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Human and gut microbiota

Rekha Seshadri, Sinead C Leahy, Graeme T Attwood, Koon Hoong Teh, Suzanne C Lambie, Adrian L Cookson, Emiley A Eloe-Fadrosh, Georgios A Pavlopoulos, Michalis Hadjithomas, Neha J Varghese, David Paez-Espino, Rechelle Perry, Gemma Henderson, Christopher J Creevey, Nicolas Terrapon, Pascal Lapebie, Elodie Drula, Vincent Lombard, Edward Rubin, Nikos C Kyrpides, Bernard Henrissat, Tanja Woyke, Natalia N Ivanova, William J Kelly
Productivity of ruminant livestock depends on the rumen microbiota, which ferment indigestible plant polysaccharides into nutrients used for growth. Understanding the functions carried out by the rumen microbiota is important for reducing greenhouse gas production by ruminants and for developing biofuels from lignocellulose. We present 410 cultured bacteria and archaea, together with their reference genomes, representing every cultivated rumen-associated archaeal and bacterial family. We evaluate polysaccharide degradation, short-chain fatty acid production and methanogenesis pathways, and assign specific taxa to functions...
March 19, 2018: Nature Biotechnology
Andrew K Fuller, Benjamin D Bice, Ashlee R Venancio, Olivia M Crowley, Ambur M Staab, Stephanie J Georges, Julio R Hidalgo, Annika V Warncke, Melinda L Angus-Hill
Several recent studies have illustrated the beneficial effects of living in an enriched environment on improving human disease. In mice, environmental enrichment (EE) reduces tumorigenesis by activating the mouse immune system, or affects tumor bearing animal survival by stimulating the wound repair response, including improved microbiome diversity, in the tumor microenvironment. Provided here is a detailed procedure to assess the effects of environmental enrichment on the biodiversity of the microbiome in a mouse colon tumor model...
February 28, 2018: Journal of Visualized Experiments: JoVE
Cheng-En Dai, Hai-Long Li, Xiao-Ping He, Fen-Fen Zheng, Hua-Liu Zhu, Liang-Feng Liu, Wei Du
The pharmacological activity of active ingredients from Chinese medicine depends greatly on the microecological environment of probiotics in the human body. After effective ingredients from traditional Chinese medicines are metabolized or biotransformed by probiotics, their metabolites can increase pharmacological activity, and can be absorbed more easily to improve the bioavailability. Therefore, the combination of Chinese medicines with probiotics is the innovation point in R&D of functional food and Chinese medicines, and also a new thinking for the modernization of Chinese medicine...
January 2018: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
Zachary Js Mays, Nikhil U Nair
The trillions of microbes hosted by humans can dictate health or illness depending on a multitude of genetic, environmental, and lifestyle factors that help define the human ecosystem. As the human microbiota is characterized, so can the interconnectivity of microbe-host-disease be realized and manipulated. Designing microbes as therapeutic agents can not only enable targeted drug delivery but also restore homeostasis within a perturbed microbial community. Used for centuries in fermentation and preservation of food, lactic acid bacteria (LAB) have a long history of safe, and occasionally health promoting, interactions with the human gut, making them ideal candidates for engineered functionality...
March 15, 2018: Current Opinion in Biotechnology
David N Bolam, Bert van den Berg
The lower human gastro-intestinal tract is inhabited by an extremely high density of micro-organisms, collectively termed the colonic microbiota. Just two bacterial phyla dominate this habitat, the Gram-positive Firmicutes and the Gram-negative Bacteroidetes. The colon is further characterised by a relative lack of small, easily accessible nutrients such as simple sugars, lipids and amino acids. Instead, a plethora of diet-derived and host polysaccharides constitute the main source of nutrients. Due to their size and complexity, the uptake of such glycans for metabolic utilisation is an energy-dependent process, which in Bacteroides spp...
March 15, 2018: Current Opinion in Structural Biology
Nuria Farré, Ramon Farré, David Gozal
Obstructive Sleep Apnea (OSA) has emerged as a highly prevalent public health problem that imposes important mid-term and long-term consequences, namely cardiovascular, metabolic, cognitive and cancer-related alterations. OSA is characterized by increased upper airway resistance, alveolar hypoventilation, and recurrent upper airway obstruction during sleep. Recurrent collapse of the upper airway develops with sleep onset, and is associated with both intermittent hypoxemia and sleep fragmentation. The microbiome is a vast and complex polymicrobial ecosystem that coexists with the human organism, and has been identified as playing significant roles in the development of host immunological phenotypes...
