Mark P Simons
- Naval Medical Research Center, Silver Spring, Maryland, USA
| | - Patrick Connor
- Department of Military Medicine, Royal Centre for Defense Medicine, Birmingham, UK
| | - Jamie Fraser
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA.,Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Angela R Melton-Celsa
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - David R Tribble
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Mark S Riddle
- Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA.,Department of Internal Medicine, University of Nevada Reno, School of Medicine, Reno, Nevada, USA
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27
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Sambon M, Wins P, Bettendorff L. Neuroprotective Effects of Thiamine and Precursors with Higher Bioavailability: Focus on Benfotiamine and Dibenzoylthiamine. Int J Mol Sci 2021; 22:ijms22115418. [PMID: 34063830 PMCID: PMC8196556 DOI: 10.3390/ijms22115418] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/10/2021] [Accepted: 05/18/2021] [Indexed: 11/25/2022] Open
Abstract
Thiamine (vitamin B1) is essential for brain function because of the coenzyme role of thiamine diphosphate (ThDP) in glucose and energy metabolism. In order to compensate thiamine deficiency, several thiamine precursors with higher bioavailability were developed since the 1950s. Among these, the thioester benfotiamine (BFT) has been extensively studied and has beneficial effects both in rodent models of neurodegeneration and in human clinical studies. BFT has antioxidant and anti-inflammatory properties that seem to be mediated by a mechanism independent of the coenzyme function of ThDP. BFT has no adverse effects and improves cognitive outcome in patients with mild Alzheimer’s disease (AD). Recent in vitro studies show that another thiamine thioester, dibenzoylthiamine (DBT) is even more efficient that BFT, especially with respect to its anti-inflammatory potency. Thiamine thioesters have pleiotropic properties linked to an increase in circulating thiamine concentrations and possibly in hitherto unidentified metabolites in particular open thiazole ring derivatives. The identification of the active neuroprotective derivatives and the clarification of their mechanism of action open extremely promising perspectives in the field of neurodegenerative, neurodevelopmental and psychiatric conditions.
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28
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Rajeev R, Seethalakshmi PS, Jena PK, Prathiviraj R, Kiran GS, Selvin J. Gut microbiome responses in the metabolism of human dietary components: Implications in health and homeostasis. Crit Rev Food Sci Nutr 2021; 62:7615-7631. [PMID: 34016000 DOI: 10.1080/10408398.2021.1916429] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The gut microbiome and its link with human health and disease have gained a lot of attention recently. The microbiome executes its functions in the host by carrying out the transformation of dietary components and/or de novo synthesis of various essential nutrients. The presence of complex microbial communities makes it difficult to understand the host-microbiome interplay in the metabolism of dietary components. This review attempts to uncover the incredible role of the gut microbiome in the metabolism of dietary components, diet-microbiome interplay, and restoration of the microbiome. The in silico analysis performed in this study elucidates the functional description of essential/hub genes involved in the amino acid degradation pathway, which are mutually present in the host and its gut microbiome. Hence, the computational model helps comprehend the inter-and intracellular molecular networks between humans and their microbial partners.
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Affiliation(s)
- Riya Rajeev
- Department of Microbiology, Pondicherry University, Puducherry, India
| | - P S Seethalakshmi
- Department of Microbiology, Pondicherry University, Puducherry, India
| | - Prasant Kumar Jena
- Immunology and infectious disease research, Department of Pediatrics, Cedars Sinai Medical Center, Los Angeles, California, USA
| | - R Prathiviraj
- Department of Microbiology, Pondicherry University, Puducherry, India
| | - George Seghal Kiran
- Department of Food Science and Technology, Pondicherry University, Puducherry, India
| | - Joseph Selvin
- Department of Microbiology, Pondicherry University, Puducherry, India
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29
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Wang Q, Charmchi Z, George IC. Restrictive diet in a patient with irritable bowel syndrome leading to Wernicke encephalopathy. BMC Gastroenterol 2021; 21:179. [PMID: 33879093 PMCID: PMC8056557 DOI: 10.1186/s12876-021-01758-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 04/09/2021] [Indexed: 12/02/2022] Open
Abstract
Background We present a case of a woman with a past medical history of irritable bowel syndrome (IBS) and anxiety, who presents with ophthalmoplegia, ataxia and memory loss, characteristic of Wernicke encephalopathy. Case presentation A 64-year-old woman presented with double vision, unsteady gait and memory loss. These symptoms began after 3 months on an unfortified restricted diet, which she initiated to alleviate IBS symptoms. Magnetic resonance imaging of the brain demonstrated hyperintense T2-weighted signal in the dorsomedial aspect of bilateral thalami, periaqueductal grey matter and around the third ventricle. The patient’s visual symptoms improved significantly after thiamine supplementation, although her memory deficits persisted. Conclusion Although WE is often associated with chronic alcohol abuse, this case demonstrates the importance of recognizing WE in any patient with a restricted diet and subsequent timely initiation of thiamine.
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Affiliation(s)
- Qiang Wang
- Department of Neurology, Kings County Hospital Center, SUNY Downstate Medical Center and Maimonides Medical Center, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - Zeinab Charmchi
- Department of Neurology, Kings County Hospital Center, SUNY Downstate Medical Center and Maimonides Medical Center, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - Ilena C George
- Department of Neurology, Massachusetts General Hospital, 55 Fruit St, Boston, MA, 02114, USA.
