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Nishiyama K, Murakami R, Nakahata M, Zhou B, Hashikura N, Kaneko H, Namai F, Ikeda-Ohtsubo W, Xiao JZ, Kitazawa H, Odamaki T. Exploring strain-level diversity in the gut microbiome through mucin particle adhesion. Appl Environ Microbiol 2024; 90:e0123524. [PMID: 39133001 PMCID: PMC11409716 DOI: 10.1128/aem.01235-24] [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: 06/26/2024] [Accepted: 06/30/2024] [Indexed: 08/13/2024] Open
Abstract
Mucin glycoproteins are a significant source of carbon for the gut bacteria. Various gut microbial species possess diverse hydrolytic enzymes and catabolic pathways for breaking down mucin glycans, resulting in competition for the limited nutrients within the gut environment. Adherence to mucin glycans represents a crucial strategy used by gut microbes to access nutrient reservoirs. Understanding these properties is pivotal for comprehending the survival mechanisms of bacteria in the gastrointestinal tract. However, characterization of individual strains within the vast array of coexisting bacteria in the microbiome is challenging. To investigate this, we developed mucin-immobilized particles by immobilizing porcine gastric mucin (PGM) onto glass beads chemically modified with boronic acid. These PGM-immobilized particles were then anaerobically cultured with human fecal microbiota, and the bacteria adhering to PGM were isolated. Interestingly, the microbiome composition remained largely unchanged irrespective of PGM immobilization. Nonetheless, bacteria isolated from PGM-immobilized glass particles exhibited notably higher N-acetylgalactosaminidase activity compared to the control beads. Furthermore, Bacteroides strains isolated from PGM-immobilized glass particles displayed enhanced adhesive and metabolic properties to PGM. These findings underscore the utility of PGM particles in enriching and isolating specific microbes. Moreover, they highlight substantial differences in microbial properties at the strain level. We anticipate that PGM-immobilized particles will advance culture-based microbiome research, emphasizing the significance of strain-level characterization. IMPORTANCE Metabolism of mucin glycans by gut bacteria represents a crucial strategy for accessing nutrient reservoirs. The efficacy of mucin glycan utilization among gut bacteria hinges on the metabolic capabilities of individual strains, necessitating meticulous strain-level characterization. In this investigation, we used glass beads chemically immobilized with mucins to selectively enrich bacteria from fecal fermentation cultures, based on their superior adhesion to and metabolism of mucin glycoproteins. These findings lend support to the hypothesis that the physical interactions between bacteria and mucin glycoprotein components directly correlate with their capacity to utilize mucins as nutrient sources. Furthermore, our study implies that physical proximity may significantly influence bacterial nutrient acquisition within the ecosystem, facilitating gut bacteria's access to carbohydrate components.
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Affiliation(s)
- Keita Nishiyama
- Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai, Japan
- International Education and Research Center for Food Agricultural Immunology (CFAI), Tohoku University, Aoba-ku, Sendai, Japan
| | - Ryuta Murakami
- Next Generation Science Institute, Morinaga Milk Industry Co., Ltd, Zama, Kanagawa, Japan
| | - Masaki Nakahata
- Department of Macromolecular Science, Osaka University, Toyonaka, Osaka, Japan
| | - Binghui Zhou
- Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai, Japan
- International Education and Research Center for Food Agricultural Immunology (CFAI), Tohoku University, Aoba-ku, Sendai, Japan
| | - Nanami Hashikura
- Next Generation Science Institute, Morinaga Milk Industry Co., Ltd, Zama, Kanagawa, Japan
| | - Hiroki Kaneko
- Next Generation Science Institute, Morinaga Milk Industry Co., Ltd, Zama, Kanagawa, Japan
| | - Fu Namai
- Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai, Japan
- International Education and Research Center for Food Agricultural Immunology (CFAI), Tohoku University, Aoba-ku, Sendai, Japan
| | - Wakako Ikeda-Ohtsubo
- Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai, Japan
- International Education and Research Center for Food Agricultural Immunology (CFAI), Tohoku University, Aoba-ku, Sendai, Japan
| | - Jin-Zhong Xiao
- Next Generation Science Institute, Morinaga Milk Industry Co., Ltd, Zama, Kanagawa, Japan
| | - Haruki Kitazawa
- Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai, Japan
- International Education and Research Center for Food Agricultural Immunology (CFAI), Tohoku University, Aoba-ku, Sendai, Japan
| | - Toshitaka Odamaki
- Next Generation Science Institute, Morinaga Milk Industry Co., Ltd, Zama, Kanagawa, Japan
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Jensen N, Maldonado-Gomez M, Krishnakumar N, Weng CY, Castillo J, Razi D, Kalanetra K, German JB, Lebrilla CB, Mills DA, Taft DH. Dietary fiber monosaccharide content alters gut microbiome composition and fermentation. Appl Environ Microbiol 2024; 90:e0096424. [PMID: 39007602 PMCID: PMC11337808 DOI: 10.1128/aem.00964-24] [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: 05/14/2024] [Accepted: 06/18/2024] [Indexed: 07/16/2024] Open
Abstract
Members of the mammalian gut microbiota metabolize diverse complex carbohydrates that are not digested by the host, which are collectively labeled "dietary fiber." While the enzymes and transporters that each strain uses to establish a nutrient niche in the gut are often exquisitely specific, the relationship between carbohydrate structure and microbial ecology is imperfectly understood. The present study takes advantage of recent advances in complex carbohydrate structure determination to test the effects of fiber monosaccharide composition on microbial fermentation. Fifty-five fibers with varied monosaccharide composition were fermented by a pooled feline fecal inoculum in a modified MiniBioReactor array system over a period of 72 hours. The content of the monosaccharides glucose and xylose was significantly associated with the reduction of pH during fermentation, which was also predictable from the concentrations of the short-chain fatty acids lactic acid, propionic acid, and the signaling molecule indole-3-acetic acid. Microbiome diversity and composition were also predictable from monosaccharide content and SCFA concentration. In particular, the concentrations of lactic acid and propionic acid correlated with final alpha diversity and were significantly associated with the relative abundance of several of the genera, including Lactobacillus and Dubosiella. Our results suggest that monosaccharide composition offers a generalizable method to compare any dietary fiber of interest and uncover links between diet, gut microbiota, and metabolite production. IMPORTANCE The survival of a microbial species in the gut depends on the availability of the nutrients necessary for that species to survive. Carbohydrates in the form of non-host digestible fiber are of particular importance, and the set of genes possessed by each species for carbohydrate consumption can vary considerably. Here, differences in the monosaccharides that are the building blocks of fiber are considered for their impact on both the survival of different species of microbes and on the levels of microbial fermentation products produced. This work demonstrates that foods with similar monosaccharide content will have consistent effects on the survival of microbial species and on the production of microbial fermentation products.
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Affiliation(s)
- Nick Jensen
- Department of Food Science and Technology, University of California, Davis, California, USA
- Foods for Health Institute, University of California, Davis, California, USA
| | - Maria Maldonado-Gomez
- Department of Food Science and Technology, University of California, Davis, California, USA
- Foods for Health Institute, University of California, Davis, California, USA
| | - Nithya Krishnakumar
- Department of Food Science and Technology, University of California, Davis, California, USA
- Foods for Health Institute, University of California, Davis, California, USA
| | - Cheng-Yu Weng
- Department of Chemistry, University of California, Davis, California, USA
| | - Juan Castillo
- Department of Chemistry, University of California, Davis, California, USA
| | - Dale Razi
- Foods for Health Institute, University of California, Davis, California, USA
| | - Karen Kalanetra
- Department of Food Science and Technology, University of California, Davis, California, USA
- Foods for Health Institute, University of California, Davis, California, USA
| | - J. Bruce German
- Department of Food Science and Technology, University of California, Davis, California, USA
- Foods for Health Institute, University of California, Davis, California, USA
| | - Carlito B. Lebrilla
- Foods for Health Institute, University of California, Davis, California, USA
- Department of Chemistry, University of California, Davis, California, USA
| | - David A. Mills
- Department of Food Science and Technology, University of California, Davis, California, USA
- Foods for Health Institute, University of California, Davis, California, USA
| | - Diana H. Taft
- Department of Food Science and Human Nutrition, University of Florida, Gainsville, Florida, USA
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Sokou R, Moschari E, Palioura AE, Palioura AP, Mpakosi A, Adamakidou T, Vlachou E, Theodoraki M, Iacovidou N, Tsartsalis AN. The Impact of Gestational Diabetes Mellitus (GDM) on the Development and Composition of the Neonatal Gut Microbiota: A Systematic Review. Microorganisms 2024; 12:1564. [PMID: 39203408 PMCID: PMC11356352 DOI: 10.3390/microorganisms12081564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 07/23/2024] [Accepted: 07/29/2024] [Indexed: 09/03/2024] Open
Abstract
Gestational diabetes mellitus (GDM) is an important health issue, as it is connected with adverse effects to the mother as well as the fetus. A factor of essence for the pathology of this disorder is the gut microbiota, which seems to have an impact on the development and course of GDM. The role of the gut microbiota on maternal reproductive health and all the changes that happen during pregnancy as well as during the neonatal period is of high interest. The correct establishment and maturation of the gut microbiota is of high importance for the development of basic biological systems. The aim of this study is to provide a systematic review of the literature on the effect of GDM on the gut microbiota of neonates, as well as possible links to morbidity and mortality of neonates born to mothers with GDM. Systematic research took place in databases including PubMed and Scopus until June 2024. Data that involved demographics, methodology, and changes to the microbiota were derived and divided based on patients with exposure to or with GDM. The research conducted on online databases revealed 316 studies, of which only 16 met all the criteria and were included in this review. Research from the studies showed great heterogeneity and varying findings at the level of changes in α and β diversity and enrichment or depletion in phylum, gene, species, and operational taxonomic units in the neonatal gut microbiota of infants born to mothers with GDM. The ways in which the microbiota of neonates and infants are altered due to GDM remain largely unclear and require further investigation. Future studies are needed to explore and clarify these mechanisms.
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Affiliation(s)
- Rozeta Sokou
- Neonatal Intensive Care Unit, General Hospital of Nikea “Agios Panteleimon”, 18454 Piraeus, Greece; (E.M.); (A.E.P.); (A.-P.P.); (M.T.)
- Neonatal Department, National and Kapodistrian University of Athens, Aretaieio Hospital, 11528 Athens, Greece;
| | - Eirini Moschari
- Neonatal Intensive Care Unit, General Hospital of Nikea “Agios Panteleimon”, 18454 Piraeus, Greece; (E.M.); (A.E.P.); (A.-P.P.); (M.T.)
| | - Alexia Eleftheria Palioura
- Neonatal Intensive Care Unit, General Hospital of Nikea “Agios Panteleimon”, 18454 Piraeus, Greece; (E.M.); (A.E.P.); (A.-P.P.); (M.T.)
| | - Aikaterini-Pothiti Palioura
- Neonatal Intensive Care Unit, General Hospital of Nikea “Agios Panteleimon”, 18454 Piraeus, Greece; (E.M.); (A.E.P.); (A.-P.P.); (M.T.)
| | - Alexandra Mpakosi
- Department of Microbiology, General Hospital of Nikea “Agios Panteleimon”, 18454 Piraeus, Greece;
| | - Theodoula Adamakidou
- Department of Nursing, School of Health Sciences, University of West Attica, Ag. Spydironos 28, 12243 Athens, Greece; (T.A.); (E.V.)
| | - Eugenia Vlachou
- Department of Nursing, School of Health Sciences, University of West Attica, Ag. Spydironos 28, 12243 Athens, Greece; (T.A.); (E.V.)
| | - Martha Theodoraki
- Neonatal Intensive Care Unit, General Hospital of Nikea “Agios Panteleimon”, 18454 Piraeus, Greece; (E.M.); (A.E.P.); (A.-P.P.); (M.T.)
| | - Nicoletta Iacovidou
- Neonatal Department, National and Kapodistrian University of Athens, Aretaieio Hospital, 11528 Athens, Greece;
| | - Athanasios N. Tsartsalis
- Department of Endocrinology Diabetes and Metabolism, Naval Hospital of Athens, Dinokratous 70, 11521 Athens, Greece;
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Dmytriv TR, Storey KB, Lushchak VI. Intestinal barrier permeability: the influence of gut microbiota, nutrition, and exercise. Front Physiol 2024; 15:1380713. [PMID: 39040079 PMCID: PMC11260943 DOI: 10.3389/fphys.2024.1380713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 05/29/2024] [Indexed: 07/24/2024] Open
Abstract
The intestinal wall is a selectively permeable barrier between the content of the intestinal lumen and the internal environment of the body. Disturbances of intestinal wall permeability can potentially lead to unwanted activation of the enteric immune system due to excessive contact with gut microbiota and its components, and the development of endotoxemia, when the level of bacterial lipopolysaccharides increases in the blood, causing chronic low-intensity inflammation. In this review, the following aspects are covered: the structure of the intestinal wall barrier; the influence of the gut microbiota on the permeability of the intestinal wall via the regulation of functioning of tight junction proteins, synthesis/degradation of mucus and antioxidant effects; the molecular mechanisms of activation of the pro-inflammatory response caused by bacterial invasion through the TLR4-induced TIRAP/MyD88 and TRAM/TRIF signaling cascades; the influence of nutrition on intestinal permeability, and the influence of exercise with an emphasis on exercise-induced heat stress and hypoxia. Overall, this review provides some insight into how to prevent excessive intestinal barrier permeability and the associated inflammatory processes involved in many if not most pathologies. Some diets and physical exercise are supposed to be non-pharmacological approaches to maintain the integrity of intestinal barrier function and provide its efficient operation. However, at an early age, the increased intestinal permeability has a hormetic effect and contributes to the development of the immune system.
