151
|
Nakayama-Imaohji H, Hirota K, Yamasaki H, Yoneda S, Nariya H, Suzuki M, Secher T, Miyake Y, Oswald E, Hayashi T, Kuwahara T. DNA Inversion Regulates Outer Membrane Vesicle Production in Bacteroides fragilis. PLoS One 2016; 11:e0148887. [PMID: 26859882 PMCID: PMC4747536 DOI: 10.1371/journal.pone.0148887] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 01/25/2016] [Indexed: 02/06/2023] Open
Abstract
Phase changes in Bacteroides fragilis, a member of the human colonic microbiota, mediate variations in a vast array of cell surface molecules, such as capsular polysaccharides and outer membrane proteins through DNA inversion. The results of the present study show that outer membrane vesicle (OMV) formation in this anaerobe is also controlled by DNA inversions at two distantly localized promoters, IVp-I and IVp-II that are associated with extracellular polysaccharide biosynthesis and the expression of outer membrane proteins. These promoter inversions are mediated by a single tyrosine recombinase encoded by BF2766 (orthologous to tsr19 in strain NCTC9343) in B. fragilis YCH46, which is located near IVp-I. A series of BF2766 mutants were constructed in which the two promoters were locked in different configurations (IVp-I/IVp-II = ON/ON, OFF/OFF, ON/OFF or OFF/ON). ON/ON B. fragilis mutants exhibited hypervesiculating, whereas the other mutants formed only a trace amount of OMVs. The hypervesiculating ON/ON mutants showed higher resistance to treatment with bile, LL-37, and human β-defensin 2. Incubation of wild-type cells with 5% bile increased the population of cells with the ON/ON genotype. These results indicate that B. fragilis regulates the formation of OMVs through DNA inversions at two distantly related promoter regions in response to membrane stress, although the mechanism underlying the interplay between the two regions controlled by the invertible promoters remains unknown.
Collapse
Affiliation(s)
- Haruyuki Nakayama-Imaohji
- Department of Microbiology, Faculty of Medicine, Kagawa University, 1750–1 Miki, Kagawa 761–0793, Japan
| | - Katsuhiko Hirota
- Department of Oral Microbiology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770–8503, Japan
| | - Hisashi Yamasaki
- Department of Cellular and Molecular Medicine, Wakayama Medical University Graduate School of Medicine, Wakayama 641–8509, Japan
| | - Saori Yoneda
- Department of Microbiology, Faculty of Medicine, Kagawa University, 1750–1 Miki, Kagawa 761–0793, Japan
| | - Hirofumi Nariya
- Department of Microbiology, Faculty of Medicine, Kagawa University, 1750–1 Miki, Kagawa 761–0793, Japan
| | - Motoo Suzuki
- Department of Microbiology, Faculty of Medicine, Kagawa University, 1750–1 Miki, Kagawa 761–0793, Japan
| | - Thomas Secher
- Inserm UMR1043 Toulouse, France
- INRA USC 1360 Toulouse, France
- CNRS UMR5282 Toulouse, France
- Université de Toulouse, UPS, Centre de Physiopathologie de Toulouse Purpan (CPTP), Toulouse, France
| | - Yoichiro Miyake
- Department of Oral Microbiology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770–8503, Japan
| | - Eric Oswald
- Inserm UMR1043 Toulouse, France
- INRA USC 1360 Toulouse, France
- CNRS UMR5282 Toulouse, France
- Université de Toulouse, UPS, Centre de Physiopathologie de Toulouse Purpan (CPTP), Toulouse, France
- CHU Toulouse, Hôpital Purpan, Service de bactériologie-hygiène, Toulouse, France
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka 812–8582, Japan
| | - Tomomi Kuwahara
- Department of Microbiology, Faculty of Medicine, Kagawa University, 1750–1 Miki, Kagawa 761–0793, Japan
- * E-mail:
| |
Collapse
|
152
|
Rehman A, Rausch P, Wang J, Skieceviciene J, Kiudelis G, Bhagalia K, Amarapurkar D, Kupcinskas L, Schreiber S, Rosenstiel P, Baines JF, Ott S. Geographical patterns of the standing and active human gut microbiome in health and IBD. Gut 2016; 65:238-48. [PMID: 25567118 DOI: 10.1136/gutjnl-2014-308341] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 11/30/2014] [Indexed: 12/12/2022]
Abstract
OBJECTIVE A global increase of IBD has been reported, especially in countries that previously had low incidence rates. Also, the knowledge of the human gut microbiome is steadily increasing, however, limited information regarding its variation on a global scale is available. In the light of the microbial involvement in IBDs, we aimed to (1) identify shared and distinct IBD-associated mucosal microbiota patterns from different geographical regions including Europe (Germany, Lithuania) and South Asia (India) and (2) determine whether profiling based on 16S rRNA transcripts provides additional resolution, both of which may hold important clinical relevance. DESIGN In this study, we analyse a set of 89 mucosal biopsies sampled from individuals of German, Lithuanian and Indian origins, using bacterial community profiling of a roughly equal number of healthy controls, patients with Crohn's disease and UC from each location, and analyse 16S rDNA and rRNA as proxies for standing and active microbial community structure, respectively. RESULTS We find pronounced population-specific as well as general disease patterns in the major phyla and patterns of diversity, which differ between the standing and active communities. The geographical origin of samples dominates the patterns of β diversity with locally restricted disease clusters and more pronounced effects in the active microbial communities. However, two genera belonging to the Clostridium leptum subgroup, Faecalibacteria and Papillibacter, display consistent patterns with respect to disease status and may thus serve as reliable 'microbiomarkers'. CONCLUSIONS These analyses reveal important interactions of patients' geographical origin and disease in the interpretation of disease-associated changes in microbial communities and highlight the added value of analysing communities on both the 16S rRNA gene (DNA) and transcript (RNA) level.
Collapse
Affiliation(s)
- Ateequr Rehman
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Philipp Rausch
- Max Planck Institute for Evolutionary Biology, Plön, Germany Institute for Experimental Medicine, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Jun Wang
- Max Planck Institute for Evolutionary Biology, Plön, Germany Institute for Experimental Medicine, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Jurgita Skieceviciene
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany Institute for Digestive Research, Medical Academy, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Gediminas Kiudelis
- Department of Gastroenterology, Medical Academy, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Ketan Bhagalia
- Bombay Hospital and Medical Research Center, Mumbai, India
| | | | - Limas Kupcinskas
- Institute for Digestive Research, Medical Academy, Lithuanian University of Health Sciences, Kaunas, Lithuania Department of Gastroenterology, Medical Academy, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany Department of General Internal Medicine, Christian-Albrechts-University of Kiel, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - John F Baines
- Max Planck Institute for Evolutionary Biology, Plön, Germany Institute for Experimental Medicine, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Stephan Ott
- Department of General Internal Medicine, Christian-Albrechts-University of Kiel, University Hospital Schleswig-Holstein, Kiel, Germany
| |
Collapse
|
153
|
Aziz F, Parrado Rubio J, Ouazzani N, Dary M, Manyani H, Rodríguez Morgado B, Mandi L. Sanitary impact evaluation of drinking water in storage reservoirs in Moroccan rural area. Saudi J Biol Sci 2016; 24:767-777. [PMID: 28490945 PMCID: PMC5415126 DOI: 10.1016/j.sjbs.2016.01.034] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Revised: 12/29/2015] [Accepted: 01/19/2016] [Indexed: 12/04/2022] Open
Abstract
In Morocco, storage reservoirs are particular systems of water supply in rural areas. These reservoirs are fed with rainwater and/or directly from the river, which are very contaminated by several pathogenic bacteria. They are used without any treatment as a drinking water by the surrounding population. In this context, the aim of this study is to evaluate the impact of consuming contaminated water stored in reservoirs on health status for six rural communities located in Assif El Mal, Southern East of Marrakech. This was investigated using a classical methodology based on population survey and by molecular approach using PCR–DGGE technique to determine the intestinal bacterial diversity of consumers. The survey showed that, the residents of the studied area suffered from numerous health problems (diarrheal diseases, vomiting or hepatitis A) due to the lack of waste management infrastructures. The consumer’s stool analysis by molecular approach revealed that numbers of Escherichia coli, Aeromonas hydrophila and Clostridia, were significantly higher in the diarrheal feces. In addition, PCR–DGGE study of the prevalence and distribution of bacteria causing human diseases, confirmed that, there is a relationship between water bacterial contaminations of storage reservoirs and microbial disease related health status. Therefore, water reservoir consumption is assumed to be the mean way of exposure for this population. It’s clear that this approach gives a very helpful tool to confirm without any doubt the relationship between water bacterial contamination and health status.
Collapse
Affiliation(s)
- Faissal Aziz
- National Center for Research and Studies on Water and Energy, University Cadi Ayyad, Marrakech, Morocco.,Laboratory of Hydrobiology, Ecotoxicology & Sanitation (LHEA, URAC 33), Faculty of Sciences Semlalia, Marrakech, Morocco
| | - Juan Parrado Rubio
- Department of Biochemical and Molecular Biology, Faculty of Pharmacy, University of Seville, Spain
| | - Naaila Ouazzani
- National Center for Research and Studies on Water and Energy, University Cadi Ayyad, Marrakech, Morocco.,Laboratory of Hydrobiology, Ecotoxicology & Sanitation (LHEA, URAC 33), Faculty of Sciences Semlalia, Marrakech, Morocco
| | - Mohammed Dary
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, Spain
| | - Hamid Manyani
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, Spain
| | - Bruno Rodríguez Morgado
- Department of Biochemical and Molecular Biology, Faculty of Pharmacy, University of Seville, Spain
| | - Laila Mandi
- National Center for Research and Studies on Water and Energy, University Cadi Ayyad, Marrakech, Morocco.,Laboratory of Hydrobiology, Ecotoxicology & Sanitation (LHEA, URAC 33), Faculty of Sciences Semlalia, Marrakech, Morocco
| |
Collapse
|
154
|
Praveen V, Praveen S. Microbiome-Gut-Brain Axis: A Pathway for Improving Brainstem Serotonin Homeostasis and Successful Autoresuscitation in SIDS-A Novel Hypothesis. Front Pediatr 2016; 4:136. [PMID: 28111624 PMCID: PMC5216028 DOI: 10.3389/fped.2016.00136] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 11/30/2016] [Indexed: 12/16/2022] Open
Abstract
Sudden infant death syndrome (SIDS) continues to be a major public health issue. Following its major decline since the "Back to Sleep" campaign, the incidence of SIDS has plateaued, with an annual incidence of about 1,500 SIDS-related deaths in the United States and thousands more throughout the world. The etiology of SIDS, the major cause of postneonatal mortality in the western world, is still poorly understood. Although sleeping in prone position is a major risk factor, SIDS continues to occur even in the supine sleeping position. The triple-risk model of Filiano and Kinney emphasizes the interaction between a susceptible infant during a critical developmental period and stressor/s in the pathogenesis of SIDS. Recent evidence ranges from dysregulated autonomic control to findings of altered neurochemistry, especially the serotonergic system that plays an important role in brainstem cardiorespiratory/thermoregulatory centers. Brainstem serotonin (5-HT) and tryptophan hydroxylase-2 (TPH-2) levels have been shown to be lower in SIDS, supporting the evidence that defects in the medullary serotonergic system play a significant role in SIDS. Pathogenic bacteria and their enterotoxins have been associated with SIDS, although no direct evidence has been established. We present a new hypothesis that the infant's gut microbiome, and/or its metabolites, by its direct effects on the gut enterochromaffin cells, stimulates the afferent gut vagal endings by releasing serotonin (paracrine effect), optimizing autoresuscitation by modulating brainstem 5-HT levels through the microbiome-gut-brain axis, thus playing a significant role in SIDS during the critical period of gut flora development and vulnerability to SIDS. The shared similarities between various risk factors for SIDS and their relationship with the infant gut microbiome support our hypothesis. Comprehensive gut-microbiome studies are required to test our hypothesis.