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30
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Pollet RM, Martin LM, Koropatkin NM. TonB-dependent transporters in the Bacteroidetes: Unique domain structures and potential functions. Mol Microbiol 2021; 115:490-501. [PMID: 33448497 DOI: 10.1111/mmi.14683] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 01/10/2021] [Accepted: 01/11/2021] [Indexed: 12/26/2022]
Abstract
The human gut microbiota endows the host with a wealth of metabolic functions central to health, one of which is the degradation and fermentation of complex carbohydrates. The Bacteroidetes are one of the dominant bacterial phyla of this community and possess an expanded capacity for glycan utilization. This is mediated via the coordinated expression of discrete polysaccharide utilization loci (PUL) that invariantly encode a TonB-dependent transporter (SusC) that works with a glycan-capturing lipoprotein (SusD). More broadly within Gram-negative bacteria, TonB-dependent transporters (TBDTs) are deployed for the uptake of not only sugars, but also more often for essential nutrients such as iron and vitamins. Here, we provide a comprehensive look at the repertoire of TBDTs found in the model gut symbiont Bacteroides thetaiotaomicron and the range of predicted functional domains associated with these transporters and SusD proteins for the uptake of both glycans and other nutrients. This atlas of the B. thetaiotaomicron TBDTs reveals that there are at least three distinct subtypes of these transporters encoded within its genome that are presumably regulated in different ways to tune nutrient uptake.
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Affiliation(s)
| | - Lauryn M Martin
- Department of Biology, Alcorn State University, Alcorn, MS, USA
| | - Nicole M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
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31
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Kundra P, Rachmühl C, Lacroix C, Geirnaert A. Role of Dietary Micronutrients on Gut Microbial Dysbiosis and Modulation in Inflammatory Bowel Disease. Mol Nutr Food Res 2021. [DOI: 10.1002/mnfr.201901271] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Palni Kundra
- Laboratory of Food Biotechnology Institute of Food Nutrition and Health Schmelzbergstrasse 7 Zürich 8092 Switzerland
| | - Carole Rachmühl
- Laboratory of Food Biotechnology Institute of Food Nutrition and Health Schmelzbergstrasse 7 Zürich 8092 Switzerland
| | - Christophe Lacroix
- Laboratory of Food Biotechnology Institute of Food Nutrition and Health Schmelzbergstrasse 7 Zürich 8092 Switzerland
| | - Annelies Geirnaert
- Laboratory of Food Biotechnology Institute of Food Nutrition and Health Schmelzbergstrasse 7 Zürich 8092 Switzerland
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32
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Mayengbam S, Chleilat F, Reimer RA. Dietary Vitamin B6 Deficiency Impairs Gut Microbiota and Host and Microbial Metabolites in Rats. Biomedicines 2020; 8:biomedicines8110469. [PMID: 33147768 PMCID: PMC7693528 DOI: 10.3390/biomedicines8110469] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/28/2020] [Accepted: 10/30/2020] [Indexed: 12/15/2022] Open
Abstract
Vitamin B6 plays a crucial role as a cofactor in various enzymatic reactions but bacteria-produced vitamin B6 is not sufficient to meet host requirements. Our objective was to assess the impact of diet-derived vitamin B6 on gut microbiota and host serum metabolomics. Sprague–Dawley rats (n = 47) were fed a control, low B6 (LB6) or high B6 (HB6) diet for six weeks. Serum and cecal samples were collected for biochemical, metabolomics and gut microbiota profiling. There was a significant sex effect for gut microbiota and several metabolic markers. Bodyweight and percent body fat were significantly reduced in LB6 compared to control and HB6 rats. Microbial beta-diversity differed significantly between LB6 and the control and HB6 rats in both sexes. Lachnospiraceae_NK4A136_group and Bacteroides were the primary taxa driving the difference between LB6 and control. There was a significant separation of cecal and serum metabolites of LB6 compared to control and HB6 rats. In the cecum, arginine biosynthesis was impaired, while vitamin B6 metabolism, lysine degradation and nicotinate and nicotinamide metabolism were impaired in serum metabolite profiles. Cecal propionate and butyrate were significantly reduced in LB6 rats irrespective of sex. Host vitamin B6 deficiency but not excess significantly alters gut microbial composition and its metabolites.