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Affiliation(s)
- Tetiana R. Dmytriv
- Department of Biochemistry and Biotechnology, Vasyl Stefanyk Precarpathian National University, Ivano-Frankivsk, Ukraine
- Research and Development University, Ivano-Frankivsk, Ukraine
| | | | - Volodymyr I. Lushchak
- Department of Biochemistry and Biotechnology, Vasyl Stefanyk Precarpathian National University, Ivano-Frankivsk, Ukraine
- Research and Development University, Ivano-Frankivsk, Ukraine
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5
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Yang X, Zhang J, Zhu J, Yang R, Tong Y. Molecular insights into FucR transcription factor to control the metabolism of L-fucose in Bifidobacterium longum subsp. infantis. Microbiol Res 2024; 283:127709. [PMID: 38593579 DOI: 10.1016/j.micres.2024.127709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 03/27/2024] [Accepted: 03/30/2024] [Indexed: 04/11/2024]
Abstract
Bifidobacterium longum subsp. infantis commonly colonizes the human gut and is capable of metabolizing L-fucose, which is abundant in the gut. Multiple studies have focused on the mechanisms of L-fucose utilization by B. longum subsp. infantis, but the regulatory pathways governing the expression of these catabolic processes are still unclear. In this study, we have conducted a structural and functional analysis of L-fucose metabolism transcription factor FucR derived from B. longum subsp. infantis Bi-26. Our results indicated that FucR is a L-fucose-sensitive repressor with more α-helices, fewer β-sheets, and β-turns. Transcriptional analysis revealed that FucR displays weak negative self-regulation, which is counteracted in the presence of L-fucose. Isothermal titration calorimetry indicated that FucR has a 2:1 stoichiometry with L-fucose. The key amino acid residues for FucR binding L-fucose are Asp280 and Arg331, with mutation of Asp280 to Ala resulting in a decrease in the affinity between FucR and L-fucose with the Kd value from 2.58 to 11.68 μM, and mutation of Arg331 to Ala abolishes the binding ability of FucR towards L-fucose. FucR specifically recognized and bound to a 20-bp incomplete palindrome sequence (5'-ACCCCAATTACGAAAATTTTT-3'), and the affinity of the L-fucose-loaded FucR for the DNA fragment was lower than apo-FucR. The results provided new insights into the regulating L-fucose metabolism by B. longum subsp. infantis.
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Affiliation(s)
- Xiaojun Yang
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Jing Zhang
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Jing Zhu
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Ruijin Yang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yanjun Tong
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China.
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6
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Zhao T, Liu S, Ma X, Shuai Y, He H, Guo T, Huang W, Wang Q, Liu S, Wang Z, Gong G, Huang L. Lycium barbarum arabinogalactan alleviates intestinal mucosal damage in mice by restoring intestinal microbes and mucin O-glycans. Carbohydr Polym 2024; 330:121882. [PMID: 38368089 DOI: 10.1016/j.carbpol.2024.121882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/25/2024] [Accepted: 01/26/2024] [Indexed: 02/19/2024]
Abstract
Structurally defined arabinogalactan (LBP-3) from Lycium barbarum have effect on improving intestinal barrier function. However, whether its intestinal barrier function depended on the changes of intestinal mucin O-glycans have not been investigated. A dextran sodium sulfate-induced acute colitis mouse model was employed to test prevention and treatment with LBP-3. The intestinal microbiota as well as colonic mucin O-glycan profiles were analyzed. Supplementation with LBP-3 inhibited harmful bacteria, including Desulfovibrionaceae, Enterobacteriaceae, and Helicobacteraceae while significantly increased the abundance of beneficial bacteria (e.g., Lachnospiraceae, Ruminococcaceae, and Lactobacillaceae). Notably, LBP-3 augmented the content of neutral O-glycans by stimulating the fucosylation glycoforms (F1H1N2 and F1H2N2), short-chain sulfated O-glycans (S1F1H1N2, S1H1N2, and S1H2N3), and sialylated medium- and long-chain O-glycans (F1H2N2A1, H2N3A1, and F1H3N2A1). In summary, we report that supplement LBP-3 significantly reduced pathological symptoms, restored the bacterial community, and promoted the expression of O-glycans to successfully prevent and alleviate colitis in a mouse model, especially in the LBP-3 prevention testing group. The underlying mechanism of action was investigated using glycomics to better clarify which the structurally defined LBP-3 were responsible for its beneficial effect against ulcerative colitis and assess its use as a functional food or pharmaceutical supplement.
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Affiliation(s)
- Tong Zhao
- Shaanxi Natural Carbohydrate Resource Engineering Research Center, College of Food Science and Technology, Northwest University, Xi'an 710069, China
| | - Sining Liu
- Shaanxi Natural Carbohydrate Resource Engineering Research Center, College of Food Science and Technology, Northwest University, Xi'an 710069, China
| | - Xiaoran Ma
- Shaanxi Natural Carbohydrate Resource Engineering Research Center, College of Food Science and Technology, Northwest University, Xi'an 710069, China
| | - Yutong Shuai
- Shaanxi Natural Carbohydrate Resource Engineering Research Center, College of Food Science and Technology, Northwest University, Xi'an 710069, China
| | - Houde He
- Shaanxi Natural Carbohydrate Resource Engineering Research Center, College of Food Science and Technology, Northwest University, Xi'an 710069, China
| | - Tongyi Guo
- Shaanxi Natural Carbohydrate Resource Engineering Research Center, College of Food Science and Technology, Northwest University, Xi'an 710069, China
| | - Wenqi Huang
- Shaanxi Natural Carbohydrate Resource Engineering Research Center, College of Food Science and Technology, Northwest University, Xi'an 710069, China
| | - Qian Wang
- Shaanxi Natural Carbohydrate Resource Engineering Research Center, College of Food Science and Technology, Northwest University, Xi'an 710069, China
| | - Shan Liu
- Tianren Goji Biotechnology Co., Ltd, Ningxia, China
| | - Zhongfu Wang
- Shaanxi Natural Carbohydrate Resource Engineering Research Center, College of Food Science and Technology, Northwest University, Xi'an 710069, China
| | - Guiping Gong
- Shaanxi Natural Carbohydrate Resource Engineering Research Center, College of Food Science and Technology, Northwest University, Xi'an 710069, China.
| | - Linjuan Huang
- Shaanxi Natural Carbohydrate Resource Engineering Research Center, College of Food Science and Technology, Northwest University, Xi'an 710069, China.
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Candeliere F, Musmeci E, Sola L, Amaretti A, Raimondi S, Rossi M. Genomic and functional analysis of the mucinolytic species Clostridium celatum, Clostridium tertium, and Paraclostridium bifermentans. Front Microbiol 2024; 15:1359726. [PMID: 38511005 PMCID: PMC10952124 DOI: 10.3389/fmicb.2024.1359726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 02/28/2024] [Indexed: 03/22/2024] Open
Abstract
Mucins are large glycoproteins whose degradation requires the expression of several glycosil hydrolases to catalyze the cleavage of the oligosaccharide chains and release monosaccharides that can be assimilated. In this study, we present a characterization on the strains Clostridium celatum WC0700, Clostridium tertium WC0709, and Paraclostridium bifermentans WC0705. These three strains were previously isolated from enrichment cultures on mucin of fecal samples from healthy subjects and can use mucin as sole carbon and nitrogen source. Genome analysis and in vitro functional analysis of these strains elucidated their physiological and biochemical features. C. celatum WC0700 harbored the highest number of glycosyl hydrolases specific for mucin degradation, while P. bifermentans WC0705 had the least. These predicted differences were confirmed growing the strains on 5 mucin-decorating monosaccharides (L-fucose, N-Acetylneuraminic acid, galactose, N-acetylgalactosamine, and N-acetylglucosamine) as only source of carbon. Fermenting mucin, they all produced formic, acetic, propionic, butyric, isovaleric, and lactic acids, and ethanol; acetic acid was the main primary metabolite. Further catabolic capabilities were investigated, as well as antibiotic susceptibility, biofilm formation, tolerance to oxygen and temperature. The potential pathogenicity of the strains was evaluated through in silico research of virulence factors. The merge between comparative and functional genomics and biochemical/physiological characterization provided a comprehensive view of these mucin degraders, reassuring on the safety of these species and leaving ample scope for deeper investigations on the relationship with the host and for assessing if some relevant health-promoting effect could be ascribed to these SCFA producing species.
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Affiliation(s)
- Francesco Candeliere
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Eliana Musmeci
- Department of Civil, Chemical, Environmental and Material Engineering (DICAM), Alma Mater Studiorum University of Bologna, Bologna, Italy
| | - Laura Sola
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Alberto Amaretti
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
- Biogest Siteia, University of Modena and Reggio Emilia, Reggio Emilia, Italy
| | - Stefano Raimondi
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
- Biogest Siteia, University of Modena and Reggio Emilia, Reggio Emilia, Italy
| | - Maddalena Rossi
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
- Biogest Siteia, University of Modena and Reggio Emilia, Reggio Emilia, Italy
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8
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McDonald AG, Lisacek F. Simulated digestions of free oligosaccharides and mucin-type O-glycans reveal a potential role for Clostridium perfringens. Sci Rep 2024; 14:1649. [PMID: 38238389 PMCID: PMC10796942 DOI: 10.1038/s41598-023-51012-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 12/29/2023] [Indexed: 01/22/2024] Open
Abstract
The development of a stable human gut microbiota occurs within the first year of life. Many open questions remain about how microfloral species are influenced by the composition of milk, in particular its content of human milk oligosaccharides (HMOs). The objective is to investigate the effect of the human HMO glycome on bacterial symbiosis and competition, based on the glycoside hydrolase (GH) enzyme activities known to be present in microbial species. We extracted from UniProt a list of all bacterial species catalysing glycoside hydrolase activities (EC 3.2.1.-), cross-referencing with the BRENDA database, and obtained a set of taxonomic lineages and CAZy family data. A set of 13 documented enzyme activities was selected and modelled within an enzyme simulator according to a method described previously in the context of biosynthesis. A diverse population of experimentally observed HMOs was fed to the simulator, and the enzymes matching specific bacterial species were recorded, based on their appearance of individual enzymes in the UniProt dataset. Pairs of bacterial species were identified that possessed complementary enzyme profiles enabling the digestion of the HMO glycome, from which potential symbioses could be inferred. Conversely, bacterial species having similar GH enzyme profiles were considered likely to be in competition for the same set of dietary HMOs within the gut of the newborn. We generated a set of putative biodegradative networks from the simulator output, which provides a visualisation of the ability of organisms to digest HMO and mucin-type O-glycans. B. bifidum, B. longum and C. perfringens species were predicted to have the most diverse GH activity and therefore to excel in their ability to digest these substrates. The expected cooperative role of Bifidobacteriales contrasts with the surprising capacities of the pathogen. These findings indicate that potential pathogens may associate in human gut based on their shared glycoside hydrolase digestive apparatus, and which, in the event of colonisation, might result in dysbiosis. The methods described can readily be adapted to other enzyme categories and species as well as being easily fine-tuneable if new degrading enzymes are identified and require inclusion in the model.
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Affiliation(s)
- Andrew G McDonald
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, 1211, Geneva, Switzerland.
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland.
| | - Frédérique Lisacek
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, 1211, Geneva, Switzerland.
- Computer Science Department, University of Geneva, Geneva, Switzerland.
- Section of Biology, University of Geneva, Geneva, Switzerland.
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9
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Aziz K, Zaidi A, Rehman N. Probiotic profiling of bifidobacteria indigenous to the human intestinal mucosa shows alleviation of dysbiosis-associated pathogen biofilms. Arch Microbiol 2023; 205:176. [PMID: 37027059 DOI: 10.1007/s00203-023-03487-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 03/13/2023] [Accepted: 03/14/2023] [Indexed: 04/08/2023]
Abstract
The present study was undertaken to isolate bifidobacterial probiotics and characterize the biodiversity of mucosal bacteria in the human distal gut through 16S rRNA amplicon sequencing. Bifidobacterial strains obtained by selective culturing were investigated for biofilms and probiotic characteristics. Both culture-dependent and culture-independent approaches revealed substantial microbial diversity. Bifidobacterium strains yielded robust biofilms with predominantly exopolysaccharides and eDNA matrix. Microscopy revealed species-dependent spatial arrangement of microcolonies. Following probiotic profiling and safety assessment, the inter- and intra-specific interactions in in dual strain bifidobacterial biofilms were studied. As a species, only strains of B. bifidum exhibited exclusively inductive type of interactions whereas in other species, the interactions were more varied. On the other hand, in dual species biofilms, a preponderance of inductive interactions was evident between B. adolescentis, B. thermophilum, B. bifidum, and B. longum. The strong biofilm-formers also diminished pathogenic biofilm viability, and some were proficient in cholesterol removal in vitro. None of the strains exhibited harmful enzymatic activities associated with disease pathology. Interaction between biofilm-forming bifidobacterial strains provides an understanding of their functionality and persistence in the human host, and food or medicine. Their anti-pathogenic activity represents a therapeutic strategy against drug-resistant pathogenic biofilms.
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Affiliation(s)
- Kanwal Aziz
- National Probiotic Lab-National Institute for Biotechnology and Genetic Engineering-College (NIBGE-C), Jhang Road, Faisalabad, 38000, Punjab, Pakistan
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, 45650, Pakistan
| | - Arsalan Zaidi
- National Probiotic Lab-National Institute for Biotechnology and Genetic Engineering-College (NIBGE-C), Jhang Road, Faisalabad, 38000, Punjab, Pakistan.
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, 45650, Pakistan.
| | - Nadeem Rehman
- Kulsum International Hospital (KIH), 2020 Blue Area, Islamabad, Pakistan
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10
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Tran NTD, Chaidee A, Surapinit A, Yingklang M, Roytrakul S, Charoenlappanit S, Pinlaor P, Hongsrichan N, Anutrakulchai S, Cha'on U, Pinlaor S. Chronic Strongyloides stercoralis infection increases presence of the Ruminococcus torques group in the gut and alters the microbial proteome. Sci Rep 2023; 13:4216. [PMID: 36918707 PMCID: PMC10012286 DOI: 10.1038/s41598-023-31118-5] [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: 11/28/2022] [Accepted: 03/07/2023] [Indexed: 03/15/2023] Open
Abstract
We explored the impact of chronic Strongyloides stercoralis infection on the gut microbiome and microbial activity in a longitudinal study. At baseline (time-point T0), 42 fecal samples from matched individuals (21 positive for strongyloidiasis and 21 negative) were subjected to microbiome 16S-rRNA sequencing. Those positive at T0 (untreated then because of COVID19 lockdowns) were retested one year later (T1). Persistent infection in these individuals indicated chronic strongyloidiasis: they were treated with ivermectin and retested four months later (T2). Fecal samples at T1 and T2 were subjected to 16S-rRNA sequencing and LC-MS/MS to determine microbial diversity and proteomes. No significant alteration of indices of gut microbial diversity was found in chronic strongyloidiasis. However, the Ruminococcus torques group was highly over-represented in chronic infection. Metaproteome data revealed enrichment of Ruminococcus torques mucin-degrader enzymes in infection, possibly influencing the ability of the host to expel parasites. Metaproteomics indicated an increase in carbohydrate metabolism and Bacteroidaceae accounted for this change in chronic infection. STITCH interaction networks explored highly expressed microbial proteins before treatment and short-chain fatty acids involved in the synthesis of acetate. In conclusion, our data indicate that chronic S. stercoralis infection increases Ruminococcus torques group and alters the microbial proteome.