Collapse
Affiliation(s)
| | - Shama Praveen
- Providence Little Company of Mary Medical Center , Torrance, CA , USA
| |
Collapse
|
155
|
Song H, Han W, Yan F, Xu D, Chu Q, Zheng X. Dietary Phaseolus vulgaris extract alleviated diet-induced obesity, insulin resistance and hepatic steatosis and alters gut microbiota composition in mice. J Funct Foods 2016. [DOI: 10.1016/j.jff.2015.10.022] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
|
156
|
Tsurumaki M, Kotake M, Iwasaki M, Saito M, Tanaka K, Aw W, Fukuda S, Tomita M. The application of omics technologies in the functional evaluation of inulin and inulin-containing prebiotics dietary supplementation. Nutr Diabetes 2015; 5:e185. [PMID: 26619369 PMCID: PMC4672356 DOI: 10.1038/nutd.2015.35] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 09/23/2015] [Accepted: 10/19/2015] [Indexed: 12/25/2022] Open
Abstract
Inulin, a natural renewable polysaccharide resource produced by various plants in nature, has been reported to possess a significant number of diverse pharmaceutical and food applications. Recently, there has been rapid progress in high-throughput technologies and platforms to assay global mRNA, proteins, metabolites and gut microbiota. In this review, we will describe the current status of utilizing omics technologies of elucidating the impact of inulin and inulin-containing prebiotics at the transcriptome, proteome, metabolome and gut microbiome levels. Although many studies in this review have addressed the impact of inulin comprehensively, these omics technologies only enable us to understand physiological information at each different stage of mRNA, protein, metabolite and gut microbe. We believe that a synergistic approach is vital in order to fully illustrate the intricate beauty behind the relatively modest influence of food factors like inulin on host health.
Collapse
Affiliation(s)
- M Tsurumaki
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan
| | - M Kotake
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan
| | - M Iwasaki
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan
| | - M Saito
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan
| | - K Tanaka
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan
| | - W Aw
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - S Fukuda
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - M Tomita
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| |
Collapse
|
157
|
Characterization of a sialate-O-acetylesterase (NanS) from the oral pathogen Tannerella forsythia that enhances sialic acid release by NanH, its cognate sialidase. Biochem J 2015; 472:157-67. [DOI: 10.1042/bj20150388] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 09/16/2015] [Indexed: 12/11/2022]
Abstract
We characterize a novel bacterial sialate-O-acetylesterase potentially important for the nutrition of oral pathogens causing periodontal disease by enhancing their ability to harvest sialic acid sugar. Its high activity and stability indicate that it can also be used in glycan pharmacoanalytics.
Collapse
|
158
|
Aw W, Fukuda S. An Integrated Outlook on the Metagenome and Metabolome of Intestinal Diseases. Diseases 2015; 3:341-359. [PMID: 28943629 PMCID: PMC5548254 DOI: 10.3390/diseases3040341] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 10/30/2015] [Accepted: 11/02/2015] [Indexed: 01/08/2023] Open
Abstract
Recently, metagenomics and metabolomics are the two most rapidly advancing “omics” technologies. Metagenomics seeks to characterize the composition of microbial communities, their operations, and their dynamically co-evolving relationships with the habitats they occupy, whereas metabolomics studies unique chemical endpoints (metabolites) that specific cellular processes leave behind. Remarkable progress in DNA sequencing and mass spectrometry technologies has enabled the comprehensive collection of information on the gut microbiome and its metabolome in order to assess the influence of the gut microbiota on host physiology on a whole-systems level. Our gut microbiota, which consists of prokaryotic cells together with its metabolites, creates a unique gut ecosystem together with the host eukaryotic cells. In this review, we will highlight the detailed relationships between gut microbiota and its metabolites on host health and the pathogenesis of various intestinal diseases such as inflammatory bowel disease and colorectal cancer. Therapeutic interventions such as probiotic and prebiotic administrations and fecal microbiota transplantations will also be discussed. We would like to promote this unique biology-wide approach of incorporating metagenome and metabolome information as we believe that this can help us understand the intricate interplay between gut microbiota and host metabolism to a greater extent. This novel integration of microbiome, metatranscriptome, and metabolome information will help us have an improved holistic understanding of the complex mammalian superorganism, thereby allowing us to gain new and unprecedented insights to providing exciting novel therapeutic approaches for optimal intestinal health.
Collapse
Affiliation(s)
- Wanping Aw
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan.
| | - Shinji Fukuda
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan.
- RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| |
Collapse
|
159
|
Abstract
The contribution of intestinal bacterial strains (gut microbiota) to the development of obesity and obesity-related disorders is increasingly recognized as a potential diagnostic and pharmacologic target. Alterations in the intestinal bacterial composition have been associated with presence of chronic low-grade inflammation, a known feature of insulin resistance and type 2 diabetes mellitus. However, causality still needs to be proven. Fecal transplantation studies in germ-free mice have provided crucial insight into the causality of gut microbiota in development of obesity and obesity-related disorders. Moreover, fecal transplantation studies in conjunction with fecal sampling in prospectively followed cohorts will help identify causally involved intestinal bacterial strains in human obesity. Results from these studies will lead to characterization of novel diagnostic markers as well as therapeutic strategies that aim to treat obesity and obesity-related disorders.
Collapse
|
160
|
Chang C, Tesar C, Li X, Kim Y, Rodionov DA, Joachimiak A. A novel transcriptional regulator of L-arabinose utilization in human gut bacteria. Nucleic Acids Res 2015; 43:10546-59. [PMID: 26438537 PMCID: PMC4666351 DOI: 10.1093/nar/gkv1005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 09/23/2015] [Indexed: 01/08/2023] Open
Abstract
Carbohydrate metabolism plays a crucial role in the ecophysiology of human gut microbiota. Mechanisms of transcriptional regulation of sugar catabolism in commensal and prevalent human gut bacteria such as Bacteroides thetaiotaomicron remain mostly unknown. By a combination of bioinformatics and experimental approaches, we have identified an NrtR family transcription factor (BT0354 in B. thetaiotaomicron, BtAraR) as a novel regulator controlling the arabinose utilization genes. L-arabinose was confirmed to be a negative effector of BtAraR. We have solved the crystal structures of the apo and L-arabinose-bound BtAraR proteins, as well as the complex of apo-protein with a specific DNA operator. BtAraR forms a homodimer with each subunit comprised of the ligand-binding Nudix hydrolase-like domain and the DNA-binding winged-helix-turn-helix (wHTH) domain. We have identified the residues involved in binding of L-arabinose and recognition of DNA. The majority of these residues are well conserved in the AraR orthologs in Bacteroidetes. In the structure of the BtAraR-DNA complex, we found the unique interaction of arginine intercalating its guanidinum moiety into the base pair stacking of B-DNA. L-arabinose binding induces movement of wHTH domains, resulting in a conformation unsuitable for DNA binding. Our analysis facilitates reconstruction of the metabolic and regulatory networks involved in carbohydrate utilization in human gut Bacteroides.
Collapse
Affiliation(s)
- Changsoo Chang
- Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, IL 60439, USA Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Christine Tesar
- Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Xiaoqing Li
- Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA
| | - Youngchang Kim
- Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, IL 60439, USA Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Dmitry A Rodionov
- Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127994, Russia
| | - Andrzej Joachimiak
- Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, IL 60439, USA Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| |
Collapse
|
161
|
Rosenbaum M, Knight R, Leibel RL. The gut microbiota in human energy homeostasis and obesity. Trends Endocrinol Metab 2015; 26:493-501. [PMID: 26257300 PMCID: PMC4862197 DOI: 10.1016/j.tem.2015.07.002] [Citation(s) in RCA: 283] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Revised: 07/03/2015] [Accepted: 07/10/2015] [Indexed: 12/15/2022]
Abstract
Numerous studies of rodents suggest that the gut microbiota populations are sensitive to genetic and environmental influences, and can produce or influence afferent signals that directly or indirectly impinge on energy homeostatic systems affecting both energy balance (weight gain or loss) and energy stores. Fecal transplants from obese and lean human, and from mouse donors to gnotobiotic mice, result in adoption of the donor somatotype by the formerly germ-free rodents. Thus, the microbiota is certainly implicated in the development of obesity, adiposity-related comorbidities, and the response to interventions designed to achieve sustained weight reduction in mice. More studies are needed to determine whether the microbiota plays a similarly potent role in human body-weight regulation and obesity.
Collapse
Affiliation(s)
- Michael Rosenbaum
- Columbia University, Department of Pediatrics, Division of Molecular Genetics, New York, NY 10032, USA.
| | - Rob Knight
- Departments of Pediatrics and Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Rudolph L Leibel
- Columbia University, Department of Pediatrics, Division of Molecular Genetics, New York, NY 10032, USA
| |
Collapse
|
162
|
Kim DH, Chon JW, Kim H, Seo KH. Modulation of intestinal microbiota in mice by kefir administration. Food Sci Biotechnol 2015. [DOI: 10.1007/s10068-015-0179-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
|
163
|
Cuív PÓ, Smith WJ, Pottenger S, Burman S, Shanahan ER, Morrison M. Isolation of Genetically Tractable Most-Wanted Bacteria by Metaparental Mating. Sci Rep 2015; 5:13282. [PMID: 26293474 PMCID: PMC4642544 DOI: 10.1038/srep13282] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 07/16/2015] [Indexed: 01/03/2023] Open
Abstract
Metagenomics has rapidly advanced our inventory and appreciation of the genetic potential inherent to the gut microbiome. However it is widely accepted that two key constraints to further genetic dissection of the gut microbiota and host-microbe interactions have been our inability to recover new isolates from the human gut, and the paucity of genetically tractable gut microbes. To address this challenge we developed a modular RP4 mobilisable recombinant vector system and an approach termed metaparental mating to support the rapid and directed isolation of genetically tractable fastidious gut bacteria. Using this approach we isolated transconjugants affiliated with Clostridium cluster IV (Faecalibacterium and Oscillibacter spp.), Clostridium cluster XI (Anaerococcus) and Clostridium XIVa (Blautia spp.) and group 2 ruminococci amongst others, and demonstrated that the recombinant vectors were stably maintained in their recipient hosts. By a similar approach we constructed fluorescently labelled bacterial transconjugants affiliated with Clostridium cluster IV (including Flavonifractor and Pseudoflavonifractor spp.), Clostridium XIVa (Blautia spp.) and Clostridium cluster XVIII (Clostridium ramosum) that expressed a flavin mononucleotide-based reporter gene (evoglow-C-Bs2). Our approach will advance the integration of bacterial genetics with metagenomics and realize new directions to support a more mechanistic dissection of host-microbe associations relevant to human health and disease.