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Affiliation(s)
- Shyamchand Mayengbam
- Department of Biochemistry, Memorial University of Newfoundland, St. John’s, NL A1C 5S7, Canada;
| | - Faye Chleilat
- Faculty of Kinesiology, University of Calgary, Calgary, AB T2N 1N4, Canada;
| | - Raylene A. Reimer
- Faculty of Kinesiology, University of Calgary, Calgary, AB T2N 1N4, Canada;
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
- Correspondence:
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33
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Zafar H, Saier MH. Comparative Genomics of the Transport Proteins of Ten Lactobacillus Strains. Genes (Basel) 2020; 11:genes11101234. [PMID: 33096690 PMCID: PMC7593918 DOI: 10.3390/genes11101234] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 10/13/2020] [Accepted: 10/16/2020] [Indexed: 12/24/2022] Open
Abstract
The genus Lactobacillus includes species that may inhabit different anatomical locations in the human body, but the greatest percentage of its species are inhabitants of the gut. Lactobacilli are well known for their probiotic characteristics, although some species may become pathogenic and exert negative effects on human health. The transportome of an organism consists of the sum of the transport proteins encoded within its genome, and studies on the transportome help in the understanding of the various physiological processes taking place in the cell. In this communication we analyze the transport proteins and predict probable substrate specificities of ten Lactobacillus strains. Six of these strains (L. brevis, L. bulgaricus, L. crispatus, L. gasseri, L. reuteri, and L. ruminis) are currently believed to be only probiotic (OP). The remaining four strains (L. acidophilus, L. paracasei, L. planatarum, and L. rhamnosus) can play dual roles, being both probiotic and pathogenic (PAP). The characteristics of the transport systems found in these bacteria were compared with strains (E. coli, Salmonella, and Bacteroides) from our previous studies. Overall, the ten lactobacilli contain high numbers of amino acid transporters, but the PAP strains contain higher number of sugar, amino acid and peptide transporters as well as drug exporters than their OP counterparts. Moreover, some of the OP strains contain pore-forming toxins and drug exporters similar to those of the PAP strains, thus indicative of yet unrecognized pathogenic potential. The transportomes of the lactobacilli seem to be finely tuned according to the extracellular and probiotic lifestyles of these organisms. Taken together, the results of this study help to reveal the physiological and pathogenic potential of common prokaryotic residents in the human body.
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Affiliation(s)
- Hassan Zafar
- Department of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0116, USA
- Department of Microbiology and Molecular Genetics, Faculty of Life Sciences, University of Okara, Okara, Punjab 56300, Pakistan
- Correspondence: (H.Z.); (M.H.S.J.); Tel.: +1-858-534-4084 (M.H.S.J.); Fax: +1-858-534-7108 (M.H.S.J.)
| | - Milton H. Saier
- Department of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0116, USA
- Correspondence: (H.Z.); (M.H.S.J.); Tel.: +1-858-534-4084 (M.H.S.J.); Fax: +1-858-534-7108 (M.H.S.J.)
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34
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Ryan D, Prezza G, Westermann AJ. An RNA-centric view on gut Bacteroidetes. Biol Chem 2020; 402:55-72. [PMID: 33544493 DOI: 10.1515/hsz-2020-0230] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 08/21/2020] [Indexed: 01/26/2023]
Abstract
Bacteria employ noncoding RNAs to maintain cellular physiology, adapt global gene expression to fluctuating environments, sense nutrients, coordinate their interaction with companion microbes and host cells, and protect themselves against bacteriophages. While bacterial RNA research has made fundamental contributions to biomedicine and biotechnology, the bulk of our knowledge of RNA biology stems from the study of a handful of aerobic model species. In comparison, RNA research is lagging in many medically relevant obligate anaerobic species, in particular the numerous commensal bacteria comprising our gut microbiota. This review presents a guide to RNA-based regulatory mechanisms in the phylum Bacteroidetes, focusing on the most abundant bacterial genus in the human gut, Bacteroides spp. This includes recent case reports on riboswitches, an mRNA leader, cis- and trans-encoded small RNAs (sRNAs) in Bacteroides spp., and a survey of CRISPR-Cas systems across Bacteroidetes. Recent work from our laboratory now suggests the existence of hundreds of noncoding RNA candidates in Bacteroides thetaiotaomicron, the emerging model organism for functional microbiota research. Based on these collective observations, we predict mechanistic and functional commonalities and differences between Bacteroides sRNAs and those of other model bacteria, and outline open questions and tools needed to boost Bacteroidetes RNA research.
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Affiliation(s)
- Daniel Ryan
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Josef-Schneider-Str. 2/D15, D-97080, Würzburg, Germany
| | - Gianluca Prezza
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Josef-Schneider-Str. 2/D15, D-97080, Würzburg, Germany
| | - Alexander J Westermann
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Josef-Schneider-Str. 2/D15, D-97080, Würzburg, Germany.,Institute of Molecular Infection Biology (IMIB), University of Würzburg, Josef-Schneider-Str. 2/D15, D-97080, Würzburg, Germany
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Uebanso T, Shimohata T, Mawatari K, Takahashi A. Functional Roles of B‐Vitamins in the Gut and Gut Microbiome. Mol Nutr Food Res 2020; 64:e2000426. [DOI: 10.1002/mnfr.202000426] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 07/31/2020] [Indexed: 01/19/2023]
Affiliation(s)
- Takashi Uebanso
- Department of Preventive Environment and Nutrition, Institute of Biomedical Sciences Tokushima University Graduate School Tokushima 770–8503 Japan
| | - Takaaki Shimohata
- Department of Preventive Environment and Nutrition, Institute of Biomedical Sciences Tokushima University Graduate School Tokushima 770–8503 Japan
| | - Kazuaki Mawatari
- Department of Preventive Environment and Nutrition, Institute of Biomedical Sciences Tokushima University Graduate School Tokushima 770–8503 Japan
| | - Akira Takahashi
- Department of Preventive Environment and Nutrition, Institute of Biomedical Sciences Tokushima University Graduate School Tokushima 770–8503 Japan