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Affiliation(s)
- Na T D Tran
- Department of Parasitology, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand.,Chronic Kidney Disease Prevention in Northeastern Thailand, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Apisit Chaidee
- Department of Parasitology, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand.,Chronic Kidney Disease Prevention in Northeastern Thailand, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Achirawit Surapinit
- Department of Parasitology, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
| | | | - Sitiruk Roytrakul
- Functional Proteomics Technology Laboratory, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Sawanya Charoenlappanit
- Functional Proteomics Technology Laboratory, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Porntip Pinlaor
- Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, 40002, Thailand.,Chronic Kidney Disease Prevention in Northeastern Thailand, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Nuttanan Hongsrichan
- Department of Parasitology, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand.,Chronic Kidney Disease Prevention in Northeastern Thailand, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Sirirat Anutrakulchai
- Department of Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand.,Chronic Kidney Disease Prevention in Northeastern Thailand, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Ubon Cha'on
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand.,Chronic Kidney Disease Prevention in Northeastern Thailand, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Somchai Pinlaor
- Department of Parasitology, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand. .,Chronic Kidney Disease Prevention in Northeastern Thailand, Khon Kaen University, Khon Kaen, 40002, Thailand.
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11
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Janapatla RP, Dudek A, Chen CL, Chuang CH, Chien KY, Feng Y, Yeh YM, Wang YH, Chang HJ, Lee YC, Chiu CH. Marine prebiotics mediate decolonization of Pseudomonas aeruginosa from gut by inhibiting secreted virulence factor interactions with mucins and enriching Bacteroides population. J Biomed Sci 2023; 30:9. [PMID: 36732731 PMCID: PMC9896862 DOI: 10.1186/s12929-023-00902-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 01/12/2023] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Pseudomonas aeruginosa intestinal carriage rates are significantly higher in immunosuppressed individuals and hospitalized patients who therefore have increased risk of infections and antibiotic-associated diarrhea. To combat intestinal dysbiosis and decolonize P. aeruginosa from gastrointestinal tract, we investigated the anti-adherence and gut microbiota modulation properties of marine prebiotic fucoidans. METHODS Proteomic analysis of culture supernatant was performed by LC-MS/MS. Using lectin-based enzyme-linked immunosorbent assay, hemagglutinin domain interaction and inhibition with biomolecules were studied. We investigated the role of nutritional grade fucoidans in a mouse model and used 16S ribosomal RNA sequencing to examine fecal microbiota composition. RESULTS Analysis of culture supernatant proteins indicated the secretion of two-partner secretion (TPS) family proteins, including TpsA1/CdiA2 and TpsA2/CdiA1. Lectin like activity at the N-terminal of TpsA due to a conserved hemagglutinin domain (Pfam identifier [ID] PF05860) mediates binding to mucins that carry multiple fucosylated glycans. Fucose-rich sulfated polysaccharides (fucoidans) and sulfated dextrans were found to be potent inhibitors of the recombinant N-terminal hemagglutinin domain of TpsA (TpsA-NT-HAD) binding to mucins. In a mouse model, antibiotic-induced dysbiosis was essential for P. aeruginosa gastrointestinal colonization. After prophylactic oral fucoidans supplementation, a higher proportion (60%) of the mice were decolonized over time and resisted re-colonization, this was associated with remarkable expansion of Bacteroides (post-infection day-3 abundance, 29-50%) and consequential reductions in bloom of Enterobacteriaceae and Enterococcaceae populations. In the non-supplemented group, Parabacteroides mediated recovery from dysbiosis but failed to decolonize P. aeruginosa. CONCLUSIONS Supplementing diet with marine prebiotic fucoidans can mediate earlier recovery from dysbiosis and decolonization of P. aeruginosa from gut by inhibiting secreted virulence factor (TpsA/CdiA) interaction with mucins and promoting the growth of beneficial Bacteroides population. We suggest the prophylactic use of nutritional grade fucoidans to decolonize P. aeruginosa from gastrointestinal tract of at-risk individuals to prevent infection and transmission of colonizing P. aeruginosa.
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Affiliation(s)
- Rajendra Prasad Janapatla
- grid.413801.f0000 0001 0711 0593Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Anna Dudek
- grid.413801.f0000 0001 0711 0593Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Chyi-Liang Chen
- grid.413801.f0000 0001 0711 0593Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | | | - Kun-Yi Chien
- grid.145695.a0000 0004 1798 0922Graduate Institute of Biomedical Sciences, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Ye Feng
- grid.13402.340000 0004 1759 700XInstitute for Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Yuan-Ming Yeh
- grid.413801.f0000 0001 0711 0593Chang Gung Microbiota Therapy Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Yi-Hsin Wang
- grid.413801.f0000 0001 0711 0593Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Hsin-Ju Chang
- grid.413801.f0000 0001 0711 0593Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Yuan-Chuan Lee
- grid.21107.350000 0001 2171 9311Department of Biology, Johns Hopkins University, Baltimore, MD USA
| | - Cheng-Hsun Chiu
- grid.413801.f0000 0001 0711 0593Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan ,grid.413801.f0000 0001 0711 0593Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
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12
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Huang L, Chen C. Employing pigs to decipher the host genetic effect on gut microbiome: advantages, challenges, and perspectives. Gut Microbes 2023; 15:2205410. [PMID: 37122143 PMCID: PMC10153013 DOI: 10.1080/19490976.2023.2205410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
The gut microbiota is a complex and diverse ecosystem comprised of trillions of microbes and plays an essential role in host's immunity, metabolism, and even behaviors. Environmental and host factors drive the huge variations in the gut microbiome among individuals. Here, we summarize accumulated evidences about host genetic effect on the gut microbial compositions with emphases on the correlation between host genetic kinship and the similarity of microbial compositions, heritability estimates of microbial taxa, and identification of genomic variants associated with the gut microbiome in pigs as well as in humans. A proportion of bacterial taxa have been reported to be heritable, and numerous variants associated with the diversity of the gut microbiota or specific taxa have been identified in both humans and pigs. LCT and ABO gene have been replicated in multiple studies, and its mechanism have been elucidated clearly. We also discuss the main advantages and challenges using pigs as experimental animals in exploring host genetic effect on the gut microbial composition and provided our insights on the perspectives in this area.
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Affiliation(s)
- Lusheng Huang
- National Key Laboratory of Pig Genetic Improvement, Jiangxi Agricultural University, Nanchang, China
| | - Congying Chen
- National Key Laboratory of Pig Genetic Improvement, Jiangxi Agricultural University, Nanchang, China
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13
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Deswal G, Selwal MK, Nirvan H, Selwal KK. Priestia flexa KS1: A new bacterial strain isolated from human faeces implicated in mucin degradation. Int Microbiol 2022:10.1007/s10123-022-00312-2. [PMID: 36502447 DOI: 10.1007/s10123-022-00312-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 11/29/2022] [Accepted: 12/02/2022] [Indexed: 12/14/2022]
Abstract
The human gut acts as a habitat for diverse microbial communities, including mucin utilizers that play a significant role in host health and diseases. In this study, a gram-positive, rod-shaped mucin degrading bacterium was isolated from human faeces that belonged to the Priestia flexa species. Priestia isolate was analyzed for mucin-degrading ability and found that the KS1 strain could grow on mucin as the sole carbon source. The experimental results of the mucolytic zone around the colony and a 58% decrease in carbohydrate concentration confirmed the ability of Priestia to degrade mucin. The intracellular and extracellular glycosidase assay data supported the above results suggesting the ability of P. flexa to produce glycan hydrolysis enzymes that convert complex mucin oligosaccharide chains into simple glycans. The survival ability of the KS1 strain in simulated gastrointestinal conditions revealed that it could tolerate low pH (≥ 50% cell viability at pH 1.0) and 0.5% bile salt concentration (≥ 85% cell viability). The strain showed low hydrophobicity towards n-hexadecane (26.51 ± 0.92%) and xylene (21.71 ± 0.54%). Moreover, the KS1 culture was resistant to cefixime, clavulanic acid/ceftazidime, nafallin, methicillin, trimethoprim, kanamycin, and nalidixic antibiotic. Our results highlight the isolation of P. flexa KS1 strain that degrade mucin under in vitro conditions and show its better acclimatization within the GI environment. Further studies are required to unearth the molecular mechanisms involved in the degradation of mucin oligosaccharides in the human gut, advancing our understanding of health and disease.
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14
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Wang X, Li Z, Li W, Li C, Liu J, Lu Y, Fan J, Ren H, Huang L, Wang Z. Gestational diabetes mellitus affects the fucosylation and sialylation levels of N/O-glycans in human milk glycoproteins. Carbohydr Polym 2022; 301:120312. [DOI: 10.1016/j.carbpol.2022.120312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/24/2022] [Accepted: 11/02/2022] [Indexed: 11/09/2022]
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15
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Pan M, Barua N, Ip M. Mucin-degrading gut commensals isolated from healthy faecal donor suppress intestinal epithelial inflammation and regulate tight junction barrier function. Front Immunol 2022; 13:1021094. [PMID: 36311778 PMCID: PMC9597641 DOI: 10.3389/fimmu.2022.1021094] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 09/16/2022] [Indexed: 11/24/2022] Open
Abstract
The intestinal epithelium surface is covered by a layer of mucus that harbors a complex and dynamic population of bacteria termed gut microbiota. In particular, some gut bacteria have the ability to degrade the mucin glycan for nutritional sources. However, the bacterial diversity of mucin-degrading bacteria in human gut microbiota and their role in the gut remains unclear. In this study, we characterized the diversity of mucin-degrading bacteria in the human gut microbiota by an established cultivation-based molecular profiling method. The results showed the gut commensals having the mucin degrading ability were widely distributed in the gut microbiota and were more abundant than previously thought. In addition, many previously uncharacterized mucin degraders were isolated from faecals samples, suggesting the mucin-degrading gut commensals were underappreciated. To gain a better understanding of the interaction between these mucin-degrading gut commensals and the host, the effect of the commensals on intestinal epithelial cells were examined, and the results revealed that the commensals (8 Bacteroides spp., 2 Parabacteroides spp, Akkermanisa muciniphila and Bifidobacterial dentium) incited low level of inflammatory response (IL-8 and TNF-α) but suppressed the inflammatory response induced by E. coli through downregulating the NF-κB pathway. The presence of gut commensals also showed potential in enhancing the epithelial tight junction (TJ) barrier function through regulating the mRNA expression of TJ protein genes such as Zo-1, Occludin, Claudin-1 and E-cadherin. Furthermore, the presence of commensal bacteria P. distasonis, B. thetaiotaomicron and A. muciniphila completely or partly restored the pro-inflammatory cytokine IL-1β induced TJ barrier disruption. In conclusion, these findings indicate that mucin-degrading gut commensals were widely distributed in the gut microbiota and showed anti-inflammatory effect against pathogen infection and potential in modulating the epithelial barrier function.
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Affiliation(s)
- Mingfang Pan
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Nilakshi Barua
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Margaret Ip
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Centre for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- *Correspondence: Margaret Ip,
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16
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N-glycosylation of cervicovaginal fluid reflects microbial community, immune activity, and pregnancy status. Sci Rep 2022; 12:16948. [PMID: 36216861 PMCID: PMC9551102 DOI: 10.1038/s41598-022-20608-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 09/15/2022] [Indexed: 12/29/2022] Open
Abstract
Human cervicovaginal fluid (CVF) is a complex, functionally important and glycan rich biological fluid, fundamental in mediating physiological events associated with reproductive health. Using a comprehensive glycomic strategy we reveal an extremely rich and complex N-glycome in CVF of pregnant and non-pregnant women, abundant in paucimannose and high mannose glycans, complex glycans with 2-4 N-Acetyllactosamine (LacNAc) antennae, and Poly-LacNAc glycans decorated with fucosylation and sialylation. N-glycosylation profiles were observed to differ in relation to pregnancy status, microbial composition, immune activation, and pregnancy outcome. Compared to CVF from women experiencing term birth, CVF from women who subsequently experienced preterm birth showed lower sialylation, which correlated to the presence of a diverse microbiome, and higher fucosylation, which correlated positively to pro-inflammatory cytokine concentration. This study is the first step towards better understanding the role of cervicovaginal glycans in reproductive health, their contribution to the mechanism of microbial driven preterm birth, and their potential for preventative therapy.
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17
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Exploring Bacterial Attributes That Underpin Symbiont Life in the Monogastric Gut. Appl Environ Microbiol 2022; 88:e0112822. [PMID: 36036591 PMCID: PMC9499014 DOI: 10.1128/aem.01128-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The large bowel of monogastric animals, such as that of humans, is home to a microbial community (microbiota) composed of a diversity of mostly bacterial species. Interrelationships between the microbiota as an entity and the host are complex and lifelong and are characteristic of a symbiosis. The relationships may be disrupted in association with disease, resulting in dysbiosis. Modifications to the microbiota to correct dysbiosis require knowledge of the fundamental mechanisms by which symbionts inhabit the gut. This review aims to summarize aspects of niche fitness of bacterial species that inhabit the monogastric gut, especially of humans, and to indicate the research path by which progress can be made in exploring bacterial attributes that underpin symbiont life in the gut.