Collapse
Affiliation(s)
- Páraic Ó Cuív
- CSIRO Preventative Health Flagship Research Program, Queensland, Australia.,The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Queensland, Australia
| | - Wendy J Smith
- CSIRO Preventative Health Flagship Research Program, Queensland, Australia
| | - Sian Pottenger
- The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Queensland, Australia
| | - Sriti Burman
- The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Queensland, Australia
| | - Erin R Shanahan
- The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Queensland, Australia.,Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Queensland, Australia
| | - Mark Morrison
- CSIRO Preventative Health Flagship Research Program, Queensland, Australia.,The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Queensland, Australia
| |
Collapse
|
164
|
Chen HM, Liu XW, Sun RJ, Fang JY. A survey on the developmental intestinal microbiota research in China: The history, funding, and frontiers of gut bacteria. J Dig Dis 2015. [PMID: 26215325 DOI: 10.1111/1751-2980.12274] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Up to 100 trillion bacteria are harbored in the human intestine with a mutualistic and interdependent relationship with the host during a long period of co-evolution. The so-called intestinal microbiota (IM) fulfill important metabolic tasks and the impaired stability may lead to IM-related diseases, including inflammatory bowel disease (IBD), colorectal cancer (CRC), metabolic syndrome (MS), liver diseases, and so on. Here, we review the past and development of IM research in China, including the achievements that Chinese researchers have made both in basic and clinical scientific field. Moreover, we evaluate the contributions of the National Natural Science Foundation of China (NSFC), the 973 National Basic Research Program of China (973 Program), the 863 National High Technology Research and Development Program of China (863 Program), and funds from the public health industry in the field of IM research.
Collapse
Affiliation(s)
- Hui Min Chen
- State Key Laboratory of Oncogene and Related Genes, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Xiao Wei Liu
- Division of Digestive Disease, The Second Xiangya Hospital of Central South University, Changsha, Hunan Province, China.,National Natural Science Foundation of China, Beijing, China
| | - Rui Juan Sun
- National Natural Science Foundation of China, Beijing, China
| | - Jing Yuan Fang
- State Key Laboratory of Oncogene and Related Genes, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute, Shanghai Institute of Digestive Disease, Shanghai, China
| |
Collapse
|
165
|
Blatchford P, Stoklosinski H, Walton G, Swann J, Gibson G, Gearry R, Ansell J. Kiwifruit fermentation drives positive gut microbial and metabolic changes irrespective of initial microbiota composition. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.bcdf.2015.07.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
|
166
|
Blatchford P, Bentley-Hewitt KL, Stoklosinski H, McGhie T, Gearry R, Gibson G, Ansell J. In vitro characterisation of the fermentation profile and prebiotic capacity of gold-fleshed kiwifruit. Benef Microbes 2015; 6:829-39. [PMID: 26123782 DOI: 10.3920/bm2015.0006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
A new Actinidia chinensis gold-fleshed kiwifruit cultivar 'Zesy002' was tested to investigate whether it could positively modulate the composition of the human colonic microbiota. Digested Zesy002 kiwifruit was added to in vitro pH-controlled anaerobic batch fermenters that were inoculated with representative human faecal microbiota. Alterations to the gut microbial ecology were determined by 16S rRNA gene sequencing and metabolic end products were measured using gas chromatography and liquid chromatography - mass spectrometry. Results indicated a substantial shift in the composition of bacteria within the gut models caused by kiwifruit supplementation. Zesy002 supplemented microbiota had a significantly higher abundance of Bacteroides spp., Parabacteroides spp. and Bifidobacterium spp. after 48 h of fermentation compared with the start of the fermentation. Organic acids from kiwifruit were able to endure simulated gastrointestinal digestion and were detectable in the first 10 h of fermentation. The fermentable carbohydrates were converted to beneficial organic acids with a particular predilection for propionate production, corresponding with the rise in Bacteroides spp. and Parabacteroides spp. These results support the claim that Zesy002 kiwifruit non-digestible fractions can effect favourable changes to the human colonic microbial community and primary metabolites, and demonstrate a hitherto unknown effect of Zesy002 on colonic microbiota under in vitro conditions.
Collapse
Affiliation(s)
- P Blatchford
- 1 The New Zealand Institute for Plant and Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand.,2 Department of Food and Nutritional Sciences, The University of Reading, Reading RG6 6AP, United Kingdom
| | - K L Bentley-Hewitt
- 1 The New Zealand Institute for Plant and Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand
| | - H Stoklosinski
- 1 The New Zealand Institute for Plant and Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand
| | - T McGhie
- 1 The New Zealand Institute for Plant and Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand
| | - R Gearry
- 3 Department of Gastroenterology, Christchurch Hospital, Private Bag 4710, Christchurch, New Zealand
| | - G Gibson
- 2 Department of Food and Nutritional Sciences, The University of Reading, Reading RG6 6AP, United Kingdom
| | - J Ansell
- 4 Zespri International Limited, 400 Maunganui Road, P.O. Box 4043, Mt Maunganui 3149, New Zealand
| |
Collapse
|
167
|
Peng B, Huang S, Liu T, Geng A. Bacterial xylose isomerases from the mammal gut Bacteroidetes cluster function in Saccharomyces cerevisiae for effective xylose fermentation. Microb Cell Fact 2015; 14:70. [PMID: 25981595 PMCID: PMC4436767 DOI: 10.1186/s12934-015-0253-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 05/06/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Xylose isomerase (XI) catalyzes the conversion of xylose to xylulose, which is the key step for anaerobic ethanolic fermentation of xylose. Very few bacterial XIs can function actively in Saccharomyces cerevisiae. Here, we illustrate a group of XIs that would function for xylose fermentation in S. cerevisiae through phylogenetic analysis, recombinant yeast strain construction, and xylose fermentation. RESULTS Phylogenetic analysis of deposited XI sequences showed that XI evolutionary relationship was highly consistent with the bacterial taxonomic orders and quite a few functional XIs in S. cerevisiae were clustered with XIs from mammal gut Bacteroidetes group. An XI from Bacteroides valgutus in this cluster was actively expressed in S. cerevisiae with an activity comparable to the fungal XI from Piromyces sp. Two XI genes were isolated from the environmental metagenome and they were clustered with XIs from environmental Bacteroidetes group. These two XIs could not be expressed in yeast with activity. With the XI from B. valgutus expressed in S. cerevisiae, background yeast strains were optimized by pentose metabolizing pathway enhancement and adaptive evolution in xylose medium. Afterwards, more XIs from the mammal gut Bacteroidetes group, including those from B. vulgatus, Tannerella sp. 6_1_58FAA_CT1, Paraprevotella xylaniphila and Alistipes sp. HGB5, were individually transformed into S. cerevisiae. The known functional XI from Orpinomyces sp. ukk1, a mammal gut fungus, was used as the control. All the resulting recombinant yeast strains were able to ferment xylose. The respiration-deficient strains harboring B. vulgatus and Alistipes sp. HGB5 XI genes respectively obtained specific xylose consumption rate of 0.662 and 0.704 g xylose gcdw(-1) h(-1), and ethanol specific productivity of 0.277 and 0.283 g ethanol gcdw(-1) h(-1), much comparable to those obtained by the control strain carrying Orpinomyces sp. ukk1 XI gene. CONCLUSIONS This study demonstrated that XIs clustered in the mammal gut Bacteroidetes group were able to be expressed functionally in S. cerevisiae and background strain anaerobic adaptive evolution in xylose medium is essential for the screening of functional XIs. The methods outlined in this paper are instructive for the identification of novel XIs that are functional in S. cerevisiae.
Collapse
Affiliation(s)
- Bingyin Peng
- School of Life Sciences and Chemical Technology, Ngee Ann Polytechnic, Singapore, Singapore.
| | - Shuangcheng Huang
- School of Life Sciences and Chemical Technology, Ngee Ann Polytechnic, Singapore, Singapore. .,School of Chemical Engineering and Pharmacy, Key Laboratory for Green Chemical Process of Ministry of Education, Wuhan Institute of Technology, Wuhan, 430073, Peoples Republic of China.
| | - Tingting Liu
- School of Life Sciences and Chemical Technology, Ngee Ann Polytechnic, Singapore, Singapore. .,School of Chemical Engineering and Pharmacy, Key Laboratory for Green Chemical Process of Ministry of Education, Wuhan Institute of Technology, Wuhan, 430073, Peoples Republic of China.
| | - Anli Geng
- School of Life Sciences and Chemical Technology, Ngee Ann Polytechnic, Singapore, Singapore.
| |
Collapse
|
168
|
Kumar PS, Mason MR. Mouthguards: does the indigenous microbiome play a role in maintaining oral health? Front Cell Infect Microbiol 2015; 5:35. [PMID: 26000251 PMCID: PMC4422079 DOI: 10.3389/fcimb.2015.00035] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 03/25/2015] [Indexed: 01/23/2023] Open
Abstract
The existence of symbiotic relationships between bacteria and their hosts in various ecosystems have long been known to science. The human body also hosts vast numbers of bacteria in several habitats. Emerging evidence from the gastro-intestinal tract, genito-urinary tract and respiratory indicates that there are several health benefits to hosting a complex and diverse microbial community. Bacteria colonize the oral cavity within a few minutes after birth and form stable communities. Our knowledge of the oral microbiome has expanded exponentially with development of novel exploratory methods that allow us to examine diversity, structure, function, and topography without the need to cultivate the individual components of the biofilm. The purpose of this perspective, therefore, is to examine the strength of current evidence supporting a role for the oral microbiome in maintaining oral health. While several lines of evidence are emerging to suggest that indigenous oral microbiota may have a role in immune education and preventing pathogen expansion, much more work is needed to definitively establish whether oral bacteria do indeed contribute to sustaining oral health, and if so, the mechanisms underlying this role.