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36
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Heravi FS, Zakrzewski M, Vickery K, Malone M, Hu H. Metatranscriptomic Analysis Reveals Active Bacterial Communities in Diabetic Foot Infections. Front Microbiol 2020; 11:1688. [PMID: 32793159 PMCID: PMC7387423 DOI: 10.3389/fmicb.2020.01688] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 06/29/2020] [Indexed: 01/13/2023] Open
Abstract
Despite the extended view of the composition of diabetic foot infections (DFIs), little is known about which transcriptionally active bacterial communities are pertinent to infection, and if any differences are associated with increased infection severity. We applied a RNA sequencing approach to analyze the composition, function, and pathogenicity of the active bacterial communities in DFIs. Taxonomic profiling of bacterial transcripts revealed the presence of 14 bacterial phyla in DFIs. The abundance of the Spiroplasma, Vibrio, and Mycoplasma were significantly different in different infection severities (P < 0.05). Mild and severe stages of infections were dominated by Staphylococcus aureus and Porphyromonas asaccharolytica, respectively. A total of 132 metabolic pathways were identified of which ribosome and thiamin being among the most highly transcribed pathways. Moreover, a total of 131 antibiotic resistance genes, primarily involved in the multidrug efflux pumps/exporters, were identified. Furthermore, iron acquisition systems (synthesize and regulation of siderophores) and pathways involved in the synthesis and regulation of cell-surface components associated with adhesion, colonization, and movement of bacterial cells were the most common virulence factors. These virulence factors may help bacteria compete for scares resources and survive the host wound proteases. Characterization of transcriptionally active bacterial communities can help to provide an understanding of the role of key pathogens in the development of DFIs. Such information can be clinically useful allowing replacement of DFIs empirical therapy with targeted treatment.
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Affiliation(s)
- Fatemah Sadeghpour Heravi
- Surgical Infection Research Group, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
| | | | - Karen Vickery
- Surgical Infection Research Group, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
| | - Matthew Malone
- Infectious Diseases and Microbiology, School of Medicine, Western Sydney University, Sydney, NSW, Australia.,Liverpool Hospital, South Western Sydney LHD, Sydney, NSW, Australia.,Liverpool Diabetes Collaborative Research Unit, Ingham Institute for Applied Medical Research, Sydney, NSW, Australia
| | - Honghua Hu
- Surgical Infection Research Group, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
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A high-resolution transcriptome map identifies small RNA regulation of metabolism in the gut microbe Bacteroides thetaiotaomicron. Nat Commun 2020; 11:3557. [PMID: 32678091 PMCID: PMC7366714 DOI: 10.1038/s41467-020-17348-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 06/23/2020] [Indexed: 12/15/2022] Open
Abstract
Bacteria of the genus Bacteroides are common members of the human intestinal microbiota and important degraders of polysaccharides in the gut. Among them, the species Bacteroides thetaiotaomicron has emerged as the model organism for functional microbiota research. Here, we use differential RNA sequencing (dRNA-seq) to generate a single-nucleotide resolution transcriptome map of B. thetaiotaomicron grown under defined laboratory conditions. An online browser, called ‘Theta-Base’ (www.helmholtz-hiri.de/en/datasets/bacteroides), is launched to interrogate the obtained gene expression data and annotations of ~4500 transcription start sites, untranslated regions, operon structures, and 269 noncoding RNA elements. Among the latter is GibS, a conserved, 145 nt-long small RNA that is highly expressed in the presence of N-acetyl-D-glucosamine as sole carbon source. We use computational predictions and experimental data to determine the secondary structure of GibS and identify its target genes. Our results indicate that sensing of N-acetyl-D-glucosamine induces GibS expression, which in turn modifies the transcript levels of metabolic enzymes. Bacteroides thetaiotaomicron is a human gut microbe and an emergent model organism. Here, Ryan et al. generate single-nucleotide resolution RNA-seq data for this bacterium and map transcription start sites and noncoding RNAs, one of which modulates expression of metabolic enzymes.
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38
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Righetti F, Materne SL, Boss J, Eichner H, Charpentier E, Loh E. Characterization of a transcriptional TPP riboswitch in the human pathogen Neisseria meningitidis. RNA Biol 2020; 17:718-730. [PMID: 32079473 PMCID: PMC7237195 DOI: 10.1080/15476286.2020.1727188] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Increasing evidence has demonstrated that regulatory RNA elements such as riboswitches (RS) play a pivotal role in the fine-tuning of bacterial gene expression. In this study, we investigated and characterized a novel transcriptional thiamine pyrophosphate (TPP) RS in the obligate human pathogen N. meningitidis MC58 (serogroup B). This RS is located in the 5´ untranslated region upstream of thiC gene, encoding a protein involved in TPP biosynthesis, an essential cofactor for all living beings. Primer extension revealed the transcriptional start site of thiC. Northern blot analysis of thiC mRNA and reporter gene studies confirmed the presence of an active TPP-sensing RS. Expression patterns of the wild-type RS and site-specific mutants showed that it is an OFF switch that controls transcription elongation of thiC mRNA. Interestingly, the regulatory mechanism of the meningococcal thiC RS resembles the Gram-positive Bacillus subtilis thiC RS rather than the Gram-negative Escherichia coli thiC RS. Therefore, the meningococcal thiC RS represents a rare example of transcriptional RS in a Gram-negative bacterium. We further observed that the RS is actively involved in modulating gene expression in response to different growth media and to supplemented bacterial and eukaryotic cell lysates as possible sources of nutrients in the nasopharynx. Our results suggest that RS-mediated gene regulation could influence meningococcal fitness, through the fine-tuning of biosynthesis and scavenging of nutrients and cofactors, such as thiamine.