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18
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Xia B, Zhong R, Wu W, Luo C, Meng Q, Gao Q, Zhao Y, Chen L, Zhang S, Zhao X, Zhang H. Mucin O-glycan-microbiota axis orchestrates gut homeostasis in a diarrheal pig model. MICROBIOME 2022; 10:139. [PMID: 36045454 PMCID: PMC9429786 DOI: 10.1186/s40168-022-01326-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 07/13/2022] [Indexed: 05/03/2023]
Abstract
BACKGROUND Post-weaning diarrhea in piglets reduces growth performance and increases mortality, thereby causing serious economic losses. The intestinal epithelial cells and microbiota reciprocally regulate each other in order to maintain intestinal homeostasis and control inflammation. However, a relative paucity of research has been focused on the host-derived regulatory network that controls mucin O-glycans and thereby changes gut microbiota during diarrhea in infancy. At the development stage just after birth, the ontogeny of intestinal epithelium, immune system, and gut microbiota appear similar in piglets and human infants. Here, we investigated the changes of mucin O-glycans associated with gut microbiota using a diarrheal post-weaned piglet model. RESULTS We found that diarrhea disrupted the colonic mucus layer and caused aberrant mucin O-glycans, including reduced acidic glycans and truncated glycans, leading to an impaired gut microenvironment. Subsequently, the onset of diarrhea, changes in microbiota and bacterial translocation, resulting in compromised epithelial barrier integrity, enhanced susceptibility to inflammation, and mild growth faltering. Furthermore, we found the activation of NLRP3 inflammasome complexes in the diarrheal piglets when compared to the healthy counterparts, triggered the release of proinflammatory cytokines IL-1β and IL-18, and diminished autophagosome formation, specifically the defective conversion of LC3A/B I into LC3A/B II and the accumulation of p62. Additionally, selective blocking of the autophagy pathway by 3-MA led to the reduction in goblet cell-specific gene transcript levels in vitro. CONCLUSIONS We observed that diarrheal piglets exhibited colonic microbiota dysbiosis and mucosal barrier dysfunction. Our data demonstrated that diarrhea resulted in the activation of inflammasomes and autophagy restriction along with aberrant mucin O-glycans including reduced acidic glycans and truncated glycans. The results suggested the mucin O-glycans-microbiota axis is likely associated with diarrheal pathogenesis. Our study provides novel insights into the pathophysiology of early-weaning-induced diarrheal disease in piglets and potentially understanding of disease mechanisms of diarrhea for human infants. Understanding the molecular pathology and pathogenesis of diarrhea is a prerequisite for the development of novel and effective therapies. Our data suggest that facilitating O-glycan elongation, modifying the microbiota, and developing specific inhibitors to some key inflammasomes could be the options for therapy of diarrhea including human infants. Video abstract.
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Affiliation(s)
- Bing Xia
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, 102206 China
| | - Ruqing Zhong
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Weida Wu
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Chengzeng Luo
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Qingshi Meng
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Qingtao Gao
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Yong Zhao
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Liang Chen
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Sheng Zhang
- Institute of Biotechnology, Cornell University, Ithaca, NY 14853 USA
| | - Xin Zhao
- Department of Animal Science, McGill University, Montreal, Quebec H9X3V9 Canada
| | - Hongfu Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
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19
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Greene LK, Andriambeloson JB, Rasoanaivo HA, Yoder AD, Blanco MB. Variation in gut microbiome structure across the annual hibernation cycle in a wild primate. FEMS Microbiol Ecol 2022; 98:6604834. [PMID: 35679092 DOI: 10.1093/femsec/fiac070] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 05/07/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
The gut microbiome can mediate host metabolism, including facilitating energy-saving strategies like hibernation. The dwarf lemurs of Madagascar (Cheirogaleus spp.) are the only obligate hibernators among primates. They also hibernate in the subtropics, and unlike temperate hibernators, fatten by converting fruit sugars to lipid deposits, torpor at relatively warm temperatures, and forage for a generalized diet after emergence. Despite these ecological differences, we might expect hibernation to shape the gut microbiome in similar ways across mammals. We, therefore, compare gut microbiome profiles, determined by amplicon sequencing of rectal swabs, in wild furry-eared dwarf lemurs (C. crossleyi) during fattening, hibernation, and after emergence. The dwarf lemurs exhibited reduced gut microbial diversity during fattening, intermediate diversity and increased community homogenization during hibernation, and greatest diversity after emergence. The Mycoplasma genus was enriched during fattening, whereas the Aerococcaceae and Actinomycetaceae families, and not Akkermansia, bloomed during hibernation. As expected, the dwarf lemurs showed seasonal reconfigurations of the gut microbiome; however, the patterns of microbial diversity diverged from temperate hibernators, and better resembled the shifts associated with dietary fruits and sugars in primates and model organisms. Our results thus highlight the potential for dwarf lemurs to probe microbiome-mediated metabolism in primates under contrasting conditions.
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Affiliation(s)
- Lydia K Greene
- The Duke Lemur Center, 3705 Erwin Road, Durham, NC 27705, United States.,Department of Biology, Duke University, Durham, NC 27708, United States
| | - Jean-Basile Andriambeloson
- Department of Zoology and Animal Biodiversity, Faculty of Science, University of Antananarivo, Antananarivo, Madagascar
| | - Hoby A Rasoanaivo
- Department of Science and Veterinary Medicine, Faculty of Medicine, University of Antananarivo, Antananarivo, Madagascar
| | - Anne D Yoder
- Department of Biology, Duke University, Durham, NC 27708, United States
| | - Marina B Blanco
- The Duke Lemur Center, 3705 Erwin Road, Durham, NC 27705, United States.,Department of Biology, Duke University, Durham, NC 27708, United States
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20
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Ge X, Pereira FC, Mitteregger M, Berry D, Zhang M, Hausmann B, Zhang J, Schintlmeister A, Wagner M, Cheng JX. SRS-FISH: A high-throughput platform linking microbiome metabolism to identity at the single-cell level. Proc Natl Acad Sci U S A 2022; 119:e2203519119. [PMID: 35727976 PMCID: PMC9245642 DOI: 10.1073/pnas.2203519119] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/08/2022] [Indexed: 12/26/2022] Open
Abstract
One of the biggest challenges in microbiome research in environmental and medical samples is to better understand functional properties of microbial community members at a single-cell level. Single-cell isotope probing has become a key tool for this purpose, but the current detection methods for determination of isotope incorporation into single cells do not allow high-throughput analyses. Here, we report on the development of an imaging-based approach termed stimulated Raman scattering-two-photon fluorescence in situ hybridization (SRS-FISH) for high-throughput metabolism and identity analyses of microbial communities with single-cell resolution. SRS-FISH offers an imaging speed of 10 to 100 ms per cell, which is two to three orders of magnitude faster than achievable by state-of-the-art methods. Using this technique, we delineated metabolic responses of 30,000 individual cells to various mucosal sugars in the human gut microbiome via incorporation of deuterium from heavy water as an activity marker. Application of SRS-FISH to investigate the utilization of host-derived nutrients by two major human gut microbiome taxa revealed that response to mucosal sugars tends to be dominated by Bacteroidales, with an unexpected finding that Clostridia can outperform Bacteroidales at foraging fucose. With high sensitivity and speed, SRS-FISH will enable researchers to probe the fine-scale temporal, spatial, and individual activity patterns of microbial cells in complex communities with unprecedented detail.
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Affiliation(s)
- Xiaowei Ge
- Department of Electrical & Computer Engineering, Boston University, Boston, MA 02215
| | - Fátima C. Pereira
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, 1030 Vienna, Austria
| | - Matthias Mitteregger
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, 1030 Vienna, Austria
| | - David Berry
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, 1030 Vienna, Austria
| | - Meng Zhang
- Department of Electrical & Computer Engineering, Boston University, Boston, MA 02215
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, 1030 Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria
| | - Jing Zhang
- Department of Biomedical Engineering, Photonics Center, Boston University, Boston, MA 02215
| | - Arno Schintlmeister
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, 1030 Vienna, Austria
| | - Michael Wagner
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, 1030 Vienna, Austria
- Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark
| | - Ji-Xin Cheng
- Department of Electrical & Computer Engineering, Boston University, Boston, MA 02215
- Department of Biomedical Engineering, Photonics Center, Boston University, Boston, MA 02215
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21
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Amandine C, Ebert D, Stukenbrock E, Rodríguez de la Vega RC, Tiffin P, Croll D, Tellier A. Unraveling coevolutionary dynamics using ecological genomics. Trends Genet 2022; 38:1003-1012. [PMID: 35715278 DOI: 10.1016/j.tig.2022.05.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 05/08/2022] [Accepted: 05/10/2022] [Indexed: 11/27/2022]
Abstract
Coevolutionary interactions, from the delicate co-dependency in mutualistic interactions to the antagonistic relationship of hosts and parasites, are a ubiquitous driver of adaptation. Surprisingly, little is known about the genomic processes underlying coevolution in an ecological context. However, species comprise genetically differentiated populations that interact with temporally variable abiotic and biotic environments. We discuss the recent advances in coevolutionary theory and genomics as well as shortcomings, to identify coevolving genes that take into account this spatial and temporal variability of coevolution, and propose a practical guide to understand the dynamic of coevolution using an ecological genomics lens.
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Affiliation(s)
- Cornille Amandine
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190 Gif-sur-Yvette, France.
| | - Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland
| | - Eva Stukenbrock
- Max Planck Institute for Terrestrial Microbiology, Max Planck Research Group, Fungal Biodiversity, Marburg, Germany
| | | | - Peter Tiffin
- Department of Plant and Microbial Biology, 250 Biological Sciences, 1445 Gortner Ave., University of Minnesota, Saint Paul, MN 55108, USA
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland.
| | - Aurélien Tellier
- Population Genetics, Department of Life Science Systems, Technical University of Munich, Liesel-Beckman-Str. 2, 85354 Freising, Germany.
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22
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ABO genotype alters the gut microbiota by regulating GalNAc levels in pigs. Nature 2022; 606:358-367. [PMID: 35477154 PMCID: PMC9157047 DOI: 10.1038/s41586-022-04769-z] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 04/19/2022] [Indexed: 12/12/2022]
Abstract
The composition of the intestinal microbiome varies considerably between individuals and is correlated with health1. Understanding the extent to which, and how, host genetics contributes to this variation is essential yet has proved to be difficult, as few associations have been replicated, particularly in humans2. Here we study the effect of host genotype on the composition of the intestinal microbiota in a large mosaic pig population. We show that, under conditions of exacerbated genetic diversity and environmental uniformity, microbiota composition and the abundance of specific taxa are heritable. We map a quantitative trait locus affecting the abundance of Erysipelotrichaceae species and show that it is caused by a 2.3 kb deletion in the gene encoding N-acetyl-galactosaminyl-transferase that underpins the ABO blood group in humans. We show that this deletion is a ≥3.5-million-year-old trans-species polymorphism under balancing selection. We demonstrate that it decreases the concentrations of N-acetyl-galactosamine in the gut, and thereby reduces the abundance of Erysipelotrichaceae that can import and catabolize N-acetyl-galactosamine. Our results provide very strong evidence for an effect of the host genotype on the abundance of specific bacteria in the intestine combined with insights into the molecular mechanisms that underpin this association. Our data pave the way towards identifying the same effect in rural human populations. The host blood-type-associated ABO genotype affects the abundance of specific bacteria in the pig intestine.
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23
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Glover JS, Ticer TD, Engevik MA. Characterizing the mucin-degrading capacity of the human gut microbiota. Sci Rep 2022; 12:8456. [PMID: 35589783 PMCID: PMC9120202 DOI: 10.1038/s41598-022-11819-z] [Citation(s) in RCA: 91] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 04/01/2022] [Indexed: 01/09/2023] Open
Abstract
Mucin-degrading microbes are known to harbor glycosyl hydrolases (GHs) which cleave specific glycan linkages. Although several microbial species have been identified as mucin degraders, there are likely many other members of the healthy gut community with the capacity to degrade mucins. The aim of the present study was to systematically examine the CAZyme mucin-degrading profiles of the human gut microbiota. Within the Verrucomicrobia phylum, all Akkermansia glycaniphila and muciniphila genomes harbored multiple gene copies of mucin-degrading GHs. The only representative of the Lentisphaerae phylum, Victivallales, harbored a GH profile that closely mirrored Akkermansia. In the Actinobacteria phylum, we found several Actinomadura, Actinomyces, Bifidobacterium, Streptacidiphilus and Streptomyces species with mucin-degrading GHs. Within the Bacteroidetes phylum, Alistipes, Alloprevotella, Bacteroides, Fermenitomonas Parabacteroides, Prevotella and Phocaeicola species had mucin degrading GHs. Firmicutes contained Abiotrophia, Blautia, Enterococcus, Paenibacillus, Ruminococcus, Streptococcus, and Viridibacillus species with mucin-degrading GHs. Interestingly, far fewer mucin-degrading GHs were observed in the Proteobacteria phylum and were found in Klebsiella, Mixta, Serratia and Enterobacter species. We confirmed the mucin-degrading capability of 23 representative gut microbes using a chemically defined media lacking glucose supplemented with porcine intestinal mucus. These data greatly expand our knowledge of microbial-mediated mucin degradation within the human gut microbiota.
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Affiliation(s)
- Janiece S Glover
- Department of Regenerative Medicine & Cell Biology, Medical University of South Carolina, Charleston, SC, USA
| | - Taylor D Ticer
- Department of Regenerative Medicine & Cell Biology, Medical University of South Carolina, Charleston, SC, USA
- Department of Microbiology & Immunology, Medical University of South Carolina, Charleston, SC, USA
| | - Melinda A Engevik
- Department of Regenerative Medicine & Cell Biology, Medical University of South Carolina, Charleston, SC, USA.
- Department of Microbiology & Immunology, Medical University of South Carolina, Charleston, SC, USA.