Collapse
Affiliation(s)
- Purnima S. Kumar
- Division of Periodontology, College of Dentistry, The Ohio State UniversityColumbus, OH, USA
| | - Matthew R. Mason
- Division of Biosciences, College of Dentistry, The Ohio State UniversityColumbus, OH, USA
| |
Collapse
|
169
|
Lu L, Yu Y, Guo Y, Wang Y, Chang EB, Claud EC. Transcriptional modulation of intestinal innate defense/inflammation genes by preterm infant microbiota in a humanized gnotobiotic mouse model. PLoS One 2015; 10:e0124504. [PMID: 25928420 PMCID: PMC4415773 DOI: 10.1371/journal.pone.0124504] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 03/02/2015] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND AND AIMS It is known that postnatal functional maturation of the small intestine is facilitated by microbial colonization of the gut. Preterm infants exhibit defects in gut maturation, weak innate immunity against intestinal infection and increased susceptibility to inflammatory disorders, all of which may be related to the inappropriate microbial colonization of their immature intestines. The earliest microbes to colonize the preterm infant gut encounter a naïve, immature intestine. Thus this earliest microbiota potentially has the greatest opportunity to fundamentally influence intestinal development and immune function. The aim of this study was to characterize the effect of early microbial colonization on global gene expression in the distal small intestine during postnatal gut development. METHODS Gnotobiotic mouse models with experimental colonization by early (prior to two weeks of life) intestinal microbiota from preterm human infants were utilized. Microarray analysis was used to assess global gene expression in the intestinal epithelium. RESULTS AND CONCLUSION Multiple intestinal genes involved in metabolism, cell cycle regulation, cell-cell or cell-extracellular matrix communication, and immune function are developmental- and intestinal microbiota- regulated. Using a humanized gnotobiotic mouse model, we demonstrate that certain early preterm infant microbiota from prior to 2 weeks of life specifically induce increased NF-κB activation and a phenotype of increased inflammation whereas other preterm microbiota specifically induce decreased NF-κB activation. These fundamental differences correlate with altered clinical outcomes and suggest the existence of optimal early microbial communities to improve health outcomes.
Collapse
Affiliation(s)
- Lei Lu
- Department of Pediatrics/Neonatology, University of Chicago, Chicago Illinois, United States of America
| | - Yueyue Yu
- Department of Pediatrics/Neonatology, University of Chicago, Chicago Illinois, United States of America
| | - Yuee Guo
- Department of Pediatrics/Neonatology, University of Chicago, Chicago Illinois, United States of America
| | - Yunwei Wang
- Internal Medicine Residency Program at Reno, University of Nevada School of Medicine, Reno Nevada, United States of America
| | - Eugene B. Chang
- Department of Medicine/Gastroenterology, University of Chicago, Chicago Illinois, United States of America
| | - Erika C. Claud
- Department of Pediatrics/Neonatology, University of Chicago, Chicago Illinois, United States of America
- Department of Medicine/Gastroenterology, University of Chicago, Chicago Illinois, United States of America
- * E-mail:
| |
Collapse
|
170
|
Xu C, Huang R, Teng L, Jing X, Hu J, Cui G, Wang Y, Cui Q, Xu J. Cellulosome stoichiometry in Clostridium cellulolyticum is regulated by selective RNA processing and stabilization. Nat Commun 2015; 6:6900. [PMID: 25908225 PMCID: PMC4423207 DOI: 10.1038/ncomms7900] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 03/11/2015] [Indexed: 01/23/2023] Open
Abstract
The mechanism, physiological relevance and evolutionary implication of selective RNA processing and stabilization (SRPS) remain elusive. Here we report the genome-wide maps of transcriptional start sites (TSs) and post-transcriptional processed sites (PSs) for Clostridium cellulolyticum. The PS-associated genes are preferably associated with subunits of heteromultimeric protein complexes, and the intergenic PSs (iPSs) are enriched in operons exhibiting highly skewed transcript-abundance landscape. Stem-loop structures associated with those iPSs located at 3′ termini of highly transcribed genes exhibit folding free energy negatively correlated with transcript-abundance ratio of flanking genes. In the cellulosome-encoding cip-cel operon, iPSs and stem-loops precisely regulate structure and abundance of the subunit-encoding transcripts processed from a primary polycistronic RNA, quantitatively specifying cellulosome stoichiometry. Moreover, cellulosome evolution is shaped by the number, position and biophysical nature of TSs, iPSs and stem-loops. Our findings unveil a genome-wide RNA-encoded strategy controlling in vivo stoichiometry of protein complexes. Selective RNA processing and stabilization (SRPS) can regulate bacterial operons, but the process is not well understood. Here, the authors show that the stoichiometry of cellulosome, a 12-subunit protein complex expressed from an operon in Gram-positive Clostridium cellullolyticum, is regulated by SRPS.
Collapse
Affiliation(s)
- Chenggang Xu
- Single-Cell Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China.,CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
| | - Ranran Huang
- Single-Cell Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China.,CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lin Teng
- Single-Cell Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China.,CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoyan Jing
- Single-Cell Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China.,CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
| | - Jianqiang Hu
- Single-Cell Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China.,CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guzhen Cui
- CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
| | - Yilin Wang
- Single-Cell Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China.,CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiu Cui
- CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
| | - Jian Xu
- Single-Cell Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China.,CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
| |
Collapse
|
171
|
Inter-individual differences in the gene content of human gut bacterial species. Genome Biol 2015; 16:82. [PMID: 25896518 PMCID: PMC4428241 DOI: 10.1186/s13059-015-0646-9] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 04/01/2015] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Gene content differences in human gut microbes can lead to inter-individual phenotypic variations such as digestive capacity. It is unclear whether gene content variation is caused by differences in microbial species composition or by the presence of different strains of the same species; the extent of gene content variation in the latter is unknown. Unlike pan-genome studies of cultivable strains, the use of metagenomic data can provide an unbiased view of structural variation of gut bacterial strains by measuring them in their natural habitats, the gut of each individual in this case, representing native boundaries between gut bacterial populations. We analyzed publicly available metagenomic data from fecal samples to characterize inter-individual variation in gut bacterial species. RESULTS A comparison of 11 abundant gut bacterial species showed that the gene content of strains from the same species differed, on average, by 13% between individuals. This number is based on gene deletions only and represents a lower limit, yet the variation is already in a similar range as observed between completely sequenced strains of cultivable species. We show that accessory genes that differ considerably between individuals can encode important functions, such as polysaccharide utilization and capsular polysaccharide synthesis loci. CONCLUSION Metagenomics can yield insights into gene content variation of strains in complex communities, which cannot be predicted by phylogenetic marker genes alone. The large degree of inter-individual variability in gene content implies that strain resolution must be considered in order to fully assess the functional potential of an individual's human gut microbiome.
Collapse
|
172
|
Goh YJ, Klaenhammer TR. Genetic Mechanisms of Prebiotic Oligosaccharide Metabolism in Probiotic Microbes. Annu Rev Food Sci Technol 2015; 6:137-56. [DOI: 10.1146/annurev-food-022814-015706] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Yong Jun Goh
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina 27695; ,
| | - Todd R. Klaenhammer
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina 27695; ,
| |
Collapse
|
173
|
The sweet tooth of bacteria: common themes in bacterial glycoconjugates. Microbiol Mol Biol Rev 2015; 78:372-417. [PMID: 25184559 DOI: 10.1128/mmbr.00007-14] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Humans have been increasingly recognized as being superorganisms, living in close contact with a microbiota on all their mucosal surfaces. However, most studies on the human microbiota have focused on gaining comprehensive insights into the composition of the microbiota under different health conditions (e.g., enterotypes), while there is also a need for detailed knowledge of the different molecules that mediate interactions with the host. Glycoconjugates are an interesting class of molecules for detailed studies, as they form a strain-specific barcode on the surface of bacteria, mediating specific interactions with the host. Strikingly, most glycoconjugates are synthesized by similar biosynthesis mechanisms. Bacteria can produce their major glycoconjugates by using a sequential or an en bloc mechanism, with both mechanistic options coexisting in many species for different macromolecules. In this review, these common themes are conceptualized and illustrated for all major classes of known bacterial glycoconjugates, with a special focus on the rather recently emergent field of glycosylated proteins. We describe the biosynthesis and importance of glycoconjugates in both pathogenic and beneficial bacteria and in both Gram-positive and -negative organisms. The focus lies on microorganisms important for human physiology. In addition, the potential for a better knowledge of bacterial glycoconjugates in the emerging field of glycoengineering and other perspectives is discussed.
Collapse
|
174
|
Peterson DA, Planer JD, Guruge JL, Xue L, Downey-Virgin W, Goodman AL, Seedorf H, Gordon JI. Characterizing the interactions between a naturally primed immunoglobulin A and its conserved Bacteroides thetaiotaomicron species-specific epitope in gnotobiotic mice. J Biol Chem 2015; 290:12630-49. [PMID: 25795776 DOI: 10.1074/jbc.m114.633800] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Indexed: 12/13/2022] Open
Abstract
The adaptive immune response to the human gut microbiota consists of a complex repertoire of antibodies interacting with a broad range of taxa. Fusing intestinal lamina propria lymphocytes from mice monocolonized with Bacteroides thetaiotaomicron to a myeloma fusion partner allowed us to recover hybridomas that captured naturally primed, antigen-specific antibody responses representing multiple isotypes, including IgA. One of these hybridomas, 260.8, produced a monoclonal antibody that recognizes an epitope specific for B. thetaiotaomicron isolates in a large panel of hospital- and community-acquired Bacteroides. Whole genome transposon mutagenesis revealed a 19-gene locus, involved in LPS O-antigen polysaccharide synthesis and conserved among multiple B. thetaiotaomicron isolates, that is required for 260.8 epitope expression. Mutants in this locus exhibited marked fitness defects in vitro during growth in rich medium and in gnotobiotic mice colonized with defined communities of human gut symbionts. Expression of the 260.8 epitope was sustained during 10 months of daily passage in vitro and during 14 months of monocolonization of gnotobiotic wild-type, Rag1-/-, or Myd88-/- mice. Comparison of gnotobiotic Rag1-/- mice with and without subcutaneous 260.8 hybridomas disclosed that this IgA did not affect B. thetaiotaomicron population density or suppress 260.8 epitope production but did affect bacterial gene expression in ways emblematic of a diminished host innate immune response. Our study illustrates an approach for (i) generating diagnostic antibodies, (ii) characterizing IgA responses along a continuum of specificity/degeneracy that defines the IgA repertoire to gut symbionts, and (iii) identifying immunogenic epitopes that affect competitiveness and help maintain host-microbe mutualism.
Collapse
Affiliation(s)
- Daniel A Peterson
- From the Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63108 and Department of Pathology, The Johns Hopkins University, Baltimore, Maryland 21205
| | - Joseph D Planer
- From the Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63108 and
| | - Janaki L Guruge
- From the Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63108 and
| | - Lai Xue
- From the Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63108 and
| | - Whitt Downey-Virgin
- From the Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63108 and
| | - Andrew L Goodman
- From the Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63108 and
| | - Henning Seedorf
- From the Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63108 and
| | - Jeffrey I Gordon
- From the Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63108 and
| |
Collapse
|
175
|
Xu B, Xu W, Li J, Dai L, Xiong C, Tang X, Yang Y, Mu Y, Zhou J, Ding J, Wu Q, Huang Z. Metagenomic analysis of the Rhinopithecus bieti fecal microbiome reveals a broad diversity of bacterial and glycoside hydrolase profiles related to lignocellulose degradation. BMC Genomics 2015; 16:174. [PMID: 25887697 PMCID: PMC4369366 DOI: 10.1186/s12864-015-1378-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 02/21/2015] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The animal gastrointestinal tract contains a complex community of microbes, whose composition ultimately reflects the co-evolution of microorganisms with their animal host and the diet adopted by the host. Although the importance of gut microbiota of humans has been well demonstrated, there is a paucity of research regarding non-human primates (NHPs), especially herbivorous NHPs. RESULTS In this study, an analysis of 97,942 pyrosequencing reads generated from Rhinopithecus bieti fecal DNA extracts was performed to help better understanding of the microbial diversity and functional capacity of the R. bieti gut microbiome. The taxonomic analysis of the metagenomic reads indicated that R. bieti fecal microbiomes were dominated by Firmicutes, Bacteroidetes, Proteobacteria and Actinobacteria phyla. The comparative analysis of taxonomic classification revealed that the metagenome of R. bieti was characterized by an overrepresentation of bacteria of phylum Fibrobacteres and Spirochaetes as compared with other animals. Primary functional categories were associated mainly with protein, carbohydrates, amino acids, DNA and RNA metabolism, cofactors, cell wall and capsule and membrane transport. Comparing glycoside hydrolase profiles of R. bieti with those of other animal revealed that the R. bieti microbiome was most closely related to cow rumen. CONCLUSIONS Metagenomic and functional analysis demonstrated that R. bieti possesses a broad diversity of bacteria and numerous glycoside hydrolases responsible for lignocellulosic biomass degradation which might reflect the adaptations associated with a diet rich in fibrous matter. These results would contribute to the limited body of NHPs metagenome studies and provide a unique genetic resource of plant cell wall degrading microbial enzymes. However, future studies on the metagenome sequencing of R. bieti regarding the effects of age, genetics, diet and environment on the composition and activity of the metagenomes are required.
