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Jordi Mayneris-Perxachs, David T Bolick, Joy Leng, Greg L Medlock, Glynis L Kolling, Jason A Papin, Jonathan R Swann, Richard L Guerrant
BACKGROUND: Environmental enteropathy, which is linked to undernutrition and chronic infections, affects the physical and mental growth of children in developing areas worldwide. Key to understanding how these factors combine to shape developmental outcomes is to first understand the effects of nutritional deficiencies on the mammalian system including the effect on the gut microbiota. OBJECTIVE: We dissected the nutritional components of environmental enteropathy by analyzing the specific metabolic and gut-microbiota changes that occur in weaned-mouse models of zinc or protein deficiency compared with well-nourished controls...
October 12, 2016: American Journal of Clinical Nutrition
Julien Tap, Muriel Derrien, Hans Törnblom, Rémi Brazeilles, Stéphanie Cools-Portier, Joël Doré, Stine Störsrud, Boris Le Nevé, Lena Öhman, Magnus Simrén
BACKGROUND AND AIMS: We have limited knowledge about the association between the composition of the intestinal microbiota and clinical features of irritable bowel syndrome (IBS). We collected information on the fecal and mucosa-associated microbiota of patients with IBS and evaluated whether these were associated with symptoms. METHODS: We collected fecal and mucosal samples from adult patients who met the Rome III criteria for IBS at secondary or tertiary care outpatient clinics in Sweden, as well as from healthy subjects...
October 7, 2016: Gastroenterology
Chao Kang, Yong Zhang, Xiaohui Zhu, Kai Liu, Xiaolan Wang, Mengting Chen, Jian Wang, Hua Chen, Suocheng Hui, Li Huang, Qianyong Zhang, Jundong Zhu, Bin Wang, Mantian Mi
CONTEXT: Previous population studies in evaluating the beneficial effects of capsaicin (CAP) have yielded inconclusive results, and the mechanisms responsible for possible benefit remain unclear. OBJECTIVE: The objective was to assess the impact of dietary CAP on metabolic and immune profiles and its potential associations with gut microbial patterns in healthy adults. DESIGN: In a 6-week controlled feeding trial, subjects were given the weight maintenance diet sequentially contained with 0, 5, 0 and 10 mg/d CAP from chili powder...
September 27, 2016: Journal of Clinical Endocrinology and Metabolism
Sara Vieira-Silva, Gwen Falony, Youssef Darzi, Gipsi Lima-Mendez, Roberto Garcia Yunta, Shujiro Okuda, Doris Vandeputte, Mireia Valles-Colomer, Falk Hildebrand, Samuel Chaffron, Jeroen Raes
Despite recent progress, the organization and ecological properties of the intestinal microbial ecosystem remain under-investigated. Here, using a manually curated metabolic module framework for (meta-)genomic data analysis, we studied species-function relationships in gut microbial genomes and microbiomes. Half of gut-associated species were found to be generalists regarding overall substrate preference, but we observed significant genus-level metabolic diversification linked to bacterial life strategies. Within each genus, metabolic consistency varied significantly, being low in Firmicutes genera and higher in Bacteroides...
2016: Nature Microbiology
Balázs Szalkai, Vince Grolmusz
BACKGROUND: Metagenomic analysis of environmental and clinical samples is gaining considerable importance in today's literature. Changes in the composition of the intestinal microbial communities, relative to the healthy control, are reported in numerous conditions. METHODS: We have carefully analyzed the frequencies of the short nucleotide sequences in the metagenomes of two different enterotypes; namely of Chinese and European origins. RESULTS: We have identified 255 nucleotide sequences of length up to 9, such that their frequencies significantly differ in the two enterotypes examined...
June 21, 2016: Biochimica et Biophysica Acta
Yuliaxis Ramayo-Caldas, Nuria Mach, Patricia Lepage, Florence Levenez, Catherine Denis, Gaetan Lemonnier, Jean-Jacques Leplat, Yvon Billon, Mustapha Berri, Jöel Doré, Claire Rogel-Gaillard, Jordi Estellé
The ecological interactions within the gut microbial communities are complex and far from being fully understood. Here we report the first study that aims at defining the interaction network of the gut microbiota in pigs and comparing it with the enterotype-like clustering analysis. Fecal microbiota of 518 healthy piglets was characterized by 16S ribosomal RNA gene sequencing. Two networks were constructed at the genus and operational taxonomic unit levels. Within-network interactions mirrored the human gut microbiota relationships, with a strong co-exclusion between Prevotella and Ruminococcus genera, and were consistent with the two enterotype-like clusters identified in the pig microbiota...
May 13, 2016: ISME Journal
Joshua M Stern, Saman Moazami, Yunping Qiu, Irwin Kurland, Zigui Chen, Ilir Agalliu, Robert Burk, Kelvin P Davies
The trillions of microbes that colonize our adult intestine are referred to as the gut microbiome (GMB). Functionally it behaves as a metabolic organ that communicates with, and complements, our own human metabolic apparatus. While the relationship between the GMB and kidney stone disease (KSD) has not been investigated, dysbiosis of the GMB has been associated with diabetes, obesity and cardiovascular disease. In this pilot study we sought to identify unique changes in the GMB of kidney stone patients compared to patients without KSD...