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24
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Haro C, Guzmán-López MH, Marín-Sanz M, Sánchez-León S, Vaquero L, Pastor J, Comino I, Sousa C, Vivas S, Landa BB, Barro F. Consumption of Tritordeum Bread Reduces Immunogenic Gluten Intake without Altering the Gut Microbiota. Foods 2022; 11:foods11101439. [PMID: 35627010 PMCID: PMC9142130 DOI: 10.3390/foods11101439] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/13/2022] [Accepted: 05/15/2022] [Indexed: 12/04/2022] Open
Abstract
Gluten proteins are responsible for the wheat breadmaking quality. However, gluten is also related to human pathologies for which the only treatment is a gluten-free diet (GFD). GFD has gained popularity among individuals who want to reduce their gluten intake. Tritordeum is a cereal species that originated after crossing durum wheat with wild barley and differs from bread wheat in its gluten composition. In this work, we have characterized the immunogenic epitopes of tritordeum bread and results from a four-phase study with healthy adults for preferences of bread and alterations in the gut microbiota after consuming wheat bread, gluten-free bread, and tritordeum bread are reported. Tritordeum presented fewer peptides related to gluten proteins, CD-epitopes, and IgE binding sites than bread wheat. Participants rated tritordeum bread higher than gluten-free bread. Gut microbiota analysis revealed that the adherence to a strict GFD involves some minor changes, especially altering the species producing short-chain fatty acids. However, the short-term consumption of tritordeum bread does not induce significant changes in the diversity or community composition of the intestinal microbiota in healthy individuals. Therefore, tritordeum bread could be an alternative for healthy individuals without wheat-related pathologies who want to reduce their gluten consumption without harming their gut health.
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Affiliation(s)
- Carmen Haro
- Department of Crop Protection, Institute for Sustainable Agriculture—Spanish National Research Council (IAS—CSIC), 14004 Córdoba, Spain; (C.H.); (B.B.L.)
| | - María H. Guzmán-López
- Department of Plant Breeding, Institute for Sustainable Agriculture—Spanish National Research Council (IAS—CSIC), 14004 Córdoba, Spain; (M.M.-S.); (S.S.-L.)
- Correspondence: (M.H.G.-L.); (F.B.)
| | - Miriam Marín-Sanz
- Department of Plant Breeding, Institute for Sustainable Agriculture—Spanish National Research Council (IAS—CSIC), 14004 Córdoba, Spain; (M.M.-S.); (S.S.-L.)
| | - Susana Sánchez-León
- Department of Plant Breeding, Institute for Sustainable Agriculture—Spanish National Research Council (IAS—CSIC), 14004 Córdoba, Spain; (M.M.-S.); (S.S.-L.)
| | - Luis Vaquero
- Department of Gastroenterology, Hospital of León, Biomedicine Institute, University of León, 24071 León, Spain; (L.V.); (S.V.)
| | - Jorge Pastor
- Novapan, S.L., C/Chopo, 68-70, 50171 La Puebla de Alfinden, Spain;
| | - Isabel Comino
- Department of Microbiology and Parasitology, Pharmacy Faculty, University of Seville, 41004 Seville, Spain; (I.C.); (C.S.)
| | - Carolina Sousa
- Department of Microbiology and Parasitology, Pharmacy Faculty, University of Seville, 41004 Seville, Spain; (I.C.); (C.S.)
| | - Santiago Vivas
- Department of Gastroenterology, Hospital of León, Biomedicine Institute, University of León, 24071 León, Spain; (L.V.); (S.V.)
| | - Blanca B. Landa
- Department of Crop Protection, Institute for Sustainable Agriculture—Spanish National Research Council (IAS—CSIC), 14004 Córdoba, Spain; (C.H.); (B.B.L.)
| | - Francisco Barro
- Department of Plant Breeding, Institute for Sustainable Agriculture—Spanish National Research Council (IAS—CSIC), 14004 Córdoba, Spain; (M.M.-S.); (S.S.-L.)
- Correspondence: (M.H.G.-L.); (F.B.)
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25
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Contrasting Health Effects of Bacteroidetes and Firmicutes Lies in Their Genomes: Analysis of P450s, Ferredoxins, and Secondary Metabolite Clusters. Int J Mol Sci 2022; 23:ijms23095057. [PMID: 35563448 PMCID: PMC9100364 DOI: 10.3390/ijms23095057] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 04/29/2022] [Accepted: 04/29/2022] [Indexed: 01/27/2023] Open
Abstract
Species belonging to the bacterial phyla Bacteroidetes and Firmicutes represent over 90% of the gastrointestinal microbiota. Changes in the ratio of these two bacterial groups were found to have contrasting health effects, including obesity and inflammatory diseases. Despite the availability of many bacterial genomes, comparative genomic studies on the gene pools of these two bacterial groups concerning cytochrome P450 monooxygenases (P450s), ferredoxins, and secondary metabolite biosynthetic gene clusters (smBGCs) are not reported. This study is aimed to address this research gap. The study revealed the presence of diverse sets of P450s, ferredoxins, and smBGCs in their genomes. Bacteroidetes species have the highest number of P450 families, ferredoxin cluster-types, and smBGCs compared to Firmicutes species. Only four P450 families, three ferredoxin cluster types, and five smBGCs are commonly shared between these two bacterial groups. Considering the above facts, we propose that the contrasting effects of these two bacterial groups on the host are partly due to the distinct nature of secondary metabolites produced by these organisms. Thus, the cause of the contrasting health effects of these two bacterial groups lies in their gene pools.
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26
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Wu Q, Liang Y, Kong Y, Zhang F, Feng Y, Ouyang Y, Wang C, Guo Z, Xiao J, Feng N. Role of glycated proteins in vivo: Enzymatic glycated proteins and non-enzymatic glycated proteins. Food Res Int 2022; 155:111099. [DOI: 10.1016/j.foodres.2022.111099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 02/24/2022] [Accepted: 03/03/2022] [Indexed: 11/04/2022]
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27
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Barnes NM, Wu H. Mechanisms regulating the airborne survival of Klebsiella pneumoniae under different relative humidity and temperature levels. INDOOR AIR 2022; 32:e12991. [PMID: 35225398 DOI: 10.1111/ina.12991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 12/23/2021] [Accepted: 01/20/2022] [Indexed: 06/14/2023]
Abstract
In this study, Klebsiella pneumoniae was suspended in synthetic saliva in a nebulizer (N0 ) and nebulized for 5 min (N5 ) into an aerosol chamber and further prolonged in the aerosolization phase for 15 min (A15 ) under four different conditions: 20°C, 50% relative humidity (RH); 20°C, 80% RH; 30°C, 50% RH; and 30°C, 80% RH. Samples were collected at N0 , N5 , and A15 , then subjected to survival analysis and comparative transcriptomic analysis in order to help elucidate the underlying mechanisms of airborne survival. Survival analysis shows that a higher humidity and lower temperature were favorable for the airborne survival of K. pneumoniae, and the effect of RH was more remarkable at 20°C than that at 30°C. The RNA-seq results show that during the nebulization phase (N0 vs. N5 ), a total number of 201 differentially expressed genes (DEGs) were identified (103 downregulated and 98 upregulated). Comparison between nebulization and aerosolization phases (N5 vs. A15 ) indicates up to 132 DEGs, with 46 downregulated and 86 upregulated. The most notable groups of genes are those involved in cellular remodeling, metabolism and energy processes. Alarmingly, the mbl gene, which encodes antibiotic resistance in K. pneumoniae, was upregulated during the suspension phase under all the tested conditions. This study provides insights into the control of airborne transmitted diseases.
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Affiliation(s)
- Natasha Maria Barnes
- Department of Biology, Hong Kong Special Administrative Region, Hong Kong Baptist University, Hong Kong, China
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, India
| | - Haoxiang Wu
- Department of Biology, Hong Kong Special Administrative Region, Hong Kong Baptist University, Hong Kong, China
- Institute of Bioresource and Agriculture, Hong Kong Special Administrative Region, Hong Kong Baptist University, Hong Kong, China
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28
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Abstract
The immune system in the large intestine is separated from commensal microbes and comparatively rare enteric pathogens by a monolayer of diverse epithelial cells overlaid with a compact and adherent inner mucus layer and a looser outer mucus layer. Microorganisms, collectively referred to as the mucus-associated (MA) microbiota, physically inhabit this mucus barrier, resulting in a dynamic and incessant dialog to maintain both spatial segregation and immune tolerance. Recent major findings reveal novel features of the crosstalk between the immune system and mucus-associated bacteria in health and disease, as well as disease-related peripheral immune signatures indicative of host responses to these organisms. In this brief review, we integrate these novel observations into our overall understanding of host-microbiota mutualism at the colonic mucosal border and speculate on the significance of this emerging knowledge for our understanding of the prevention, development, and progression of chronic intestinal inflammation.
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Affiliation(s)
- Qing Zhao
- Department of Medicine, University of Alabama at Birmingham, Birmingham, 35294, USA
| | - Craig L. Maynard
- Department of Medicine, University of Alabama at Birmingham, Birmingham, 35294, USA
- Department of Pathology, University of Alabama at Birmingham, Birmingham, 35294, USA
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29
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The influence of early-life microbial exposures on long-term respiratory health. Paediatr Respir Rev 2021; 40:15-23. [PMID: 34140238 DOI: 10.1016/j.prrv.2021.05.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 05/20/2021] [Indexed: 11/21/2022]
Abstract
Host-microbiome interactions exert a profound influence on human physiology and health outcomes. In particular, certain characteristics of commensal microbiota during a critical period in early life are essential for the establishment of immune tone and metabolic control. An increasing body of evidence suggests that early life exposures that disrupt these interactions can substantially influence life-long risks for respiratory disease. Here, we explore how such early life exposures, including antibiotic exposure, maternal diet, preterm birth, mode of delivery, breastfeeding, and environmental variables shape the infant microbiome, and the mechanisms by such changes can in turn impact respiratory health.
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30
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The Intestinal Dysbiosis of Mothers with Gestational Diabetes Mellitus (GDM) and Its Impact on the Gut Microbiota of Their Newborns. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2021; 2021:3044534. [PMID: 34603565 PMCID: PMC8481071 DOI: 10.1155/2021/3044534] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 09/11/2021] [Indexed: 02/06/2023]
Abstract
Gestational diabetes mellitus (GDM) is defined as “diagnosed as impaired glucose tolerance for the first time during pregnancy,” which can lead to adverse pregnancy outcomes and produces divergent effects on mothers and newborns. In recent years, with the continuous expansion of obese people, GDM shows an upward trend. The abundant and diverse members of the human gut microbiota exert critical roles in the maintenance of human health. Studies have shown that GDM may be associated with disordered gut microbiota in both mothers and newborns. Taking into account the potential effects on maternal and consequently neonatal health, in this review, we analyzed the available data and discussed the current knowledge about the potential relationship between GDM and intestinal dysbiosis in mothers and newborns. In addition, we also discussed the influencing factors derived from GDM mothers on the gut microbiome of their newborns, including the vertical transmission of microbiota from mothers, the alteration of milk components of GDM mothers, and using of probiotics. Hoping that new insights into the role of the gut microbiota in GDM could lead to the development of integrated strategies to prevent and treat these metabolic disorders.
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31
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Ijssennagger N, van Rooijen KS, Magnúsdóttir S, Ramos Pittol JM, Willemsen ECL, de Zoete MR, Baars MJD, Stege PB, Colliva C, Pellicciari R, Youssef SA, de Bruin A, Vercoulen Y, Kuipers F, van Mil SWC. Ablation of liver Fxr results in an increased colonic mucus barrier in mice. JHEP Rep 2021; 3:100344. [PMID: 34604725 PMCID: PMC8463863 DOI: 10.1016/j.jhepr.2021.100344] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/16/2021] [Accepted: 07/22/2021] [Indexed: 12/12/2022] Open
Abstract
Background & Aims The interorgan crosstalk between the liver and the intestine has been the focus of intense research. Key in this crosstalk are bile acids, which are secreted from the liver into the intestine, interact with the microbiome, and upon absorption reach back to the liver. The bile acid-activated farnesoid X receptor (Fxr) is involved in the gut-to-liver axis. However, liver-to-gut communication and the roles of bile acids and Fxr remain elusive. Herein, we aim to get a better understanding of Fxr-mediated liver-to-gut communication, particularly in colon functioning. Methods Fxr floxed/floxed mice were crossed with cre-expressing mice to yield Fxr ablation in the intestine (Fxr-intKO), liver (Fxr-livKO), or total body (Fxr-totKO). The effects on colonic gene expression (RNA sequencing), the microbiome (16S sequencing), and mucus barrier function by ex vivo imaging were analysed. Results Despite relatively small changes in biliary bile acid concentration and composition, more genes were differentially expressed in the colons of Fxr-livKO mice than in those of Fxr-intKO and Fxr-totKO mice (3272, 731, and 1824, respectively). The colons of Fxr-livKO showed increased expression of antimicrobial genes, Toll-like receptors, inflammasome-related genes and genes belonging to the ‘Mucin-type O-glycan biosynthesis’ pathway. Fxr-livKO mice have a microbiome profile favourable for the protective capacity of the mucus barrier. The thickness of the inner sterile mucus layer was increased and colitis symptoms reduced in Fxr-livKO mice. Conclusions Targeting of FXR is at the forefront in the battle against metabolic diseases. We show that ablation of Fxr in the liver greatly impacts colonic gene expression and increased the colonic mucus barrier. Increasing the mucus barrier is of utmost importance to battle intestinal diseases such as inflammatory bowel disease, and we show that this might be done by antagonising FXR in the liver. Lay summary This study shows that the communication of the liver to the intestine is crucial for intestinal health. Bile acids are key players in this liver-to-gut communication, and when Fxr, the master regulator of bile acid homoeostasis, is ablated in the liver, colonic gene expression is largely affected, and the protective capacity of the mucus barrier is increased. Fxr ablation in the mouse liver has a major impact on colonic gene expression. Fxr signalling is induced in the colons of liver Fxr knockout (Fxr-livKO) mice. In Fxr-livKO colons, expression of antimicrobial and mucus genes is increased. Microbiome of Fxr-livKO mice is indicative of enhanced mucus barrier function. Fxr-livKO mice have an increased mucus barrier.