Collapse
Affiliation(s)
- Bo Xu
- School of Life Science, Yunnan Normal University, Kunming, 650500, China. .,Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, 650500, China. .,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, 650500, China. .,Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, 650500, China.
| | - Weijiang Xu
- School of Life Science, Yunnan Normal University, Kunming, 650500, China. .,Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, 650500, China. .,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, 650500, China. .,Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, 650500, China.
| | - Junjun Li
- School of Life Science, Yunnan Normal University, Kunming, 650500, China. .,Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, 650500, China. .,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, 650500, China. .,Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, 650500, China.
| | - Liming Dai
- School of Life Science, Yunnan Normal University, Kunming, 650500, China.
| | - Caiyun Xiong
- School of Life Science, Yunnan Normal University, Kunming, 650500, China.
| | - Xianghua Tang
- School of Life Science, Yunnan Normal University, Kunming, 650500, China. .,Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, 650500, China. .,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, 650500, China. .,Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, 650500, China.
| | - Yunjuan Yang
- School of Life Science, Yunnan Normal University, Kunming, 650500, China. .,Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, 650500, China. .,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, 650500, China. .,Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, 650500, China.
| | - Yuelin Mu
- School of Life Science, Yunnan Normal University, Kunming, 650500, China. .,Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, 650500, China. .,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, 650500, China. .,Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, 650500, China.
| | - Junpei Zhou
- School of Life Science, Yunnan Normal University, Kunming, 650500, China. .,Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, 650500, China. .,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, 650500, China. .,Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, 650500, China.
| | - Junmei Ding
- School of Life Science, Yunnan Normal University, Kunming, 650500, China. .,Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, 650500, China. .,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, 650500, China. .,Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, 650500, China.
| | - Qian Wu
- School of Life Science, Yunnan Normal University, Kunming, 650500, China. .,Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, 650500, China. .,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, 650500, China. .,Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, 650500, China.
| | - Zunxi Huang
- School of Life Science, Yunnan Normal University, Kunming, 650500, China. .,Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, 650500, China. .,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, 650500, China. .,Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, 650500, China.
| |
Collapse
|
176
|
Species-specific dynamic responses of gut bacteria to a mammalian glycan. J Bacteriol 2015; 197:1538-48. [PMID: 25691527 DOI: 10.1128/jb.00010-15] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 02/06/2015] [Indexed: 12/21/2022] Open
Abstract
UNLABELLED The mammalian intestine provides nutrients to hundreds of bacterial species. Closely related species often harbor homologous nutrient utilization genes and cocolonize the gut, raising questions regarding the strategies mediating their stable coexistence. Here we reveal that related Bacteroides species that can utilize the mammalian glycan chondroitin sulfate (CS) have diverged in the manner in which they temporally regulate orthologous CS utilization genes. Whereas certain Bacteroides species display a transient surge in CS utilization transcripts upon exposure to CS, other species exhibit sustained activation of these genes. Remarkably, species-specific expression dynamics are retained even when the key players governing a particular response are replaced by those from a species with a dissimilar response. Bacteroides species exhibiting distinct expression behaviors in the presence of CS can be cocultured on CS. However, they vary in their responses to CS availability and to the composition of the bacterial community when CS is the sole carbon source. Our results indicate that diversity resulting from regulation of polysaccharide utilization genes may enable the coexistence of gut bacterial species using a given nutrient. IMPORTANCE Genes mediating a specific task are typically conserved in related microbes. For instance, gut Bacteroides species harbor orthologous nutrient breakdown genes and may face competition from one another for these nutrients. How, then, does the gut microbial composition maintain such remarkable stability over long durations? We establish that in the case of genes conferring the ability to utilize the nutrient chondroitin sulfate (CS), microbial species vary in how they temporally regulate these genes and exhibit subtle growth differences on the basis of CS availability and community composition. Similarly to how differential regulation of orthologous genes enables related species to access new environments, gut bacteria may regulate the same genes in distinct fashions to reduce the overlap with coexisting species for utilization of available nutrients.
Collapse
|
177
|
Thompson AJ, Cuskin F, Spears RJ, Dabin J, Turkenburg JP, Gilbert HJ, Davies GJ. Structure of the GH76 α-mannanase homolog, BT2949, from the gut symbiont Bacteroides thetaiotaomicron. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:408-15. [PMID: 25664752 PMCID: PMC4321491 DOI: 10.1107/s1399004714026443] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 12/01/2014] [Indexed: 01/15/2023]
Abstract
The large bowel microbiota, a complex ecosystem resident within the gastrointestinal tract of all human beings and large mammals, functions as an essential, nonsomatic metabolic organ, hydrolysing complex dietary polysaccharides and modulating the host immune system to adequately tolerate ingested antigens. A significant member of this community, Bacteroides thetaiotaomicron, has evolved a complex system for sensing and processing a wide variety of natural glycoproducts in such a way as to provide maximum benefit to itself, the wider microbial community and the host. The immense ability of B. thetaiotaomicron as a `glycan specialist' resides in its enormous array of carbohydrate-active enzymes, many of which are arranged into polysaccharide-utilization loci (PULs) that are able to degrade sugar polymers that are often inaccessible to other gut residents, notably α-mannan. The B. thetaiotaomicron genome encodes ten putative α-mannanases spread across various PULs; however, little is known about the activity of these enzymes or the wider implications of α-mannan metabolism for the health of both the microbiota and the host. In this study, SAD phasing of a selenomethionine derivative has been used to investigate the structure of one such B. thetaiotaomicron enzyme, BT2949, which belongs to the GH76 family of α-mannanases. BT2949 presents a classical (α/α)6-barrel structure comprising a large extended surface cleft common to other GH76 family members. Analysis of the structure in conjunction with sequence alignments reveals the likely location of the catalytic active site of this noncanonical GH76.
Collapse
Affiliation(s)
- Andrew J. Thompson
- Department of Chemistry, University of York, Heslington, York YO10 5DD, England
| | - Fiona Cuskin
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, England
| | - Richard J. Spears
- Department of Chemistry, University of York, Heslington, York YO10 5DD, England
| | - Jerome Dabin
- Department of Chemistry, University of York, Heslington, York YO10 5DD, England
| | - Johan P. Turkenburg
- Department of Chemistry, University of York, Heslington, York YO10 5DD, England
| | - Harry J. Gilbert
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, England
| | - Gideon J. Davies
- Department of Chemistry, University of York, Heslington, York YO10 5DD, England
| |
Collapse
|
178
|
Natarajan P, Punta M, Kumar A, Yeh AP, Godzik A, Aravind L. Structure and sequence analyses of Bacteroides proteins BVU_4064 and BF1687 reveal presence of two novel predominantly-beta domains, predicted to be involved in lipid and cell surface interactions. BMC Bioinformatics 2015; 16:7. [PMID: 25592227 PMCID: PMC4387736 DOI: 10.1186/s12859-014-0434-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 12/16/2014] [Indexed: 11/11/2022] Open
Abstract
Background N-terminal domains of BVU_4064 and BF1687 proteins from Bacteroides vulgatus and Bacteroides fragilis respectively are members of the Pfam family PF12985 (DUF3869). Proteins containing a domain from this family can be found in most Bacteroides species and, in large numbers, in all human gut microbiome samples. Both BVU_4064 and BF1687 proteins have a consensus lipobox motif implying they are anchored to the membrane, but their functions are otherwise unknown. The C-terminal half of BVU_4064 is assigned to protein family PF12986 (DUF3870); the equivalent part of BF1687 was unclassified. Results Crystal structures of both BVU_4064 and BF1687 proteins, solved at the JCSG center, show strikingly similar three-dimensional structures. The main difference between the two is that the two domains in the BVU_4064 protein are connected by a short linker, as opposed to a longer insertion made of 4 helices placed linearly along with a strand that is added to the C-terminal domain in the BF1687 protein. The N-terminal domain in both proteins, corresponding to the PF12985 (DUF3869) domain is a β–sandwich with pre-albumin-like fold, found in many proteins belonging to the Transthyretin clan of Pfam. The structures of C-terminal domains of both proteins, corresponding to the PF12986 (DUF3870) domain in BVU_4064 protein and an unclassified domain in the BF1687 protein, show significant structural similarity to bacterial pore-forming toxins. A helix in this domain is in an analogous position to a loop connecting the second and third strands in the toxin structures, where this loop is implicated to play a role in the toxin insertion into the host cell membrane. The same helix also points to the groove between the N- and C-terminal domains that are loosely held together by hydrophobic and hydrogen bond interactions. The presence of several conserved residues in this region together with these structural determinants could make it a functionally important region in these proteins. Conclusions Structural analysis of BVU_4064 and BF1687 points to possible roles in mediating multiple interactions on the cell-surface/extracellular matrix. In particular the N-terminal domain could be involved in adhesive interactions, the C-terminal domain and the inter-domain groove in lipid or carbohydrate interactions. Electronic supplementary material The online version of this article (doi:10.1186/s12859-014-0434-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Padmaja Natarajan
- Joint Center for Structural Genomics, San Diego, USA. .,Program on Bioinformatics and Systems Biology, Sanford-Burnham Medical Research Institute, La Jolla, CA, USA.
| | - Marco Punta
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
| | - Abhinav Kumar
- Joint Center for Structural Genomics, San Diego, USA. .,Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA.
| | - Andrew P Yeh
- Joint Center for Structural Genomics, San Diego, USA. .,Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA.
| | - Adam Godzik
- Joint Center for Structural Genomics, San Diego, USA. .,Program on Bioinformatics and Systems Biology, Sanford-Burnham Medical Research Institute, La Jolla, CA, USA.