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Affiliation(s)
- Francesco Righetti
- Department of Microbiology, Tumor- and Cell Biology, BioClinicum, Karolinska University Hospital, Stockholm, Sweden
| | - Solange Lise Materne
- Department of Microbiology, Tumor- and Cell Biology, BioClinicum, Karolinska University Hospital, Stockholm, Sweden
| | - John Boss
- Department of Microbiology, Tumor- and Cell Biology, BioClinicum, Karolinska University Hospital, Stockholm, Sweden
| | - Hannes Eichner
- Department of Microbiology, Tumor- and Cell Biology, BioClinicum, Karolinska University Hospital, Stockholm, Sweden
| | - Emmanuelle Charpentier
- Max Planck Unit for the Science of Pathogens, Berlin, Germany.,Department of Regulation in Infection Biology, Max Planck Institute for Infection Biology, Berlin, Germany.,Institute for Biology, Humboldt University, Berlin, Germany.,Department of Regulation in Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany.,The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Edmund Loh
- Department of Microbiology, Tumor- and Cell Biology, BioClinicum, Karolinska University Hospital, Stockholm, Sweden.,SCELSE, Nanyang Technological University, Singapore, Singapore
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40
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Otero-Bravo A, Goffredi S, Sabree ZL. Cladogenesis and Genomic Streamlining in Extracellular Endosymbionts of Tropical Stink Bugs. Genome Biol Evol 2019; 10:680-693. [PMID: 29420776 PMCID: PMC5822708 DOI: 10.1093/gbe/evy033] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/05/2018] [Indexed: 01/21/2023] Open
Abstract
Phytophagous stink bugs are globally distributed and many harbor vertically inherited bacterial symbionts that are extracellular, yet little is known about how the symbiont’s genomes have evolved under this transmission strategy. Genome reduction is common in insect intracellular symbionts but limited genome sampling of the extracellular symbionts of distantly related stink bugs has precluded inferring patterns of extracellular symbiont genome evolution. To address this knowledge gap, we completely sequenced the genomes of the uncultivable bacterial symbionts of four neotropical stink bugs of the Edessa genus. Phylogenetic and comparative analyses indicated that the symbionts form a clade within the Pantoea genus and their genomes are highly reduced (∼0.8 Mb). Furthermore, genome synteny analysis and a jackknife approach for phylogenetic reconstruction, which corrected for long branch attraction artifacts, indicated that the Edessa symbionts were the result of a single symbiotic event that was distinct from the symbiosis event giving rise to Candidatus “Pantoea carbekii,” the extracellular symbiont of the invasive pentatomid stink bug, Halyomorpha halys. Metabolic functions inferred from the Edessa symbiont genomes suggests a shift in genomic composition characteristic of its lifestyle in that they retained many host-supportive functions while undergoing dramatic gene loss and establishing a stable relationship with their host insects. Given the undersampled nature of extracellular insect symbionts, this study is the first comparative analysis of these symbiont genomes from four distinct Edessa stink bug species. Finally, we propose the candidate name “Candidatus Pantoea edessiphila” for the species of these symbionts with strain designations according to their host species.
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Affiliation(s)
| | - Shana Goffredi
- Department of Biology, Occidental College, Los Angeles, California
| | - Zakee L Sabree
- Department of Evolution, Ecology and Organismal Biology, Ohio State University
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41
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Zhang Q, Yin X, Wang H, Wu X, Li X, Li Y, Zhang X, Fu C, Li H, Qiu Y. Fecal Metabolomics and Potential Biomarkers for Systemic Lupus Erythematosus. Front Immunol 2019; 10:976. [PMID: 31130958 PMCID: PMC6509220 DOI: 10.3389/fimmu.2019.00976] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 04/16/2019] [Indexed: 01/03/2023] Open
Abstract
The role of metabolomics in autoimmune diseases has been a rapidly expanding area in researches over the last decade, while its pathophysiologic impact on systemic lupus erythematosus (SLE) remains poorly elucidated. In this study, we analyzed the metabolic profiling of fecal samples from SLE patients and healthy controls based on ultra-high-performance liquid chromatography equipped with mass spectrometry for exploring the potential biomarkers of SLE. The results showed that 23 differential metabolites and 5 perturbed pathways were identified between the two groups, including aminoacyl-tRNA biosynthesis, thiamine metabolism, nitrogen metabolism, tryptophan metabolism, and cyanoamino acid metabolism. In addition, logistic regression and ROC analysis were used to establish a diagnostic model for distinguishing SLE patients from healthy controls. The combined model of fecal PG 27:2 and proline achieved an area under the ROC curve of 0.846, and had a good diagnostic efficacy. In the present study, we analyzed the correlations between fecal metabolic perturbations and SLE pathogenesis. In summary, we firstly illustrate the comprehensive metabolic profiles of feces in SLE patients, suggesting that the fecal metabolites could be used as the potential non-invasive biomarkers for SLE.