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Key Words
- BAs, bile acids
- Colon
- DSS, dextran sodium sulfate
- FITC, fluorescein isothiocyanate
- Farnesoid X receptor
- Fgfr4, fibroblast growth factor receptor 4
- Fxr, farnesoid X receptor
- Fxr-intKO, intestine-specific Fxr knockout
- Fxr-livKO, liver-specific Fxr knockout
- Fxr-totKO, whole body Fxr knockout
- GO, Gene Ontology
- Gut microbiome
- HID, high-iron diamine
- IBD, inflammatory bowel disease
- Intestine-specific Fxr-KO mouse
- KEGG, Kyoto Encyclopedia of Genes and Genomes
- Liver-specific Fxr-KO mouse
- Liver–gut axis
- Mucus layer
- RT qPCR, real-time quantitative PCR
- fpkm, fragments per kilobase of transcript per million mapped reads
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Affiliation(s)
- Noortje Ijssennagger
- Department of Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Kristel S van Rooijen
- Department of Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Stefanía Magnúsdóttir
- Department of Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - José M Ramos Pittol
- Department of Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands.,Institute of Biochemistry, University of Innsbruck, Innsbruck, Austria
| | - Ellen C L Willemsen
- Department of Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Marcel R de Zoete
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Matthijs J D Baars
- Department of Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Paul B Stege
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | | | - Sameh A Youssef
- Non-Clinical Safety, Department of Pathology, Janssen Pharmaceutica Research and Development, Beerse, Belgium
| | - Alain de Bruin
- Departments of Pediatrics and Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Yvonne Vercoulen
- Department of Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Folkert Kuipers
- Departments of Pediatrics and Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Saskia W C van Mil
- Department of Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
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Colonized Niche, Evolution and Function Signatures of Bifidobacterium pseudolongum within Bifidobacterial Genus. Foods 2021; 10:foods10102284. [PMID: 34681333 PMCID: PMC8535030 DOI: 10.3390/foods10102284] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/12/2021] [Accepted: 09/13/2021] [Indexed: 01/07/2023] Open
Abstract
Background: Although genomic features of various bifidobacterial species have received much attention in the past decade, information on Bifidobacterium pseudolongum was limited. In this study, we retrieved 887 publicly available genomes of bifidobacterial species, and tried to elucidate phylogenetic and potential functional roles of B. pseudolongum within the Bifidobacterium genus. Results: The results indicated that B. pseudolongum formed a population structure with multiple monophyletic clades, and had established associations with different types of mammals. The abundance of B. pseudolongum was inversely correlated with that of the harmful gut bacterial taxa. We also found that B. pseudolongum showed a strictly host-adapted lifestyle with a relatively smaller genome size, and higher intra-species genetic diversity in comparison with the other tested bifidobacterial species. For functional aspects, B. pseudolongum showed paucity of specific metabolic functions, and enrichment of specific enzymes degrading complex plant carbohydrates and host glycans. In addition, B. pseudolongum possessed a unique signature of probiotic effector molecules compared with the other tested bifidobacterial species. The investigation on intra-species evolution of B. pseudolongum indicated a clear evolution trajectory in which considerable clade-specific genes, and variation on genomic diversity by clade were observed. Conclusions: These findings provide valuable information for explaining the host adaptability of B. pseudolongum, its evolutionary role, as well as its potential probiotic effects.
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Chu ND, Crothers JW, Nguyen LTT, Kearney SM, Smith MB, Kassam Z, Collins C, Xavier R, Moses PL, Alm EJ. Dynamic Colonization of Microbes and Their Functions after Fecal Microbiota Transplantation for Inflammatory Bowel Disease. mBio 2021; 12:e0097521. [PMID: 34281401 PMCID: PMC8406238 DOI: 10.1128/mbio.00975-21] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 06/09/2021] [Indexed: 12/26/2022] Open
Abstract
For fecal microbiota transplantation (FMT) to be successful in immune diseases like inflammatory bowel disease, it is assumed that therapeutic microbes and their beneficial functions and immune interactions must colonize a recipient patient and persist in sufficient quantity and for a sufficient period of time to produce a clinical benefit. Few studies, however, have comprehensively profiled the colonization and persistence of transferred microbes along with the transfer of their microbial functions and interactions with the host immune system. Using 16S, metagenomic, and immunoglobulin A (IgA) sequencing, we analyzed hundreds of longitudinal microbiome samples from a randomized controlled trial of 12 patients with ulcerative colitis who received fecal transplant or placebo for 12 weeks. We uncovered diverse competitive dynamics among donor and patient strains, showing that persistence of transferred microbes is far from static. Indeed, one patient experienced a dramatic loss of donor bacteria 10 weeks into the trial, coinciding with a bloom of pathogenic bacteria and worsening symptoms. We evaluated the transfer of microbial functions, including desired ones, such as butyrate production, and unintended ones, such as antibiotic resistance. By profiling bacteria coated with IgA, we identified bacteria associated with inflammation and found that microbial interactions with the host immune system can be transferred across people, which could play a role in gut microbiome therapeutics for immune-related diseases. Our findings shed light on the colonization dynamics of gut microbes and their functions in the context of FMT to treat a complex disease-information that may provide a foundation for developing more-targeted therapeutics. IMPORTANCE Fecal microbiota transplantation (FMT)-transferring fecal microbes from a healthy donor to a sick patient-has shown promise for gut diseases such as inflammatory bowel disease. Unlike pharmaceuticals, however, fecal transplants are complex mixtures of living organisms, which must then interact with the microbes and immune system of the recipient. We sought to understand these interactions by tracking the microbes of 12 inflammatory bowel disease patients who received fecal transplants for 12 weeks. We uncovered a range of dynamics. For example, one patient experienced successful transfer of donor bacteria, only to lose them after 10 weeks. We similarly evaluated transfer of microbial functions, including how they interacted with the recipient's immune system. Our findings shed light on the colonization dynamics of gut microbes, as well as their functions in the context of FMT-information that may provide a critical foundation for the development of more-targeted therapeutics.
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Affiliation(s)
- Nathaniel D. Chu
- Center for Microbiome Informatics and Therapeutics, Broad Institute, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Graduate Program in Microbiology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | - Le T. T. Nguyen
- Center for Microbiome Informatics and Therapeutics, Broad Institute, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Sean M. Kearney
- Center for Microbiome Informatics and Therapeutics, Broad Institute, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | - Zain Kassam
- Finch Therapeutics, Somerville, Massachusetts, USA
| | - Cheryl Collins
- Larner College of Medicine, University of Vermont, Burlington, Vermont, USA
| | - Ramnik Xavier
- Center for Microbiome Informatics and Therapeutics, Broad Institute, Cambridge, Massachusetts, USA
- Broad Institute, Cambridge, Massachusetts, USA
| | - Peter L. Moses
- Larner College of Medicine, University of Vermont, Burlington, Vermont, USA
| | - Eric J. Alm
- Center for Microbiome Informatics and Therapeutics, Broad Institute, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Graduate Program in Microbiology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Broad Institute, Cambridge, Massachusetts, USA
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Severi E, Rudden M, Bell A, Palmer T, Juge N, Thomas GH. Multiple evolutionary origins reflect the importance of sialic acid transporters in the colonization potential of bacterial pathogens and commensals. Microb Genom 2021; 7. [PMID: 34184979 PMCID: PMC8461474 DOI: 10.1099/mgen.0.000614] [Citation(s) in RCA: 4] [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
Located at the tip of cell surface glycoconjugates, sialic acids are at the forefront of host-microbe interactions and, being easily liberated by sialidase enzymes, are used as metabolites by numerous bacteria, particularly by pathogens and commensals living on or near diverse mucosal surfaces. These bacteria rely on specific transporters for the acquisition of host-derived sialic acids. Here, we present the first comprehensive genomic and phylogenetic analysis of bacterial sialic acid transporters, leading to the identification of multiple new families and subfamilies. Our phylogenetic analysis suggests that sialic acid-specific transport has evolved independently at least eight times during the evolution of bacteria, from within four of the major families/superfamilies of bacterial transporters, and we propose a robust classification scheme to bring together a myriad of different nomenclatures that exist to date. The new transporters discovered occur in diverse bacteria, including Spirochaetes, Bacteroidetes, Planctomycetes and Verrucomicrobia, many of which are species that have not been previously recognized to have sialometabolic capacities. Two subfamilies of transporters stand out in being fused to the sialic acid mutarotase enzyme, NanM, and these transporter fusions are enriched in bacteria present in gut microbial communities. Our analysis supports the increasing experimental evidence that competition for host-derived sialic acid is a key phenotype for successful colonization of complex mucosal microbiomes, such that a strong evolutionary selection has occurred for the emergence of sialic acid specificity within existing transporter architectures.
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Affiliation(s)
- Emmanuele Severi
- Department of Biology, University of York, York, UK.,Microbes in Health and Disease, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | | | - Andrew Bell
- Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Tracy Palmer
- Microbes in Health and Disease, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Nathalie Juge
- Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
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Xiao Y, Zhao J, Zhang H, Zhai Q, Chen W. Mining genome traits that determine the different gut colonization potential of Lactobacillus and Bifidobacterium species. Microb Genom 2021; 7:000581. [PMID: 34100697 PMCID: PMC8461469 DOI: 10.1099/mgen.0.000581] [Citation(s) in RCA: 4] [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: 09/04/2020] [Accepted: 04/12/2021] [Indexed: 12/11/2022] Open
Abstract
Although the beneficial effects of probiotics are likely to be associated with their ability to colonize the gut, little is known about the characteristics of good colonizers. In a systematic analysis of the comparative genomics, we tried to elucidate the genomic contents that account for the distinct host adaptability patterns of Lactobacillus and Bifidobacterium species. The Bifidobacterium species, with species-level phylogenetic structures affected by recombination among strains, broad mucin-foraging activity, and dietary-fibre-degrading ability, represented niche conservatism and tended to be host-adapted. The Lactobacillus species stretched across three lifestyles, namely free-living, nomadic and host-adapted, as characterized by the variations of bacterial occurrence time, guanine-cytosine (GC) content and genome size, evolution event frequency, and the presence of human-adapted bacterial genes. The numbers and activity of host-adapted factors, such as bile salt hydrolase and intestinal tissue-anchored elements, were distinctly distributed among the three lifestyles. The strains of the three lifestyles could be separated with such a collection of colonization-related genomic content (genes, genome size and GC content). Thus, our work provided valuable information for rational selection and gut engraftment prediction of probiotics. Here, we have found many interesting predictive results for bacterial gut fitness, which will be validated in vitro and in vivo.
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Affiliation(s)
- Yue Xiao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, PR China
- Yangzhou Institute of Food Biotechnology, Jiangnan University, Yangzhou, Jiangsu 225004, PR China
- Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch, Wuxi 214122, PR China
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
- International Joint Research Laboratory for Probiotics at Jiangnan University, Wuxi, Jiangsu 214122, PR China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, PR China
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36
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Smith NW, Shorten PR, Altermann E, Roy NC, McNabb WC. Examination of hydrogen cross-feeders using a colonic microbiota model. BMC Bioinformatics 2021; 22:3. [PMID: 33407079 PMCID: PMC7789523 DOI: 10.1186/s12859-020-03923-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 12/07/2020] [Indexed: 12/15/2022] Open
Abstract
Background Hydrogen cross-feeding microbes form a functionally important subset of the human colonic microbiota. The three major hydrogenotrophic functional groups of the colon: sulphate-reducing bacteria (SRB), methanogens and reductive acetogens, have been linked to wide ranging impacts on host physiology, health and wellbeing. Results An existing mathematical model for microbial community growth and metabolism was combined with models for each of the three hydrogenotrophic functional groups. The model was further developed for application to the colonic environment via inclusion of responsive pH, host metabolite absorption and the inclusion of host mucins. Predictions of the model, using two existing metabolic parameter sets, were compared to experimental faecal culture datasets. Model accuracy varied between experiments and measured variables and was most successful in predicting the growth of high relative abundance functional groups, such as the Bacteroides, and short chain fatty acid (SCFA) production. Two versions of the colonic model were developed: one representing the colon with sequential compartments and one utilising a continuous spatial representation. When applied to the colonic environment, the model predicted pH dynamics within the ranges measured in vivo and SCFA ratios comparable to those in the literature. The continuous version of the model simulated relative abundances of microbial functional groups comparable to measured values, but predictions were sensitive to the metabolic parameter values used for each functional group. Sulphate availability was found to strongly influence hydrogenotroph activity in the continuous version of the model, correlating positively with SRB and sulphide concentration and negatively with methanogen concentration, but had no effect in the compartmentalised model version. Conclusions Although the model predictions compared well to only some experimental measurements, the important features of the colon environment included make it a novel and useful contribution to modelling the colonic microbiota.
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Affiliation(s)
- Nick W Smith
- School of Food and Advanced Technology, Massey University, Palmerston North, New Zealand.,Riddet Institute, Massey University, Private Bag 11222, Palmerston North, 4442, New Zealand.,AgResearch, Ruakura Research Centre, Private Bag 3123, Hamilton, 3240, New Zealand
| | - Paul R Shorten
- Riddet Institute, Massey University, Private Bag 11222, Palmerston North, 4442, New Zealand. .,AgResearch, Ruakura Research Centre, Private Bag 3123, Hamilton, 3240, New Zealand.
| | - Eric Altermann
- Riddet Institute, Massey University, Private Bag 11222, Palmerston North, 4442, New Zealand.,AgResearch, Grasslands Research Centre, Private Bag 11008, Palmerston North, 4442, New Zealand.,High-Value Nutrition National Science Challenge, Auckland, New Zealand
| | - Nicole C Roy
- Riddet Institute, Massey University, Private Bag 11222, Palmerston North, 4442, New Zealand.,High-Value Nutrition National Science Challenge, Auckland, New Zealand.,Department of Human Nutrition, University of Otago, Dunedin, New Zealand.,Liggins Institute, The University of Auckland, Auckland, New Zealand
| | - Warren C McNabb
- Riddet Institute, Massey University, Private Bag 11222, Palmerston North, 4442, New Zealand.,High-Value Nutrition National Science Challenge, Auckland, New Zealand
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37
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The Role of Glycosylation in Inflammatory Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1325:265-283. [PMID: 34495540 DOI: 10.1007/978-3-030-70115-4_13] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The diversity of glycan presentation in a cell, tissue and organism is enormous, which reflects the huge amount of important biological information encoded by the glycome which has not been fully understood. A compelling body of evidence has been highlighting the fundamental role of glycans in immunity, such as in development, and in major inflammatory processes such as inflammatory bowel disease, systemic lupus erythematosus and other autoimmune disorders. Glycans play an instrumental role in the immune response, integrating the canonical circuits that regulate innate and adaptive immune responses. The relevance of glycosylation in immunity is demonstrated by the role of glycans as important danger-associated molecular patterns and pathogen-associated molecular patterns associated with the discrimination between self and non-self; also as important regulators of the threshold of T cell activation, modulating receptors signalling and the activity of both T and other immune cells. In addition, glycans are important determinants that regulate the dynamic crosstalk between the microbiome and immune response. In this chapter, the essential role of glycans in the immunopathogenesis of inflammatory disorders will be presented and its potential clinical applications (diagnosis, prognosis and therapeutics) will be highlighted.