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, Building 38A, Bethesda, MD, 20894, USA.
| |
Collapse
|
179
|
Aw W, Fukuda S. The Role of Integrated Omics in Elucidating the Gut Microbiota Health Potentials. ACTA ACUST UNITED AC 2015. [DOI: 10.1007/978-3-319-23213-3_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
|
180
|
Hansen AK, Hansen CHF, Krych L, Nielsen DS. Impact of the gut microbiota on rodent models of human disease. World J Gastroenterol 2014; 20:17727-17736. [PMID: 25548471 PMCID: PMC4273123 DOI: 10.3748/wjg.v20.i47.17727] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Revised: 09/30/2014] [Accepted: 11/19/2014] [Indexed: 02/06/2023] Open
Abstract
Traditionally bacteria have been considered as either pathogens, commensals or symbionts. The mammal gut harbors 1014 organisms dispersed on approximately 1000 different species. Today, diagnostics, in contrast to previous cultivation techniques, allow the identification of close to 100% of bacterial species. This has revealed that a range of animal models within different research areas, such as diabetes, obesity, cancer, allergy, behavior and colitis, are affected by their gut microbiota. Correlation studies may for some diseases show correlation between gut microbiota composition and disease parameters higher than 70%. Some disease phenotypes may be transferred when recolonizing germ free mice. The mechanistic aspects are not clear, but some examples on how gut bacteria stimulate receptors, metabolism, and immune responses are discussed. A more deeper understanding of the impact of microbiota has its origin in the overall composition of the microbiota and in some newly recognized species, such as Akkermansia muciniphila, Segmented filamentous bacteria and Faecalibacterium prausnitzii, which seem to have an impact on more or less severe disease in specific models. Thus, the impact of the microbiota on animal models is of a magnitude that cannot be ignored in future research. Therefore, either models with specific microbiota must be developed, or the microbiota must be characterized in individual studies and incorporated into data evaluation.
Collapse
|
181
|
Rabausch U, Ilmberger N, Streit W. The metagenome-derived enzyme RhaB opens a new subclass of bacterial B type α-l-rhamnosidases. J Biotechnol 2014; 191:38-45. [DOI: 10.1016/j.jbiotec.2014.04.024] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 04/23/2014] [Accepted: 04/28/2014] [Indexed: 11/26/2022]
|
182
|
Abstract
Holistic emerging approaches allow us to understand that every organism is the result of integration mechanisms observed at every level of nature: integration of DNA from virus and bacteria in metazoans, endosymbiotic relationships and holobionts. Horizontal gene transfer events in Bacteria, Archaea and Eukaryotes have resulted in the chimeric nature of genomes. As a continuity of this genomic landscape, the human body contains more bacterial than human cells. Human microbiome has co-evolved with the human being as a unity called holobiont. The loss of part of our microbiome along evolution can explain the continuous increasing incidence of immune and inflammatory-related diseases. Life is a continuous process in which the organism experiences its environment and this interaction impacts in the epigenetic system and the genomic structure. The emerging perspectives restitute the great importance of Lamarck's theoretical contributions (the milieu) and Darwin's pangenesis theory.
Collapse
|
183
|
Lakshminarayanan B, Stanton C, O'Toole PW, Ross RP. Compositional dynamics of the human intestinal microbiota with aging: implications for health. J Nutr Health Aging 2014. [PMID: 25389954 DOI: 10.1007/s12603-014-0513-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The human gut contains trillions of microbes which form an essential part of the complex ecosystem of the host. This microbiota is relatively stable throughout adult life, but may fluctuate over time with aging and disease. The gut microbiota serves a number of functions including roles in energy provision, nutrition and also in the maintenance of host health such as protection against pathogens. This review summarizes the age-related changes in the microbiota of the gastrointestinal tract (GIT) and the link between the gut microbiota in health and disease. Understanding the composition and function of the gut microbiota along with the changes it undergoes overtime should aid the design of novel therapeutic strategies to counteract such alterations. These strategies include probiotic and prebiotic preparations as well as targeted nutrients, designed to enrich the gut microbiota of the aging population.
Collapse
Affiliation(s)
- B Lakshminarayanan
- R. Paul Ross, Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland. , Tel: 00353 (0)25 42229, Fax: 00353 (0)25 42340
| | | | | | | |
Collapse
|
184
|
Arias MC, Danchin EGJ, Coutinho P, Henrissat B, Ball S. Eukaryote to gut bacteria transfer of a glycoside hydrolase gene essential for starch breakdown in plants. Mob Genet Elements 2014; 2:81-87. [PMID: 22934241 PMCID: PMC3429525 DOI: 10.4161/mge.20375] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Lateral gene transfer (LGT) between bacteria constitutes a strong force in prokaryote evolution, transforming the hierarchical tree of life into a network of relationships between species. In contrast, only a few cases of LGT from eukaryotes to prokaryotes have been reported so far. The distal animal intestine is predominantly a bacterial ecosystem, supplying the host with energy from dietary polysaccharides through carbohydrate-active enzymes absent from its genome. It has been suggested that LGT is particularly important for the human microbiota evolution. Here we show evidence for the first eukaryotic gene identified in multiple gut bacterial genomes. We found in the genome sequence of several gut bacteria, a typically eukaryotic glycoside-hydrolase necessary for starch breakdown in plants. The distribution of this gene is patchy in gut bacteria with presence otherwise detected only in a few environmental bacteria.
We speculate that the transfer of this gene to gut bacteria occurred by a sequence of two key LGT events; first, an original eukaryotic gene was transferred probably from Archaeplastida to environmental bacteria specialized in plant polysaccharides degradation and second, the gene was transferred from the environmental bacteria to gut microbes.
Collapse
|
185
|
Aw W, Fukuda S. Toward the comprehensive understanding of the gut ecosystem via metabolomics-based integrated omics approach. Semin Immunopathol 2014; 37:5-16. [PMID: 25338280 DOI: 10.1007/s00281-014-0456-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 10/09/2014] [Indexed: 12/27/2022]
Abstract
Recent advances in DNA sequencing and mass spectrometry technologies have allowed us to collect more data on microbiome and metabolome to assess the influence of the gut microbiota on human health at a whole-systems level. Major advances in metagenomics and metabolomics technologies have shown that the gut microbiota contributes to host overall health status to a large extent. As such, the gut microbiota is often likened to a measurable and functional organ consisting of prokaryotic cells, which creates the unique gut ecosystem together with the host eukaryotic cells. In this review, we discuss in detail the relationship between gut microbiota and its metabolites like choline, bile acids, phenols, and short-chain fatty acids in the host health and etiopathogenesis of various pathological states such as multiple sclerosis, autism, obesity, diabetes, and chronic kidney disease. By integrating metagenomic and metabolomic information on a systems biology-wide approach, we would be better able to understand this interplay between gut microbiome and host metabolism. Integration of the microbiome, metatranscriptome, and metabolome information will pave the way toward an improved holistic understanding of the complex mammalian superorganism. Through the modeling of metabolic interactions between lifestyle, diet, and microbiota, integrated omics-based understanding of the gut ecosystem is the new avenue, providing exciting novel therapeutic approaches for optimal host health.
Collapse
Affiliation(s)
- Wanping Aw
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata, 997-0052, Japan
| | | |
Collapse
|
186
|
Jiménez E, Sánchez B, Farina A, Margolles A, Rodríguez JM. Characterization of the bile and gall bladder microbiota of healthy pigs. Microbiologyopen 2014; 3:937-49. [PMID: 25336405 PMCID: PMC4263516 DOI: 10.1002/mbo3.218] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 09/21/2014] [Accepted: 09/23/2014] [Indexed: 12/12/2022] Open
Abstract
Bile is a biological fluid synthesized in the liver, stored and concentrated in the gall bladder (interdigestive), and released into the duodenum after food intake. The microbial populations of different parts of mammal's gastrointestinal tract (stomach, small and large intestine) have been extensively studied; however, the characterization of bile microbiota had not been tackled until now. We have studied, by culture-dependent techniques and a 16S rRNA gene-based analysis, the microbiota present in the bile, gall bladder mucus, and biopsies of healthy sows. Also, we have identified the most abundant bacterial proteins in the bile samples. Our data show that the gall bladder ecosystem is mainly populated by members of the phyla Proteobacteria, Firmicutes, and Bacteroidetes. Furthermore, fluorescent in situ hybridization (FISH) and transmission electron microscopy (TEM) allowed us to visualize the presence of individual bacteria of different morphological types, in close association with either the epithelium or the erythrocytes, or inside the epithelial cells. Our work has generated new knowledge of bile microbial profiles and functions and might provide the basis for future studies on the relationship between bile microbiota, gut microbiota, and health.
Collapse
Affiliation(s)
- Esther Jiménez
- Departamento de Nutrición, Bromatología y Tecnología de los Alimentos, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | | | | | | | | |
Collapse
|
187
|
Tellez G. Prokaryotes Versus Eukaryotes: Who is Hosting Whom? Front Vet Sci 2014; 1:3. [PMID: 26664911 PMCID: PMC4668860 DOI: 10.3389/fvets.2014.00003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 06/23/2014] [Indexed: 01/22/2023] Open
Abstract
Microorganisms represent the largest component of biodiversity in our world. For millions of years, prokaryotic microorganisms have functioned as a major selective force shaping eukaryotic evolution. Microbes that live inside and on animals outnumber the animals' actual somatic and germ cells by an estimated 10-fold. Collectively, the intestinal microbiome represents a "forgotten organ," functioning as an organ inside another that can execute many physiological responsibilities. The nature of primitive eukaryotes was drastically changed due to the association with symbiotic prokaryotes facilitating mutual coevolution of host and microbe. Phytophagous insects have long been used to test theories of evolutionary diversification; moreover, the diversification of a number of phytophagous insect lineages has been linked to mutualisms with microbes. From termites and honey bees to ruminants and mammals, depending on novel biochemistries provided by the prokaryotic microbiome, the association helps to metabolize several nutrients that the host cannot digest and converting these into useful end products (such as short-chain fatty acids), a process, which has huge impact on the biology and homeostasis of metazoans. More importantly, in a direct and/or indirect way, the intestinal microbiota influences the assembly of gut-associated lymphoid tissue, helps to educate immune system, affects the integrity of the intestinal mucosal barrier, modulates proliferation and differentiation of its epithelial lineages, regulates angiogenesis, and modifies the activity of enteric as well as the central nervous system. Despite these important effects, the mechanisms by which the gut microbial community influences the host's biology remain almost entirely unknown. Our aim here is to encourage empirical inquiry into the relationship between mutualism and evolutionary diversification between prokaryotes and eukaryotes, which encourage us to postulate: who is hosting whom?