October 2016: Urolithiasis
Marc Noguera-Julian, Muntsa Rocafort, Yolanda Guillén, Javier Rivera, Maria Casadellà, Piotr Nowak, Falk Hildebrand, Georg Zeller, Mariona Parera, Rocío Bellido, Cristina Rodríguez, Jorge Carrillo, Beatriz Mothe, Josep Coll, Isabel Bravo, Carla Estany, Cristina Herrero, Jorge Saz, Guillem Sirera, Ariadna Torrela, Jordi Navarro, Manel Crespo, Christian Brander, Eugènia Negredo, Julià Blanco, Francisco Guarner, Maria Luz Calle, Peer Bork, Anders Sönnerborg, Bonaventura Clotet, Roger Paredes
The precise effects of HIV-1 on the gut microbiome are unclear. Initial cross-sectional studies provided contradictory associations between microbial richness and HIV serostatus and suggested shifts from Bacteroides to Prevotella predominance following HIV-1 infection, which have not been found in animal models or in studies matched for HIV-1 transmission groups. In two independent cohorts of HIV-1-infected subjects and HIV-1-negative controls in Barcelona (n = 156) and Stockholm (n = 84), men who have sex with men (MSM) predominantly belonged to the Prevotella-rich enterotype whereas most non-MSM subjects were enriched in Bacteroides, independently of HIV-1 status, and with only a limited contribution of diet effects...
March 2016: EBioMedicine
Anastassia Gorvitovskaia, Susan P Holmes, Susan M Huse
BACKGROUND: In a series of studies of the gut microbiome, "enterotypes" have been used to classify gut microbiome samples that cluster together in ordination analyses. Initially, three distinct enterotypes were described, although later studies reduced this to two clusters, one dominated by Bacteroides or Clostridiales species found more commonly in Western (American and Western European) subjects and the other dominated by Prevotella more often associated with non-Western subjects. The two taxa, Bacteroides and Prevotella, have been presumed to represent consistent underlying microbial communities, but no one has demonstrated the presence of additional microbial taxa across studies that can define these communities...
2016: Microbiome
Burkhardt Flemer, Denise B Lynch, Jillian M R Brown, Ian B Jeffery, Feargal J Ryan, Marcus J Claesson, Micheal O'Riordain, Fergus Shanahan, Paul W O'Toole
OBJECTIVE: A signature that unifies the colorectal cancer (CRC) microbiota across multiple studies has not been identified. In addition to methodological variance, heterogeneity may be caused by both microbial and host response differences, which was addressed in this study. DESIGN: We prospectively studied the colonic microbiota and the expression of specific host response genes using faecal and mucosal samples ('ON' and 'OFF' the tumour, proximal and distal) from 59 patients undergoing surgery for CRC, 21 individuals with polyps and 56 healthy controls...
March 18, 2016: Gut
Hirokazu Toju, Satoshi Yamamoto, Akifumi S Tanabe, Takashi Hayakawa, Hiroshi S Ishii
Terrestrial plants host phylogenetically and functionally diverse groups of below-ground microbes, whose community structure controls plant growth/survival in both natural and agricultural ecosystems. Therefore, understanding the processes by which whole root-associated microbiomes are organized is one of the major challenges in ecology and plant science. We here report that diverse root-associated fungi can form highly compartmentalized networks of coexistence within host roots and that the structure of the fungal symbiont communities can be partitioned into semi-discrete types even within a single host plant population...
March 2016: Journal of the Royal Society, Interface
Takuo Emoto, Tomoya Yamashita, Naoto Sasaki, Yushi Hirota, Tomohiro Hayashi, Anna So, Kazuyuki Kasahara, Keiko Yodoi, Takuya Matsumoto, Taiji Mizoguchi, Wataru Ogawa, Ken-Ichi Hirata
AIM: Recent studies have suggested that metabolic disorders such as obesity and type 2 diabetes are associated with gut microbiota. The association between atherosclerosis and gut microbiota has also been attracting increased attention. Our aim was to specify a characteristic trend of gut microbiota in coronary artery disease (CAD). METHODS: This study included 39 CAD patients, 30 age- and sex-matched no-CAD controls (Ctrls) with coronary risk factors and 50 healthy volunteers (HVs) without coronary risk factors...
August 1, 2016: Journal of Atherosclerosis and Thrombosis
Travis E Gibson, Amir Bashan, Hong-Tai Cao, Scott T Weiss, Yang-Yu Liu
Microbiome-based stratification of healthy individuals into compositional categories, referred to as "enterotypes" or "community types", holds promise for drastically improving personalized medicine. Despite this potential, the existence of community types and the degree of their distinctness have been highly debated. Here we adopted a dynamic systems approach and found that heterogeneity in the interspecific interactions or the presence of strongly interacting species is sufficient to explain community types, independent of the topology of the underlying ecological network...