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38
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González-Morelo KJ, Vega-Sagardía M, Garrido D. Molecular Insights Into O-Linked Glycan Utilization by Gut Microbes. Front Microbiol 2020; 11:591568. [PMID: 33224127 PMCID: PMC7674204 DOI: 10.3389/fmicb.2020.591568] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 10/20/2020] [Indexed: 12/16/2022] Open
Abstract
O-linked glycosylation is a post-translational modification found mainly in eukaryotic cells, which covalently attaches oligosaccharides to secreted proteins in certain threonine or serine residues. Most of O-glycans have N-acetylgalactosamine (GalNAc) as a common core. Several glycoproteins, such as mucins (MUCs), immunoglobulins, and caseins are examples of O-glycosylated structures. These glycans are further elongated with other monosaccharides and sulfate groups. Some of them could be found in dairy foods, while others are produced endogenously, in both cases interacting with the gut microbiota. Interestingly, certain gut microbes can access, release, and consume O-linked glycans as a carbon source. Among these, Akkermansia muciniphila, Bifidobacterium bifidum, and Bacteroides thetaiotaomicron are prominent O-linked glycan utilizers. Their consumption strategies include specialized α-fucosidases and α-sialidases, in addition to endo-α-N-acetylgalactosaminidases that release galacto-N-biose (GNB) from peptides backbones. O-linked glycan utilization by certain gut microbes represents an important niche that allows them to predominate and modulate host responses such as inflammation. Here, we focus on the distinct molecular mechanisms of consumption of O-linked GalNAc glycans by prominent gut microbes, especially from mucin and casein glycomacropeptide (GMP), highlighting the potential of these structures as emerging prebiotics.
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Affiliation(s)
| | | | - Daniel Garrido
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
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39
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Zhang Y, Zhong X, Su S, Huang G. Discovery of Novel Prebiotic Carbohydrates and Sugar Mimics of BlMsmE, a Solute-Binding Protein of the ABC Transporter from Bacillus licheniformis. J Phys Chem B 2020; 124:9996-10006. [DOI: 10.1021/acs.jpcb.0c05583] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Yubo Zhang
- Department of Food Science, Foshan University, Foshan 528231, China
| | - Xianfeng Zhong
- Department of Food Science, Foshan University, Foshan 528231, China
| | - Siyun Su
- Department of Food Science, Foshan University, Foshan 528231, China
| | - Guidong Huang
- Department of Food Science, Foshan University, Foshan 528231, China
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40
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Bell A, Juge N. Mucosal glycan degradation of the host by the gut microbiota. Glycobiology 2020; 31:691-696. [PMID: 33043970 PMCID: PMC8252862 DOI: 10.1093/glycob/cwaa097] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/21/2020] [Accepted: 10/02/2020] [Indexed: 12/15/2022] Open
Abstract
The gut microbiota plays a major role in human health and an alteration in gut microbiota structure and function has been implicated in several diseases. In the colon, mucus covering the epithelium is critical to maintain a homeostatic relationship with the gut microbiota by harboring a microbial community at safe distance from the epithelium surface. The mucin glycans composing the mucus layer provide binding sites and a sustainable source of nutrients to the bacteria inhabiting the mucus niche. Access to these glycan chains requires a complement of glycoside hydrolases (GHs) produced by bacteria across the phyla constituting the human gut microbiota. Due to the increased recognition of the role of mucus-associated microbes in human health, how commensal bacteria breakdown and utilize host mucin glycans has become of increased interest and is reviewed here. This short review provides an overview of the strategies evolved by gut commensal bacteria to access this rich source of the nutrient with a focus on the GHs involved in mucin degradation.
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Affiliation(s)
- Andrew Bell
- The Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Rosalind Franklin Road Norwich Research Park, Norwich NR4 7UQ, UK
| | - Nathalie Juge
- The Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Rosalind Franklin Road Norwich Research Park, Norwich NR4 7UQ, UK
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41
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Pereira FC, Wasmund K, Cobankovic I, Jehmlich N, Herbold CW, Lee KS, Sziranyi B, Vesely C, Decker T, Stocker R, Warth B, von Bergen M, Wagner M, Berry D. Rational design of a microbial consortium of mucosal sugar utilizers reduces Clostridiodes difficile colonization. Nat Commun 2020; 11:5104. [PMID: 33037214 PMCID: PMC7547075 DOI: 10.1038/s41467-020-18928-1] [Citation(s) in RCA: 162] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 09/18/2020] [Indexed: 12/18/2022] Open
Abstract
Many intestinal pathogens, including Clostridioides difficile, use mucus-derived sugars as crucial nutrients in the gut. Commensals that compete with pathogens for such nutrients are therefore ecological gatekeepers in healthy guts, and are attractive candidates for therapeutic interventions. Nevertheless, there is a poor understanding of which commensals use mucin-derived sugars in situ as well as their potential to impede pathogen colonization. Here, we identify mouse gut commensals that utilize mucus-derived monosaccharides within complex communities using single-cell stable isotope probing, Raman-activated cell sorting and mini-metagenomics. Sequencing of cell-sorted fractions reveals members of the underexplored family Muribaculaceae as major mucin monosaccharide foragers, followed by members of Lachnospiraceae, Rikenellaceae, and Bacteroidaceae families. Using this information, we assembled a five-member consortium of sialic acid and N-acetylglucosamine utilizers that impedes C. difficile's access to these mucosal sugars and impairs pathogen colonization in antibiotic-treated mice. Our findings underscore the value of targeted approaches to identify organisms utilizing key nutrients and to rationally design effective probiotic mixtures.
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Affiliation(s)
- Fátima C Pereira
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Althanstrasse 14, 1090, Vienna, Austria
| | - Kenneth Wasmund
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Althanstrasse 14, 1090, Vienna, Austria
| | - Iva Cobankovic
- University of Vienna, Faculty of Chemistry, Department of Food Chemistry and Toxicology, Währinger Straße 38, 1090, Vienna, Austria
| | - Nico Jehmlich
- Helmholtz-Centre for Environmental Research - UFZ, Department of Molecular Systems Biology, Permoserstraße 15, 04318, Leipzig, Germany
| | - Craig W Herbold
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Althanstrasse 14, 1090, Vienna, Austria
| | - Kang Soo Lee
- Ralph M. Parsons Laboratory for Environmental Science and Engineering, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Barbara Sziranyi
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Althanstrasse 14, 1090, Vienna, Austria
| | - Cornelia Vesely
- Medical University of Vienna, Center for Anatomy and Cell Biology, Division of Cell and Developmental Biology, Vienna, Austria
| | - Thomas Decker
- Max F. Perutz Laboratories, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna, Austria
| | - Roman Stocker
- Ralph M. Parsons Laboratory for Environmental Science and Engineering, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Benedikt Warth
- University of Vienna, Faculty of Chemistry, Department of Food Chemistry and Toxicology, Währinger Straße 38, 1090, Vienna, Austria
| | - Martin von Bergen
- Helmholtz-Centre for Environmental Research - UFZ, Department of Molecular Systems Biology, Permoserstraße 15, 04318, Leipzig, Germany
| | - Michael Wagner
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Althanstrasse 14, 1090, Vienna, Austria
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, 9220, Aalborg, Denmark
| | - David Berry
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Althanstrasse 14, 1090, Vienna, Austria.
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria.
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42
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Weiss GA, Grabinger T, Glaus Garzon J, Hasler T, Greppi A, Lacroix C, Khanzhin N, Hennet T. Intestinal inflammation alters mucosal carbohydrate foraging and monosaccharide incorporation into microbial glycans. Cell Microbiol 2020; 23:e13269. [PMID: 32975882 PMCID: PMC7757161 DOI: 10.1111/cmi.13269] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 09/02/2020] [Accepted: 09/20/2020] [Indexed: 12/12/2022]
Abstract
Endogenous carbohydrates released from the intestinal mucus represent a constant source of nutrients to the intestinal microbiota. Mucus-derived carbohydrates can also be used as building blocks in the biosynthesis of bacterial cell wall components, thereby influencing host mucosal immunity. To assess the uptake of endogenous carbohydrates by gut microbes in healthy mice and during intestinal inflammation, we applied azido-monosaccharides that can be tracked on bacterial cell walls after conjugation with fluorophores. In interleukin-10 deficient mice, changes in the gut microbiota were accompanied by decreased carbohydrate hydrolase activities and increased lumenal concentrations of host glycan-derived monosaccharides. Tracking of the monosaccharide N-azidoacetylglucosamine (GlcNAz) in caecum bacteria revealed a preferential incorporation of this carbohydrate by Xanthomonadaceae in healthy mice and by Bacteroidaceae in interleukin-10 deficient mice. These GlcNAz-positive Bacteroidaceae fractions mainly belonged to the species B. acidifaciens and B. vulgatus. Growth of Bacteroides species in the presence of specific monosaccharides changed their stimulatory activity toward CD11c+ dendritic cells. Expression of activation markers and cytokine production was highest after stimulation of dendritic cells with B. vulgatus. The variable incorporation of monosaccharides by related Bacteroides species underline the necessity to investigate intestinal bacteria down to the species level when addressing microbiota-host interactions.
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Affiliation(s)
- Gisela Adrienne Weiss
- Institute of Physiology, University of Zurich, Zurich, Switzerland.,Yili Innovation Center Europe, Bronland 12E-1, 6708WH Wageningen, Netherlands
| | - Thomas Grabinger
- Institute of Physiology, University of Zurich, Zurich, Switzerland
| | | | - Tobias Hasler
- Institute of Physiology, University of Zurich, Zurich, Switzerland
| | - Anna Greppi
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, ETH-Zurich, Zurich, Switzerland
| | - Christophe Lacroix
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, ETH-Zurich, Zurich, Switzerland
| | | | - Thierry Hennet
- Institute of Physiology, University of Zurich, Zurich, Switzerland
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43
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Zabel BE, Gerdes S, Evans KC, Nedveck D, Singles SK, Volk B, Budinoff C. Strain-specific strategies of 2'-fucosyllactose, 3-fucosyllactose, and difucosyllactose assimilation by Bifidobacterium longum subsp. infantis Bi-26 and ATCC 15697. Sci Rep 2020; 10:15919. [PMID: 32985563 PMCID: PMC7522266 DOI: 10.1038/s41598-020-72792-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 09/02/2020] [Indexed: 02/07/2023] Open
Abstract
Human milk provides essential nutrients for infant nutrition. A large proportion of human milk is composed of human milk oligosaccharides (HMOs), which are resistant to digestion by the infant. Instead, HMOs act as a bioactive and prebiotic enriching HMO-utilizing bacteria and cause systematic changes in the host. Several species of Bifidobacterium have been shown to utilize HMOs by conserved, as well as species-specific pathways, but less work has been done to study variation within species or sub-species. B. longum subsp. infantis is a prevalent species in the breast-fed infant gut and the molecular mechanisms of HMO utilization for the type strain B. longum subsp. infantis ATCC 15697 (type strain) have been well characterized. We used growth, transcriptomic, and metabolite analysis to characterize key differences in the utilization of 2'FL, 3FL and DFL (FLs) between B. longum subsp. infantis Bi-26 (Bi-26) and the type strain. Bi-26 grows faster, produces unique metabolites, and has a distinct global gene transcription response to FLs compared to the type strain. Taken together the findings demonstrate major strain specific adaptations in Bi-26 to efficient utilization of FLs.
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Affiliation(s)
- Bryan E Zabel
- Genomics and Microbiome Science, DuPont Nutrition and Biosciences, Madison, WI, USA.
| | - Svetlana Gerdes
- Genomics and Microbiome Science, DuPont Nutrition and Biosciences, Madison, WI, USA
| | - Kara C Evans
- Genomics and Microbiome Science, DuPont Nutrition and Biosciences, Madison, WI, USA
| | - Derek Nedveck
- Genomics and Microbiome Science, DuPont Nutrition and Biosciences, Madison, WI, USA
| | | | - Barbara Volk
- Advanced Analytical, DuPont Nutrition and Biosciences, Wilmington, DE, USA
| | - Charles Budinoff
- Genomics and Microbiome Science, DuPont Nutrition and Biosciences, Madison, WI, USA
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44
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Metzler-Zebeli BU, Lucke A, Doupovec B, Zebeli Q, Böhm J. A multicomponent mycotoxin deactivator modifies the response of the jejunal mucosal and cecal bacterial community to deoxynivalenol contaminated feed and oral lipopolysaccharide challenge in chickens1. J Anim Sci 2020; 98:5707485. [PMID: 31944242 DOI: 10.1093/jas/skz377] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 01/15/2020] [Indexed: 12/11/2022] Open
Abstract
Mycotoxin deactivators are a widely used strategy to abrogate negative effects of mycotoxin-contaminated feed. It has not been adequately evaluated whether these deactivators may detoxify bacterial toxins in the intestinal lumen and subsequently lower the inflammatory response in chickens. The present objective was to study the effect of a multicomponent mycotoxin deactivator (B), containing a bentonite and a bacterial strain capable to enzymatically biotransform trichothecenes especially deoxynivalenol (DON), when supplemented to a DON-contaminated feed in combination with an oral lipopolysaccharide challenge on visceral organ size, expression of innate immune genes and mucosal permeability in the small intestine as well as on the cecal bacterial composition and metabolites in broiler chickens. Eighty 1-d-old male chickens were randomly allotted to four treatment groups in two replicate batches (n = 10/treatment/replicate): 1) basal diet without DON (CON), 2) CON diet supplemented with B (2.5 mg B/kg feed) (CON-B), 3) CON diet contaminated with 10 mg DON/kg feed (DON), and 4) DON diet supplemented with 2.5 mg B/kg feed (DON-B). In half of the chickens per treatment, effects were assessed under nonchallenge conditions, whereas in the other half of birds, to increase their intestinal bacterial toxin load, effects were tested after an oral challenge with 1 mg LPS/kg BW from Escherichia coli O55:B5 on the day before sampling. DON reduced (P < 0.05) the weight of bursa fabricii and thymus. DON increased the expression level of intestinal alkaline phosphatase at the duodenal mucosa (P = 0.027) but did not modify jejunal gene expression and mucosal permeability. The LPS challenge decreased the jejunal MUC2 expression but increased ZO1 and IL6 expression compared to the unchallenged animals (P < 0.05). DON × B interactions indicated lower expression of IL10 in duodenum and NFKB in jejunum with the B diet but higher expression with the DON-B diet (P = 0.050). Furthermore, the B lowered jejunal expression of NFKB and IL6 but only in LPS-challenged chickens (P < 0.05). Alterations in the cecal microbiota composition and VFA profile were likely associated with alterations in host physiology in the small intestine caused by DON, B, and LPS. According to the present data, B appeared to have potential to detoxify antigens other than DON in the intestinal lumen of chickens, whereby the toxin load may limit the efficacy of B to modify the intestinal and systemic response as indicated by interactions of DON, B, and LPS.