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Affiliation(s)
- Qiong Zhang
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xiaofeng Yin
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Haifang Wang
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xing Wu
- Longsee Biomedical Corporation, Guangzhou, China
| | - Xin Li
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yao Li
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xiaohe Zhang
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Chen Fu
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Haixia Li
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yurong Qiu
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Huayin Medical Laboratory Center Co., Ltd., Guangzhou, China
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Yoshii K, Hosomi K, Sawane K, Kunisawa J. Metabolism of Dietary and Microbial Vitamin B Family in the Regulation of Host Immunity. Front Nutr 2019; 6:48. [PMID: 31058161 PMCID: PMC6478888 DOI: 10.3389/fnut.2019.00048] [Citation(s) in RCA: 278] [Impact Index Per Article: 55.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 04/01/2019] [Indexed: 12/28/2022] Open
Abstract
Vitamins are micronutrients that have physiological effects on various biological responses, including host immunity. Therefore, vitamin deficiency leads to increased risk of developing infectious, allergic, and inflammatory diseases. Since B vitamins are synthesized by plants, yeasts, and bacteria, but not by mammals, mammals must acquire B vitamins from dietary or microbial sources, such as the intestinal microbiota. Similarly, some intestinal bacteria are unable to synthesize B vitamins and must acquire them from the host diet or from other intestinal bacteria for their growth and survival. This suggests that the composition and function of the intestinal microbiota may affect host B vitamin usage and, by extension, host immunity. Here, we review the immunological functions of B vitamins and their metabolism by intestinal bacteria with respect to the control of host immunity.
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Affiliation(s)
- Ken Yoshii
- Laboratory of Vaccine Materials, Center for Vaccine and Adjuvant Research, and Laboratory of Gut Environmental System, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
- Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Koji Hosomi
- Laboratory of Vaccine Materials, Center for Vaccine and Adjuvant Research, and Laboratory of Gut Environmental System, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Kento Sawane
- Laboratory of Vaccine Materials, Center for Vaccine and Adjuvant Research, and Laboratory of Gut Environmental System, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
- Innovation Center, Nippon Flour Mills Co., Ltd., Atsugi, Japan
| | - Jun Kunisawa
- Laboratory of Vaccine Materials, Center for Vaccine and Adjuvant Research, and Laboratory of Gut Environmental System, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
- Graduate School of Medicine, Osaka University, Osaka, Japan
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
- Graduate School of Dentistry, Osaka University, Osaka, Japan
- Department of Microbiology and Immunology, Graduate School of Medicine, Kobe University, Hyogo, Japan
- Division of Mucosal Vaccines, International Research and Development Center for Mucosal Vaccines, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
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Cheung SG, Goldenthal AR, Uhlemann AC, Mann JJ, Miller JM, Sublette ME. Systematic Review of Gut Microbiota and Major Depression. Front Psychiatry 2019; 10:34. [PMID: 30804820 PMCID: PMC6378305 DOI: 10.3389/fpsyt.2019.00034] [Citation(s) in RCA: 320] [Impact Index Per Article: 64.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 01/21/2019] [Indexed: 11/17/2022] Open
Abstract
Background: Recently discovered relationships between the gastrointestinal microbiome and the brain have implications for psychiatric disorders, including major depressive disorder (MDD). Bacterial transplantation from MDD patients to rodents produces depression-like behaviors. In humans, case-control studies have examined the gut microbiome in healthy and affected individuals. We systematically reviewed existing studies comparing gut microbial composition in MDD and healthy volunteers. Methods: A PubMed literature search combined the terms "depression," "depressive disorder," "stool," "fecal," "gut," and "microbiome" to identify human case-control studies that investigated relationships between MDD and microbiota quantified from stool. We evaluated the resulting studies, focusing on bacterial taxa that were different between MDD and healthy controls. Results: Six eligible studies were found in which 50 taxa exhibited differences (p < 0.05) between patients with MDD and controls. Patient characteristics and methodologies varied widely between studies. Five phyla-Bacteroidetes, Firmicutes, Actinobacteria, Fusobacteria, and Protobacteria-were represented; however, divergent results occurred across studies for all phyla. The largest number of differentiating taxa were within phylum Firmicutes, in which nine families and 12 genera differentiated the diagnostic groups. The majority of these families and genera were found to be statistically different between the two groups in two identified studies. Family Lachnospiraceae differentiated the diagnostic groups in four studies (with an even split in directionality). Across all five phyla, nine genera were higher in MDD (Anaerostipes, Blautia, Clostridium, Klebsiella, Lachnospiraceae incertae sedis, Parabacteroides, Parasutterella, Phascolarctobacterium, and Streptococcus), six were lower (Bifidobacterium, Dialister, Escherichia/Shigella, Faecalibacterium, and Ruminococcus), and six were divergent (Alistipes, Bacteroides, Megamonas, Oscillibacter, Prevotella, and Roseburia). We highlight mechanisms and products of bacterial metabolism as they may relate to the etiology of depression. Conclusions: No consensus has emerged from existing human studies of depression and gut microbiome concerning which bacterial taxa are most relevant to depression. This may in part be due to differences in study design. Given that bacterial functions are conserved across taxonomic groups, we propose that studying microbial functioning may be more productive than a purely taxonomic approach to understanding the gut microbiome in depression.