Collapse
Affiliation(s)
- Guillermo Tellez
- The John Kirkpatrick Skeeles Poultry Health Laboratory, Department of Poultry Science, The Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, AR, USA
| |
Collapse
|
188
|
Abstract
Systemic lupus erythematosus (SLE) is the prototypical systemic autoimmune disease in humans and is characterized by the presence of hyperactive immune cells and aberrant antibody responses to nuclear and cytoplasmic antigens, including characteristic anti–double-stranded DNA antibodies. We performed a cross-sectional study in order to determine if an SLE-associated gut dysbiosis exists in patients without active disease. A group of 20 SLE patients in remission, for which there was strict inclusion and exclusion criteria, was recruited, and we used an optimized Ion Torrent 16S rRNA gene-based analysis protocol to decipher the fecal microbial profiles of these patients and compare them with those of 20 age- and sex-matched healthy control subjects. We found diversity to be comparable based on Shannon’s index. However, we saw a significantly lower Firmicutes/Bacteroidetes ratio in SLE individuals (median ratio, 1.97) than in healthy subjects (median ratio, 4.86; P < 0.002). A lower Firmicutes/Bacteroidetes ratio in SLE individuals was corroborated by quantitative PCR analysis. Notably, a decrease of some Firmicutes families was also detected. This dysbiosis is reflected, based on in silico functional inference, in an overrepresentation of oxidative phosphorylation and glycan utilization pathways in SLE patient microbiota. Growing evidence suggests that the gut microbiota might impact symptoms and progression of some autoimmune diseases. However, how and why this microbial community influences SLE remains to be elucidated. This is the first report describing an SLE-associated intestinal dysbiosis, and it contributes to the understanding of the interplay between the intestinal microbiota and the host in autoimmune disorders.
Collapse
|
189
|
The central role of the gut microbiota in chronic inflammatory diseases. J Immunol Res 2014; 2014:689492. [PMID: 25309932 PMCID: PMC4189530 DOI: 10.1155/2014/689492] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 08/28/2014] [Indexed: 12/12/2022] Open
Abstract
The commensal microbiota is in constant interaction with the immune system, teaching immune cells to respond to antigens. Studies in mice have demonstrated that manipulation of the intestinal microbiota alters host immune cell homeostasis. Additionally, metagenomic-sequencing analysis has revealed alterations in intestinal microbiota in patients suffering from inflammatory bowel disease, asthma, and obesity. Perturbations in the microbiota composition result in a deficient immune response and impaired tolerance to commensal microorganisms. Due to altered microbiota composition which is associated to some inflammatory diseases, several strategies, such as the administration of probiotics, diet, and antibiotic usage, have been utilized to prevent or ameliorate chronic inflammatory diseases. The purpose of this review is to present and discuss recent evidence showing that the gut microbiota controls immune system function and onset, development, and resolution of some common inflammatory diseases.
Collapse
|
190
|
Anti-obesity effects of gut microbiota are associated with lactic acid bacteria. Appl Microbiol Biotechnol 2014; 98:1-10. [PMID: 24232731 DOI: 10.1007/s00253-013-5346-3] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Revised: 10/16/2013] [Accepted: 10/17/2013] [Indexed: 12/16/2022]
Abstract
The prevalence of obesity is rapidly becoming endemic in industrialized countries and continues to increase in developing countries worldwide. Obesity predisposes people to an increased risk of developing metabolic syndrome. Recent studies have described an association between obesity and certain gut microbiota, suggesting that gut microbiota might play a critical role in the development of obesity. Although probiotics have many beneficial health effects in humans and animals, attention has only recently been drawn to manipulating the gut microbiota, such as lactic acid bacteria (LAB), to influence the development of obesity. In this review, we first describe the causes of obesity, including the genetic and environmental factors. We then describe the relationship between the gut microbiota and obesity, and the mechanisms by which the gut microbiota influence energy metabolism and inflammation in obesity. Lastly, we focus on the potential role of LAB in mediating the effects of the gut microbiota in the development of obesity.
Collapse
|
191
|
Systematic analysis of the association between gut flora and obesity through high-throughput sequencing and bioinformatics approaches. BIOMED RESEARCH INTERNATIONAL 2014; 2014:906168. [PMID: 25202708 PMCID: PMC4150407 DOI: 10.1155/2014/906168] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 06/27/2014] [Indexed: 12/24/2022]
Abstract
Eighty-one stool samples from Taiwanese were collected for analysis of the association between the gut flora and obesity. The supervised analysis showed that the most, abundant genera of bacteria in normal samples (from people with a body mass index (BMI) ≤ 24) were Bacteroides (27.7%), Prevotella (19.4%), Escherichia (12%), Phascolarctobacterium (3.9%), and Eubacterium (3.5%). The most abundant genera of bacteria in case samples (with a BMI ≥ 27) were Bacteroides (29%), Prevotella (21%), Escherichia (7.4%), Megamonas (5.1%), and Phascolarctobacterium (3.8%). A principal coordinate analysis (PCoA) demonstrated that normal samples were clustered more compactly than case samples. An unsupervised analysis demonstrated that bacterial communities in the gut were clustered into two main groups: N-like and OB-like groups. Remarkably, most normal samples (78%) were clustered in the N-like group, and most case samples (81%) were clustered in the OB-like group (Fisher's P value = 1.61E − 07). The results showed that bacterial communities in the gut were highly associated with obesity. This is the first study in Taiwan to investigate the association between human gut flora and obesity, and the results provide new insights into the correlation of bacteria with the rising trend in obesity.
Collapse
|
192
|
Kumar A, Punta M, Axelrod HL, Das D, Farr CL, Grant JC, Chiu HJ, Miller MD, Coggill PC, Klock HE, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA. Crystal structures of three representatives of a new Pfam family PF14869 (DUF4488) suggest they function in sugar binding/uptake. Protein Sci 2014; 23:1380-91. [PMID: 25044324 DOI: 10.1002/pro.2522] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 07/10/2014] [Accepted: 07/11/2014] [Indexed: 12/27/2022]
Abstract
Crystal structures of three members (BACOVA_00364 from Bacteroides ovatus, BACUNI_03039 from Bacteroides uniformis and BACEGG_00036 from Bacteroides eggerthii) of the Pfam domain of unknown function (DUF4488) were determined to 1.95, 1.66, and 1.81 Å resolutions, respectively. The protein structures adopt an eight-stranded, calycin-like, β-barrel fold and bind an endogenous unknown ligand at one end of the β-barrel. The amino acids interacting with the ligand are not conserved in any other protein of known structure with this particular fold. The size and chemical environment of the bound ligand suggest binding or transport of a small polar molecule(s) as a potential function for these proteins. These are the first structural representatives of a newly defined PF14869 (DUF4488) Pfam family.
Collapse
Affiliation(s)
- Abhinav Kumar
- Joint Center for Structural Genomics, http://www.jcsg.org; Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California, 94025
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
193
|
Zhang Z, Liu Q, Hendrickson WA. Crystal structures of apparent saccharide sensors from histidine kinase receptors prevalent in a human gut symbiont. FEBS J 2014; 281:4263-79. [PMID: 24995510 DOI: 10.1111/febs.12904] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Revised: 06/19/2014] [Accepted: 06/24/2014] [Indexed: 12/14/2022]
Abstract
UNLABELLED The adult human gut is a complicated ecosystem in which host-bacterium symbiosis plays an important role. Bacteroides thetaiotaomicron is a predominant member of the gut microflora, providing the human digestive tract with a large number of glycolytic enzymes. Expression of many of these enzymes appears to be controlled by histidine kinase receptors that are fused into unusual hybrid two-component systems that share homologous periplasmic sensor domains. These sensor domains belong to the third most populated (HK3) family based on a previous unpublished bioinformatics analysis of predicted histidine kinase sensors. Here, we present the crystal structures of two sensor domains representative of the HK3 family. Each sensor is folded into three domains: two-seven-bladed β-propeller domains and one β-sandwich domain. Both sensors form dimers in crystals, and one sensor appears to be physiologically relevant. The folding characteristics in the individual domains, the domain organization, and the oligomeric architecture are all unique to HK3 sensors. Sequence analysis of the HK3 sensors indicates that these sensor domains are shared among other signaling molecules, implying combinatorial molecular evolution. DATABASE The structural data for the crystallographic results for HK3 BT4673S and HK3 BT3049S have been deposited in the Protein Data Bank under accession numbers 3OTT and 3V9F, respectively. STRUCTURED DIGITAL ABSTRACT HK3BT3049S and HK3BT3049S bind by x-ray crystallography (View interaction) HK3BT3049S and HK3BT3049S bind by molecular sieving (View interaction) HK3BT3049S and HK3BT3049S bind by cosedimentation through density gradient (View interaction) HK3BT4673s and HK3BT4673s bind by cosedimentation through density gradient (View interaction) HK3BT4673s and HK3BT4673s bind by molecular sieving (View interaction).
Collapse
Affiliation(s)
- Zhen Zhang
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | | | | |
Collapse
|
194
|
Barzegari A, Eslami S, Ghabeli E, Omidi Y. Imposition of encapsulated non-indigenous probiotics into intestine may disturb human core microbiome. Front Microbiol 2014; 5:393. [PMID: 25132834 PMCID: PMC4116782 DOI: 10.3389/fmicb.2014.00393] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 07/13/2014] [Indexed: 01/24/2023] Open
Affiliation(s)
- Abolfazl Barzegari
- Student Research Committee, Research Center for Pharmaceutical Nanotechnology, School of Advanced Biomedical Sciences, Tabriz University of Medical Sciences Tabriz, Iran
| | - Solat Eslami
- Student Research Committee, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences Tehran, Iran
| | - Elham Ghabeli
- Student Research Committee, Faculty of Medicine, Urmia University of Medical Sciences Urmia, Iran
| | - Yadollah Omidi
- Research Center for Pharmaceutical Nanotechnology, School of Advanced Biomedical Sciences, Tabriz University of Medical Sciences Tabriz, Iran
| |
Collapse
|
195
|
Paturi G, Butts CA, Bentley-Hewitt KL, Ansell J. Influence of green and gold kiwifruit on indices of large bowel function in healthy rats. J Food Sci 2014; 79:H1611-20. [PMID: 25048562 DOI: 10.1111/1750-3841.12532] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2013] [Accepted: 05/23/2014] [Indexed: 01/08/2023]
Abstract
The effects of kiwifruit on large bowel health were investigated in healthy rats. Four-week old Sprague-Dawley rats were given diets containing 10% homogenized green kiwifruit, gold kiwifruit or 10% glucose solution (control) over 4 or 6 wk. Green kiwifruit increased the fecal output compared to control. Growth of certain bacterial species in cecum was influenced by both green and gold kiwifruit. A significant increase in cecal Lachnospiraceae in rats fed the green kiwifruit diet was observed at week 4. At week 6, green and gold kiwifruit diets assisted in improving colonic barrier function by upregulating the expression of mucin (MUC)-2, MUC3, Toll-like receptor (TLR)-4 or trefoil factor-3 genes. Gold kiwifruit consumption increased the colonic goblet cells per crypt at week 6. Significant negative correlations between E. coli and β-defensin 1 and TLR4 expression were observed. Consuming green and gold kiwifruit for 6 wk significantly altered the biomarkers of large bowel health; indicating that regularly consuming kiwifruit helps attain optimal digestive health.
Collapse
Affiliation(s)
- Gunaranjan Paturi
- The New Zealand Inst. for Plant and Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand
| | | | | | | |
Collapse
|
196
|
Hobbs ME, Williams HJ, Hillerich B, Almo SC, Raushel FM. l-Galactose metabolism in Bacteroides vulgatus from the human gut microbiota. Biochemistry 2014; 53:4661-70. [PMID: 24963813 PMCID: PMC4108180 DOI: 10.1021/bi500656m] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
A previously
unknown metabolic pathway for the utilization of l-galactose
was discovered in a prevalent gut bacterium, Bacteroides vulgatus. The new pathway consists of three
previously uncharacterized enzymes that were found to be responsible
for the conversion of l-galactose to d-tagaturonate.