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Affiliation(s)
- Barbara U Metzler-Zebeli
- Department of Biomedical Sciences, Institute of Physiology, Pathophysiology and Biophysics, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Annegret Lucke
- Department for Farm Animals and Veterinary Public Health, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna, Vienna, Austria
| | | | - Qendrim Zebeli
- Department for Farm Animals and Veterinary Public Health, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Josef Böhm
- Department for Farm Animals and Veterinary Public Health, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna, Vienna, Austria
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Liu X, Shi H, He Q, Lin F, Wang Q, Xiao S, Dai Y, Zhang Y, Yang H, Zhao H. Effect of starvation and refeeding on growth, gut microbiota and non-specific immunity in hybrid grouper (Epinephelus fuscoguttatus♀×E. lanceolatus♂). FISH & SHELLFISH IMMUNOLOGY 2020; 97:182-193. [PMID: 31790749 DOI: 10.1016/j.fsi.2019.11.055] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 11/20/2019] [Accepted: 11/22/2019] [Indexed: 06/10/2023]
Abstract
Environmental changes can lead to food deprivation among aquatic animals. The main objective of this present research was to assess the effect of starvation and refeeding on growth, gut microbiota and non-specific immunity in a hybrid grouper (Epinephelus fuscoguttatus♀×E. lanceolatus♂). A total of 120 fish with an average weight of 74.16 ± 12.08 g were randomly divided into two groups (control group and fasted-refed group). The control group was fed until satiation for 60 days, while the fasted-refed group was fasted for 30 days and then fed to satiation for 30 days. The results showed that starvation led to a significantly decreased growth performance parameters [weight gain rate (WGR) and specific weight gain rate (SGR), while the feeding rate (FR) ] increased during the refeeding, non-specific immunity was significantly improved (p < 0.05) during the first 15 days of starvation, such as superoxide dismutase (SOD), glutathione peroxidase (GSH-PX), lysozyme (LYM) and catalase (CAT). However, non-specific immunity decreased at 30 days of starvation, the expression of genes related to immunity, such as TNF-α, was upregulated (p < 0.05) during starvation, while the expression levels of IL-17 and IFN-γ was reduced (p < 0.05). The expression of IFN-γ and IL-1β peaked during refeeding. Starvation led to significantly decreased abundance and diversity of intestinal microflora, with a higher abundance of Vibrio and a lower abundance of Brevibacillus, Bifidobacterium, Alloprevotella in the fasted-refed group during refeeding than in the control group. The above results reveal that starvation stimulates changes in growth, non-specific immunity, and the gut microbiota, providing new insights for the study of fish habitat selection and adaptability to environmental changes.
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Affiliation(s)
- Xiaochun Liu
- College of Marine Sciences, South China Agricultural University, Guangzhou, 510640, China
| | - Herong Shi
- Guangdong Marine Fishery Experiment Center, Huizhou, 516081, China
| | - Qi He
- College of Marine Sciences, South China Agricultural University, Guangzhou, 510640, China
| | - Fangmei Lin
- College of Marine Sciences, South China Agricultural University, Guangzhou, 510640, China
| | - Qing Wang
- College of Marine Sciences, South China Agricultural University, Guangzhou, 510640, China; Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Shiqiang Xiao
- College of Marine Sciences, South China Agricultural University, Guangzhou, 510640, China
| | - Yuantang Dai
- College of Marine Sciences, South China Agricultural University, Guangzhou, 510640, China
| | - Yanfa Zhang
- Huizhou Haiyan Aquaculture Technology Co., Ltd., Huizhou, 516081, China
| | - Huirong Yang
- College of Marine Sciences, South China Agricultural University, Guangzhou, 510640, China; Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Huihong Zhao
- College of Marine Sciences, South China Agricultural University, Guangzhou, 510640, China.
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Josenhans C, Müthing J, Elling L, Bartfeld S, Schmidt H. How bacterial pathogens of the gastrointestinal tract use the mucosal glyco-code to harness mucus and microbiota: New ways to study an ancient bag of tricks. Int J Med Microbiol 2020; 310:151392. [DOI: 10.1016/j.ijmm.2020.151392] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/28/2019] [Accepted: 12/06/2019] [Indexed: 12/13/2022] Open
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Hoang T, Toler E, DeLong K, Mafunda NA, Bloom SM, Zierden HC, Moench TR, Coleman JS, Hanes J, Kwon DS, Lai SK, Cone RA, Ensign LM. The cervicovaginal mucus barrier to HIV-1 is diminished in bacterial vaginosis. PLoS Pathog 2020; 16:e1008236. [PMID: 31971984 PMCID: PMC6999914 DOI: 10.1371/journal.ppat.1008236] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 02/04/2020] [Accepted: 11/25/2019] [Indexed: 11/19/2022] Open
Abstract
Bacterial vaginosis (BV), a condition in which the vaginal microbiota consists of community of obligate and facultative anaerobes rather than dominated by a single species of Lactobacillus, affects ~30% of women in the US. Women with BV are at 60% increased risk for HIV acquisition and are 3-times more likely to transmit HIV to an uninfected partner. As cervicovaginal mucus (CVM) is the first line of defense against mucosal pathogens and the home of the resident vaginal microbiota, we hypothesized the barrier function of CVM to HIV may be diminished in BV. Here, we characterized CVM properties including pH, lactic acid content, and Nugent score to correlate with the microbiota community composition, which was confirmed by 16S rDNA sequencing on a subset of samples. We then quantified the mobility of fluorescently-labeled HIV virions and nanoparticles to characterize the structural and adhesive barrier properties of CVM. Our analyses included women with Nugent scores categorized as intermediate (4–6) and BV (7–10), women that were either symptomatic or asymptomatic, and a small group of women before and after antibiotic treatment for symptomatic BV. Overall, we found that HIV virions had significantly increased mobility in CVM from women with BV compared to CVM from women with Lactobacillus crispatus-dominant microbiota, regardless of whether symptoms were present. We confirmed using nanoparticles and scanning electron microscopy that the impaired barrier function was due to reduced adhesive barrier properties without an obvious degradation of the physical CVM pore structure. We further confirmed a similar increase in HIV mobility in CVM from women with Lactobacillus iners-dominant microbiota, the species most associated with transitions to BV and that persists after antibiotic treatment for BV. Our findings advance the understanding of the protective role of mucus and highlight the interplay between vaginal microbiota and the innate barrier function mucus. Bacterial vaginosis (BV), a condition characterized by the depletion of lactobacillus bacteria in the vagina, is the most common vaginal condition in reproductive age women. BV has been associated with many adverse reproductive and sexual health outcomes, including increased risk of HIV infection. Cervicovaginal mucus is the home to vaginal bacteria and acts as a first line of defense to protect the underlying tissues and cells from infection. Here, we studied the barrier properties of mucus from women with BV compared to women with vaginal bacteria dominated by lactobacilli. We found that mucus from women with BV and women with Lactobacillus iners were permissive to HIV-1, which may allow the virus to more easily reach target cells. These findings are in agreement with the observed increased risk for HIV acquisition seen in women with BV and L. iners bacteria. Furthermore, we found that the barrier against HIV is diminished in women with BV regardless of whether they have symptoms. Our findings highlight the important, yet unexplored interactions between the mucus barrier and the vaginal microbiota and the implications for human health.
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Affiliation(s)
- Thuy Hoang
- The Center for Nanomedicine, The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Emily Toler
- The Center for Nanomedicine, The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Kevin DeLong
- The Center for Nanomedicine, The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Ophthalmology, The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Nomfuneko A. Mafunda
- Ragon Institute of MGH, MIT, and Harvard, Massachusetts General Hospital, Cambridge, Massachusetts, United States of America
| | - Seth M. Bloom
- Ragon Institute of MGH, MIT, and Harvard, Massachusetts General Hospital, Cambridge, Massachusetts, United States of America
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
| | - Hannah C. Zierden
- The Center for Nanomedicine, The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Thomas R. Moench
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Jenell S. Coleman
- Department of Gynecology and Obstetrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Justin Hanes
- The Center for Nanomedicine, The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Ophthalmology, The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Douglas S. Kwon
- Ragon Institute of MGH, MIT, and Harvard, Massachusetts General Hospital, Cambridge, Massachusetts, United States of America
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
| | - Samuel K. Lai
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, UNC/NCSU Joint Department of Biomedical Engineering, Department of Microbiology & Immunology, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Richard A. Cone
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Laura M. Ensign
- The Center for Nanomedicine, The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Ophthalmology, The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
- Department of Gynecology and Obstetrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University, Baltimore, Maryland, United States of America
- * E-mail:
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Zhou J, Wang Y, Fan Q, Liu Y, Liu H, Yan J, Li M, Dong W, Li W. High levels of fucosylation and sialylation of milk N-glycans from mothers with gestational diabetes mellitus alter the offspring gut microbiome and immune balance in mice. FASEB J 2020; 34:3715-3731. [PMID: 31944389 DOI: 10.1096/fj.201901674r] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 12/09/2019] [Accepted: 12/17/2019] [Indexed: 12/17/2022]
Abstract
Gestational diabetes mellitus (GDM) is significantly associated with allergen sensitization in early childhood, and this may influence the gut microbiome and immune system of the children. In addition to mother-to-child transmission of microbes, milk glycans play a pivotal role in shaping the gut microbiome of infants. A previous study has demonstrated alterations in the major milk N-glycans of mothers with GDM. However, the impact of these changes on the gut microbiome and immune response of the neonates has yet to be studied. Here, we aimed to compare the glycosylation levels of various milk glycans between normal and GDM mice, and to characterize the intestinal microbiome and immune responses of the offspring after weaning. We found that GDM mouse milk contained significantly higher concentrations of fucosylated and sialylated N-glycans than control mice, but there was no difference in the concentration of milk oligosaccharides between the groups. The differences in milk N-glycans had direct effects on the intestinal microbiome of the offspring, which in turn affected their immune response upon challenge with ovalbumin (OVA), with disruptions in the Th1/Th2 and Th17/Treg cell balances. This study lays the foundation for further research and development of specific nutritional care for the offspring of GDM mothers.
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Affiliation(s)
- Jiaorui Zhou
- Department of Microecology, College of Basic Medical Science, Dalian Medical University, Dalian, China
| | - Yue Wang
- Department of Biochemistry, College of Basic Medical Science, Dalian Medical University, Dalian, China
| | - Qingjie Fan
- Department of Microecology, College of Basic Medical Science, Dalian Medical University, Dalian, China
| | - Yinhui Liu
- Department of Microecology, College of Basic Medical Science, Dalian Medical University, Dalian, China
| | - He Liu
- Department of Microecology, College of Basic Medical Science, Dalian Medical University, Dalian, China
| | - Jingyu Yan
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Ming Li
- Department of Microecology, College of Basic Medical Science, Dalian Medical University, Dalian, China
| | - Weijie Dong
- Department of Biochemistry, College of Basic Medical Science, Dalian Medical University, Dalian, China
| | - Wenzhe Li
- Department of Biochemistry, College of Basic Medical Science, Dalian Medical University, Dalian, China
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MacMillan JL, Vicaretti SD, Noyovitz B, Xing X, Low KE, Inglis GD, Zaytsoff SJ, Boraston AB, Smith SP, Uwiera RR, Selinger LB, Zandberg WF, Abbott DW. Structural analysis of broiler chicken small intestinal mucin O-glycan modification by Clostridium perfringens. Poult Sci 2019; 98:5074-5088. [DOI: 10.3382/ps/pez297] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 05/03/2019] [Indexed: 12/12/2022] Open
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50
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Romero S, Nastasa A, Chapman A, Kwong WK, Foster LJ. The honey bee gut microbiota: strategies for study and characterization. INSECT MOLECULAR BIOLOGY 2019; 28:455-472. [PMID: 30652367 DOI: 10.1111/imb.12567] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Gut microbiota research is an emerging field that improves our understanding of the ecological and functional dynamics of gut environments. The honey bee gut microbiota is a highly rewarding community to study, as honey bees are critical pollinators of many crops for human consumption and produce valuable commodities such as honey and wax. Most significantly, unique characteristics of the Apis mellifera gut habitat make it a valuable model system. This review discusses methods and pipelines used in the study of the gut microbiota of Ap. mellifera and closely related species for four main purposes: identifying microbiota taxonomy, characterizing microbiota genomes (microbiome), characterizing microbiota-microbiota interactions and identifying functions of the microbial community in the gut. The purpose of this contribution is to increase understanding of honey bee gut microbiota, to facilitate bee microbiota and microbiome research in general and to aid design of future experiments in this growing field.
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Affiliation(s)
- S Romero
- Michael Smith Laboratories and Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - A Nastasa
- Michael Smith Laboratories and Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - A Chapman
- Michael Smith Laboratories and Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - W K Kwong
- Biodiversity Research Centre, Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - L J Foster
- Michael Smith Laboratories and Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
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