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Affiliation(s)
- Stephanie G. Cheung
- Division of Consultation-Liaison Psychiatry, Columbia University, New York, NY, United States
- Department of Psychiatry, Columbia University, New York, NY, United States
| | - Ariel R. Goldenthal
- Department of Psychiatry, Columbia University, New York, NY, United States
- Molecular Imaging & Neuropathology Area, New York State Psychiatric Institute, New York, NY, United States
| | - Anne-Catrin Uhlemann
- Division of Infectious Diseases, Department of Medicine, Columbia University, New York, NY, United States
- Microbiome & Pathogen Genomics Core, Columbia University, New York, NY, United States
| | - J. John Mann
- Department of Psychiatry, Columbia University, New York, NY, United States
- Molecular Imaging & Neuropathology Area, New York State Psychiatric Institute, New York, NY, United States
- Department of Radiology, Columbia University, New York, NY, United States
| | - Jeffrey M. Miller
- Department of Psychiatry, Columbia University, New York, NY, United States
- Molecular Imaging & Neuropathology Area, New York State Psychiatric Institute, New York, NY, United States
| | - M. Elizabeth Sublette
- Department of Psychiatry, Columbia University, New York, NY, United States
- Molecular Imaging & Neuropathology Area, New York State Psychiatric Institute, New York, NY, United States
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Bousis S, Setyawati I, Diamanti E, Slotboom DJ, Hirsch AKH. Energy-Coupling Factor Transporters as Novel Antimicrobial Targets. ADVANCED THERAPEUTICS 2019. [DOI: 10.1002/adtp.201800066] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Spyridon Bousis
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI); Department of Drug Design and Optimization; Campus Building E8.1 66123 Saarbrücken Germany
- Stratingh Institute for Chemistry; University of Groningen; Nijenborgh 7 9747AG Groningen The Netherlands
- Department of Pharmacy; Saarland University; Saarbrücken, Campus Building E8.1 66123 Saarbrücken Germany
| | - Inda Setyawati
- Groningen Biomolecular Sciences and Biotechnology Institute; University of Groningen; Nijenborgh 4 9747AG Groningen The Netherlands
- Department of Biochemistry; Bogor Agricultural University; Dramaga 16680 Bogor Indonesia
| | - Eleonora Diamanti
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI); Department of Drug Design and Optimization; Campus Building E8.1 66123 Saarbrücken Germany
- Stratingh Institute for Chemistry; University of Groningen; Nijenborgh 7 9747AG Groningen The Netherlands
| | - Dirk J. Slotboom
- Groningen Biomolecular Sciences and Biotechnology Institute; University of Groningen; Nijenborgh 4 9747AG Groningen The Netherlands
- Department of Biochemistry; Bogor Agricultural University; Dramaga 16680 Bogor Indonesia
| | - Anna K. H. Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI); Department of Drug Design and Optimization; Campus Building E8.1 66123 Saarbrücken Germany
- Stratingh Institute for Chemistry; University of Groningen; Nijenborgh 7 9747AG Groningen The Netherlands
- Department of Pharmacy; Saarland University; Saarbrücken, Campus Building E8.1 66123 Saarbrücken Germany
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Nosaka K, Uchiyama R, Tadano K, Endo Y, Hayashi M, Konno H, Mimuro H. Thiamin transport in Helicobacter pylori lacking the de novo synthesis of thiamin. MICROBIOLOGY-SGM 2019; 165:224-232. [PMID: 30620266 DOI: 10.1099/mic.0.000765] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Helicobacter pylori lacks the genes involved in the de novo synthesis of thiamin, and is therefore a thiamin auxotroph. The PnuT transporter, a member of the Pnu transporter family, mediates the uptake of thiamin across the membrane. In the genome of H. pylori, the pnuT gene is clustered with the thiamin pyrophosphokinase gene thi80. In this study, we found that [3H]thiamin is incorporated into the H. pylori SS1 strain via facilitated diffusion with a Km value of 28 µM. The incorporation of radioactive thiamin was inhibited to some extent by 2-methyl-4-amino-5-hydroxymethylpyrimidine or pyrithiamine, but was largely unaffected by thiamin phosphate or thiamin pyrophosphate. RT-PCR analysis demonstrated that the pnuT and thi80 genes are cotranscribed as a single transcript. The estimated Km value for thiamin in the thiamin pyrophosphokinase activity exerted by the recombinant Thi80 protein was 0.40 µM, which is much lower than the Km value of thiamin transport in H. pylori cells. These findings suggested that the incorporated thiamin from the environment is efficiently trapped by pyrophosphorylation to make the transport directional. In addition, the thiamin transport activity in the pnuT-deficient H. pylori strain was less than 20 % of that in the wild-type strain at extracellular thiamin concentration of 1 µM, but the incorporated scintillation signals of the pnuT-deficient strain with 100 nM [3H]thiamin were nearly at the background level. We also found that the pnuT-deficient strain required 100-times more thiamin to achieve growth equal to that of the wild-type. These findings reflect the presence of multiple routes for entry of thiamin into H. pylori, and PnuT is likely responsible for the high-affinity thiamin transport and serves as a target for antimicrobial agents against H. pylori.