Bvu0219 (l-galactose dehydrogenase) was determined to oxidize l-galactose to l-galactono-1,5-lactone with kcat and kcat/Km values of 21 s–1 and 2.0
× 105 M–1 s–1,
respectively. The kinetic product of Bvu0219 is rapidly converted
nonenzymatically to the thermodynamically more stable l-galactono-1,4-lactone.
Bvu0220 (l-galactono-1,5-lactonase) hydrolyzes both the kinetic
and thermodynamic products of Bvu0219 to l-galactonate. However, l-galactono-1,5-lactone is estimated to be hydrolyzed 300-fold
faster than its thermodynamically more stable counterpart, l-galactono-1,4-lactone. In the final step of this pathway, Bvu0222
(l-galactonate dehydrogenase) oxidizes l-galactonate
to d-tagaturonate with kcat and kcat/Km values of
0.6 s–1 and 1.7 × 104 M–1 s–1, respectively. In the reverse direction, d-tagaturonate is reduced to l-galactonate with values
of kcat and kcat/Km of 90 s–1 and 1.6
× 105 M–1 s–1,
respectively. d-Tagaturonate is subsequently converted to d-glyceraldehyde and pyruvate through enzymes encoded within
the degradation pathway for d-glucuronate and d-galacturonate.
Collapse
Affiliation(s)
- Merlin Eric Hobbs
- Department of Biochemistry and Biophysics, §Department of Chemistry, Texas A&M University , College Station, Texas 77843, United States
| | | | | | | | | |
Collapse
|
197
|
Tyler AD, Smith MI, Silverberg MS. Analyzing the human microbiome: a "how to" guide for physicians. Am J Gastroenterol 2014; 109:983-93. [PMID: 24751579 DOI: 10.1038/ajg.2014.73] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 03/11/2014] [Indexed: 02/07/2023]
Abstract
The application of high-throughput next-generation sequencing to the analysis of the human microbiome has led to a shift in our understanding of the etiology of complex diseases. In consequence, a great deal of literature can now be found exploring this complex system, and reviewing recent findings. Observations of alterations in the intestinal microbiome associating with inflammatory bowel disease and other chronic conditions are well supported and have been widely accepted by the research community. Yet, it can be difficult to objectively evaluate the importance of these results, given the wide variety of methodologies applied by different groups in the field. The aim of this review is to focus attention on the basic principles involved in microbiome analyses, and to describe factors that may have an impact on the accurate interpretation of results.
Collapse
Affiliation(s)
- Andrea D Tyler
- 1] Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada [2] Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital Inflammatory Bowel Disease Group, Toronto, Ontario, Canada
| | - Michelle I Smith
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital Inflammatory Bowel Disease Group, Toronto, Ontario, Canada
| | - Mark S Silverberg
- 1] Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada [2] Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital Inflammatory Bowel Disease Group, Toronto, Ontario, Canada
| |
Collapse
|
198
|
Briones A, Coats E, Brinkman C. Should we build "obese" or "lean" anaerobic digesters? PLoS One 2014; 9:e97252. [PMID: 24831948 PMCID: PMC4022501 DOI: 10.1371/journal.pone.0097252] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Accepted: 04/16/2014] [Indexed: 01/04/2023] Open
Abstract
Conventional anaerobic digesters (ADs) treating dairy manure are fed with raw or fermented manure rich in volatile fatty acids (VFAs). In contrast, pre-fermented AD (PF-AD) is fed with the more recalcitrant, fiber-rich fraction of manure that has been pre-fermented and depleted of VFAs. Thus, the substrate of PF-AD may be likened to a lean diet rich in fibers while the pre-fermentation stage fermenter is fed a relatively rich diet containing labile organic substances. Previous results have shown that conventional and pre-fermented ADs fed with raw or pre-fermented manure, respectively, produced comparable methane yields. The primary objective of this study was to characterize, using next-generation DNA sequencing, the bacterial communities in various bioreactors (pre-fermentation stage fermenter; various operational arrangements PF-AD; conventional single-stage AD; and a full scale AD) and compare the Firmicutes to Bacteroidetes (F/B) ratios in these different systems. Firmicutes and Bacteroidetes constituted the two most abundant phyla in all AD samples analyzed, as well as most of the samples analyzed in the fermenters and manure samples. Higher relative abundance of Bacteroidetes, ranging from 26% to 51% of bacteria, tended to be associated with PF-AD samples, while the highest relative abundance of Firmicutes occurred in the fermenter (maximum of 76% of bacteria) and manure (maximum of 66% of bacteria) samples. On average, primary stage fermenters exhibited microbiological traits linked to obesity: higher F/B ratios and a ‘diet’ that is less fibrous and more labile compared to that fed to PF-AD. On the other hand, microbial characteristics associated with leanness (lower F/B ratios combined with fibrous substrate) were associated with PF-AD. We propose that bacterial communities in AD shift depending on the quality of substrate, which ultimately results in maintaining VFA yields in PF-AD, similar to the role of bacterial communities and a high fiber diet in lean mice.
Collapse
Affiliation(s)
- Aurelio Briones
- Department of Plant, Soil and Entomological Sciences, University of Idaho, Moscow, Idaho, United States of America
- * E-mail:
| | - Erik Coats
- Department of Civil Engineering, University of Idaho, Moscow, Idaho, United States of America
| | - Cynthia Brinkman
- Department of Civil Engineering, University of Idaho, Moscow, Idaho, United States of America
| |
Collapse
|
199
|
Lennon G, Balfe Á, Earley H, Devane LA, Lavelle A, Winter DC, Coffey JC, O'Connell PR. Influences of the colonic microbiome on the mucous gel layer in ulcerative colitis. Gut Microbes 2014; 5:277-85. [PMID: 24714392 PMCID: PMC4153764 DOI: 10.4161/gmic.28793] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The colonic mucus gel layer (MGL) is a critical component of the innate immune system acting as a physical barrier to microbes, luminal insults, and toxins. Mucins are the major component of the MGL. Selected microbes have the potential to interact with, bind to, and metabolize mucins. The tolerance of the host to the presence of these microbes is critical to maintaining MGL homeostasis. In disease states such as ulcerative colitis (UC), both the mucosa associated microbes and the constituent MGL mucins have been shown to be altered. Evidence is accumulating that implicates the potential for mucin degrading bacteria to negatively impact the MGL and its stasis. These effects appear more pronounced in UC. This review is focused on the host-microbiome interactions within the setting of the MGL. Special focus is given to the mucolytic potential of microbes and their interactions in the setting of the colitic colon.
Collapse
Affiliation(s)
- Gráinne Lennon
- School of Medicine and Medical Sciences; University College Dublin; Dublin, Ireland,Centre for Colorectal Disease; St Vincent's University Hospital; Elm Park, Ireland
| | - Áine Balfe
- School of Medicine and Medical Sciences; University College Dublin; Dublin, Ireland,Centre for Colorectal Disease; St Vincent's University Hospital; Elm Park, Ireland
| | - Helen Earley
- School of Medicine and Medical Sciences; University College Dublin; Dublin, Ireland,Centre for Colorectal Disease; St Vincent's University Hospital; Elm Park, Ireland
| | - Liam A Devane
- School of Medicine and Medical Sciences; University College Dublin; Dublin, Ireland,Centre for Colorectal Disease; St Vincent's University Hospital; Elm Park, Ireland
| | - Aonghus Lavelle
- School of Medicine and Medical Sciences; University College Dublin; Dublin, Ireland,Centre for Colorectal Disease; St Vincent's University Hospital; Elm Park, Ireland
| | - Desmond C Winter
- School of Medicine and Medical Sciences; University College Dublin; Dublin, Ireland,Centre for Colorectal Disease; St Vincent's University Hospital; Elm Park, Ireland
| | - J Calvin Coffey
- Graduate Entry Medical School; University Hospital Limerick; University of Limerick; Limerick, Ireland
| | - P Ronan O'Connell
- School of Medicine and Medical Sciences; University College Dublin; Dublin, Ireland,Centre for Colorectal Disease; St Vincent's University Hospital; Elm Park, Ireland,Correspondence to: P Ronan O'Connell,
| |
Collapse
|
200
|
Maltz MA, Bomar L, Lapierre P, Morrison HG, McClure EA, Sogin ML, Graf J. Metagenomic analysis of the medicinal leech gut microbiota. Front Microbiol 2014; 5:151. [PMID: 24860552 PMCID: PMC4029005 DOI: 10.3389/fmicb.2014.00151] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 03/21/2014] [Indexed: 12/11/2022] Open
Abstract
There are trillions of microbes found throughout the human body and they exceed the number of eukaryotic cells by 10-fold. Metagenomic studies have revealed that the majority of these microbes are found within the gut, playing an important role in the host's digestion and nutrition. The complexity of the animal digestive tract, unculturable microbes, and the lack of genetic tools for most culturable microbes make it challenging to explore the nature of these microbial interactions within this niche. The medicinal leech, Hirudo verbana, has been shown to be a useful tool in overcoming these challenges, due to the simplicity of the microbiome and the availability of genetic tools for one of the two dominant gut symbionts, Aeromonas veronii. In this study, we utilize 16S rRNA gene pyrosequencing to further explore the microbial composition of the leech digestive tract, confirming the dominance of two taxa, the Rikenella-like bacterium and A. veronii. The deep sequencing approach revealed the presence of additional members of the microbial community that suggests the presence of a moderately complex microbial community with a richness of 36 taxa. The presence of a Proteus strain as a newly identified resident in the leech crop was confirmed using fluorescence in situ hybridization (FISH). The metagenome of this community was also pyrosequenced and the contigs were binned into the following taxonomic groups: Rikenella-like (3.1 MB), Aeromonas (4.5 MB), Proteus (2.9 MB), Clostridium (1.8 MB), Eryspelothrix (0.96 MB), Desulfovibrio (0.14 MB), and Fusobacterium (0.27 MB). Functional analyses on the leech gut symbionts were explored using the metagenomic data and MG-RAST. A comparison of the COG and KEGG categories of the leech gut metagenome to that of other animal digestive-tract microbiomes revealed that the leech digestive tract had a similar metabolic potential to the human digestive tract, supporting the usefulness of this system as a model for studying digestive-tract microbiomes. This study lays the foundation for more detailed metatranscriptomic studies and the investigation of symbiont population dynamics.
Collapse
Affiliation(s)
- Michele A Maltz
- Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA
| | - Lindsey Bomar
- Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA
| | - Pascal Lapierre
- Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA
| | - Hilary G Morrison
- Marine Biological Laboratory, The Josephine Bay Paul Center Woods Hole, MA, USA
| | - Emily Ann McClure
- Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA
| | - Mitchell L Sogin
- Marine Biological Laboratory, The Josephine Bay Paul Center Woods Hole, MA, USA
| | - Joerg Graf
- Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA
| |
Collapse
|