February 2016: PLoS Computational Biology
Jarosław Szefel, Wiesław J Kruszewski, Tomasz Buczek
Enteral feeding is the preferred method of nutritional therapy. Mucosal lack of contact with nutrients leads do lymphoid tissue atrophy, immune system functional decline, and intensification in bacterial translocation. Currently, it is assumed that microbiome is one of the body organs that has a significant impact on health. The composition of microbiome is not affected by age, sex, or place of residence, although it changes rapidly after diet modification. The composition of the microbiome is determined by enterotype, which is specific for each organism...
2015: Przegla̜d Gastroenterologiczny
L-J Su, Y-Q Liu, H Liu, Y Wang, Y Li, H-M Lin, F-Q Wang, A-D Song
Tsaitermes ampliceps (lower termites) and Mironasutitermes shangchengensis (higher termites) are highly eusocial insects that thrive on recalcitrant lignocellulosic diets through nutritional symbioses with gut dwelling prokaryotes and eukaryotes. We used denaturing gradient gel electrophoresis and a 16S rRNA clone library to investigate i) how microbial communities adapt to lignocellulosic diets with different cellulose and lignin content, ii) the differences in the dominant gut microbial communities of the 2 types of termites...
2015: Genetics and Molecular Research: GMR
Nan Qin, Beiwen Zheng, Jian Yao, Lihua Guo, Jian Zuo, Lingjiao Wu, Jiawei Zhou, Lin Liu, Jing Guo, Shujun Ni, Ang Li, Yixin Zhu, Weifeng Liang, Yonghong Xiao, S Dusko Ehrlich, Lanjuan Li
Between March and June, 2013, forty H7N9 patients were hospitalized in our hospital. Next-generation sequencing technologies have been used to sequence the fecal DNA samples of the patient, the within sample diversity analysis, enterotyping, functional gene and metagenomic species analysis have been carried on both the patients and healthy controls. The influence of associated treatment in H7N9 infected patients is dramatic and was firstly revealed in species level due to deep sequencing technology. We found that most of the MetaGenomic Species (MGS) enriched in the control samples were Roseburia inulinivorans DSM 16841, butyrate producing bacterium SS3/4 and most of MGS enriched in the H7N9 patients were Clostridium sp...
2015: Scientific Reports
Pål Trosvik, Eric Jacques de Muinck
BACKGROUND: Determining ecological roles of community members and the impact of specific taxa on overall biodiversity in the gastrointestinal (GI) microbiota is of fundamental importance. A step towards a systems-level understanding of the GI microbiota is characterization of biotic interactions. Community time series analysis, an approach based on statistical analysis of changing population abundances within a single system over time, is needed in order to say with confidence that one population is affecting the dynamics of another...
2015: Microbiome
Pedro Mena, Margherita Dall'Asta, Luca Calani, Furio Brighenti, Daniele Del Rio
PURPOSE: Urolithins are bioactive ellagitannin-derived metabolites showing a wide phenotypic variation in their production by the gut microbiota. This work represents a first in vitro step toward the development of new strategies focused on the oral supplementation of urolithins with the aim of overcoming their selective production and making their putative health benefits available for the whole population. METHODS: In order to study their gastrointestinal stability, urolithin A, urolithin B, and urolithin B-glucuronide, as well as ellagic acid, were subjected to a simulated gastrointestinal digestion model consisting of oral, gastric, and pancreatic steps followed by a 24-h fecal fermentation...
October 6, 2015: European Journal of Nutrition
Frédéric Raymond, Amin A Ouameur, Maxime Déraspe, Naeem Iqbal, Hélène Gingras, Bédis Dridi, Philippe Leprohon, Pier-Luc Plante, Richard Giroux, Ève Bérubé, Johanne Frenette, Dominique K Boudreau, Jean-Luc Simard, Isabelle Chabot, Marc-Christian Domingo, Sylvie Trottier, Maurice Boissinot, Ann Huletsky, Paul H Roy, Marc Ouellette, Michel G Bergeron, Jacques Corbeil
Microbiome studies have demonstrated the high inter-individual diversity of the gut microbiota. However, how the initial composition of the microbiome affects the impact of antibiotics on microbial communities is relatively unexplored. To specifically address this question, we administered a second-generation cephalosporin, cefprozil, to healthy volunteers. Stool samples gathered before antibiotic exposure, at the end of the treatment and 3 months later were analysed using shotgun metagenomic sequencing. On average, 15 billion nucleotides were sequenced for each sample...
March 2016: ISME Journal
J S Weese, J Nichols, M Jalali, A Litster
Rectal swabs were collected from 31 cats, 16 with FIV infection and 15 uninfected controls, to evaluate and compare the rectal bacterial microbiota in cats with feline immunodeficiency virus (FIV) infection and uninfected controls. The rectal microbiota was characterized via next generation sequencing of 16S rRNA gene (V4 region) polymerase chain reaction products. Eighteen different phyla were identified. Firmicutes dominated in both groups, followed by Proteobacteria and Actinobacteria, but there were no significant differences between groups...
October 22, 2015: Veterinary Microbiology
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