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Affiliation(s)
- Kazuto Nosaka
- 12nd Department of Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Mukogawa Women's University, Nishinomiya, Japan
| | - Ryosuke Uchiyama
- 12nd Department of Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Mukogawa Women's University, Nishinomiya, Japan
| | - Kyo Tadano
- 12nd Department of Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Mukogawa Women's University, Nishinomiya, Japan
| | - Yurina Endo
- 12nd Department of Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Mukogawa Women's University, Nishinomiya, Japan
| | - Maria Hayashi
- 12nd Department of Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Mukogawa Women's University, Nishinomiya, Japan
| | - Hiroyuki Konno
- 2Department of Biochemical Engineering, Graduate School of Science and Engineering, Yamagata University, Yonezawa, Japan
| | - Hitomi Mimuro
- 3Department of Infection Microbiology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.,4Division of Bacteriology, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
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Laverde Gomez JA, Mukhopadhya I, Duncan SH, Louis P, Shaw S, Collie‐Duguid E, Crost E, Juge N, Flint HJ. Formate cross-feeding and cooperative metabolic interactions revealed by transcriptomics in co-cultures of acetogenic and amylolytic human colonic bacteria. Environ Microbiol 2019; 21:259-271. [PMID: 30362296 PMCID: PMC6378601 DOI: 10.1111/1462-2920.14454] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 10/14/2018] [Accepted: 10/18/2018] [Indexed: 12/24/2022]
Abstract
Interspecies cross-feeding is a fundamental factor in anaerobic microbial communities. In the human colon, formate is produced by many bacterial species but is normally detected only at low concentrations. Ruminococcus bromii produces formate, ethanol and acetate in approximately equal molar proportions in pure culture on RUM-RS medium with 0.2% Novelose resistant starch (RS3) as energy source. Batch co-culturing on starch with the acetogen Blautia hydrogenotrophica however led to the disappearance of formate and increased levels of acetate, which is proposed to occur through the routing of formate via the Wood Ljungdahl pathway of B. hydrogenotrophica. We investigated these inter-species interactions further using RNAseq to examine gene expression in continuous co-cultures of R. bromii and B. hydrogenotrophica. Transcriptome analysis revealed upregulation of B. hydrogenotrophica genes involved in the Wood-Ljungdahl pathway and of a 10 gene cluster responsible for increased branched chain amino acid fermentation in the co-cultures. Cross-feeding between formate-producing species and acetogens may be a significant factor in short chain fatty acid formation in the colon contributing to high rates of acetate production. Transcriptome analysis also indicated competition for the vitamin thiamine and downregulation of dissimilatory sulfate reduction and key redox proteins in R. bromii in the co-cultures, thus demonstrating the wide-ranging consequences of inter-species interactions in this model system.
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Affiliation(s)
| | | | - Sylvia H. Duncan
- Gut Health GroupThe Rowett Institute, University of AberdeenAberdeenUK
| | - Petra Louis
- Gut Health GroupThe Rowett Institute, University of AberdeenAberdeenUK
| | - Sophie Shaw
- Centre for Genome Enabled Biology and MedicineUniversity of AberdeenOld AberdeenUK
| | - Elaina Collie‐Duguid
- Centre for Genome Enabled Biology and MedicineUniversity of AberdeenOld AberdeenUK
| | - Emmanuelle Crost
- The Gut Health and Food Safety Institute Strategic ProgrammeQuadram Institute BioscienceNorwichUK
| | - Nathalie Juge
- The Gut Health and Food Safety Institute Strategic ProgrammeQuadram Institute BioscienceNorwichUK
| | - Harry J. Flint
- Gut Health GroupThe Rowett Institute, University of AberdeenAberdeenUK
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A Metabologenomic Approach Reveals Changes in the Intestinal Environment of Mice Fed on American Diet. Int J Mol Sci 2018; 19:ijms19124079. [PMID: 30562947 PMCID: PMC6321133 DOI: 10.3390/ijms19124079] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 12/11/2018] [Accepted: 12/15/2018] [Indexed: 12/23/2022] Open
Abstract
Intestinal microbiota and their metabolites are strongly associated with host physiology. Developments in DNA sequencing and mass spectrometry technologies have allowed us to obtain additional data that enhance our understanding of the interactions among microbiota, metabolites, and the host. However, the strategies used to analyze these datasets are not yet well developed. Here, we describe an original analytical strategy, metabologenomics, consisting of an integrated analysis of mass spectrometry-based metabolome data and high-throughput-sequencing-based microbiome data. Using this approach, we compared data obtained from C57BL/6J mice fed an American diet (AD), which contained higher amounts of fat and fiber, to those from mice fed control rodent diet. The feces of the AD mice contained higher amounts of butyrate and propionate, and higher relative abundances of Oscillospira and Ruminococcus. The amount of butyrate positively correlated with the abundance of these bacterial genera. Furthermore, integrated analysis of the metabolome data and the predicted metagenomic data from Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) indicated that the abundance of genes associated with butyrate metabolism positively correlated with butyrate amounts. Thus, our metabologenomic approach is expected to provide new insights and understanding of intestinal metabolic dynamics in complex microbial ecosystems.
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