March 13, 2018: Chest
Neha M Sahasrabudhe, Martin Beukema, Lingmin Tian, Berit Troost, Jan Scholte, Erik Bruininx, Geert Bruggeman, Marco van den Berg, Anton Scheurink, Henk A Schols, Marijke M Faas, Paul de Vos
Dietary carbohydrate fibers are known to prevent immunological diseases common in Western countries such as allergy and asthma but the underlying mechanisms are largely unknown. Until now beneficial effects of dietary fibers are mainly attributed to fermentation products of the fibers such as anti-inflammatory short-chain fatty acids (SCFAs). Here, we found and present a new mechanism by which dietary fibers can be anti-inflammatory: a commonly consumed fiber, pectin, blocks innate immune receptors. We show that pectin binds and inhibits, toll-like receptor 2 (TLR2) and specifically inhibits the proinflammatory TLR2-TLR1 pathway while the tolerogenic TLR2-TLR6 pathway remains unaltered...
2018: Frontiers in Immunology
Khurram Muaz, Muhammad Riaz, Saeed Akhtar, Sungkwon Park, Amir Ismail
Poultry production is among the most rapidly growing industries around the globe, and poultry is one of the major sources of meat. Poultry farmers use disease preventive and growth promoter antibiotics for faster growth of chickens in the shortest possible time to increase the rate of feed assimilation and to lower the incidence of mortality caused by a pathogen attack. Antibiotics may result in dysfunctionality of beneficial gut microbiota and increase resistance among microbial pathogens in poultry. Residues of these antibiotics in poultry meat have been determined in many of the studies globally and are considered one of the possible causes of antibacterial resistance in human pathogens...
March 14, 2018: Journal of Food Protection
Rebekah C Kennedy, Russell R Fling, Michael S Robeson, Arnold M Saxton, Liesel G Schneider, John L Darcy, David A Bemis, Ling Zhao, Jiangang Chen
Widely used as an antimicrobial in antibacterial bar soaps, triclocarban (3,4,4'-trichlorocarbanilide; TCC) is effective against Gram-positive bacteria but shows little efficacy against Gram-negative strains, potentially altering the composition of indigenous microflora within and on the human body. To date, the consequence of continuous or previous nonprescription antimicrobial exposure from compounds in personal care products on commensal microflora is still elusive. Previous research has shown that TCC exposure during gestation and lactation induced dysbiosis of gut microbial communities among exposed dams and neonates...
March 13, 2018: Environmental Science and Pollution Research International
Winnie-Pui-Pui Liew, Sabran Mohd-Redzwan
The secondary metabolites produced by fungi known as mycotoxins, are capable of causing mycotoxicosis (diseases and death) in human and animals. Contamination of feedstuffs as well as food commodities by fungi occurs frequently in a natural manner and is accompanied by the presence of mycotoxins. The occurrence of mycotoxins' contamination is further stimulated by the on-going global warming as reflected in some findings. This review comprehensively discussed the role of mycotoxins (trichothecenes, zearalenone, fumonisins, ochratoxins, and aflatoxins) toward gut health and gut microbiota...
2018: Frontiers in Cellular and Infection Microbiology
Amy N Jacobson, Biswa P Choudhury, Michael A Fischbach
Lipopolysaccharide (LPS), a cell-associated glycolipid that makes up the outer leaflet of the outer membrane of Gram-negative bacteria, is a canonical mediator of microbe-host interactions. The most prevalent Gram-negative gut bacterial taxon, Bacteroides , makes up around 50% of the cells in a typical Western gut; these cells harbor ~300 mg of LPS, making it one of the highest-abundance molecules in the intestine. As a starting point for understanding the biological function of Bacteroides LPS, we have identified genes in Bacteroides thetaiotaomicron VPI 5482 involved in the biosynthesis of its lipid A core and glycan, generated mutants that elaborate altered forms of LPS, and used matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry to interrogate the molecular features of these variants...
March 13, 2018: MBio
Ilias Kounatidis, Lauren Ames, Rupal Mistry, Hsueh-Lui Ho, Ken Haynes, Petros Ligoxygakis
Candida glabrata ( C. glabrata ) forms part of the normal human gut microbiota but can cause life-threatening invasive infections in immune-compromised individuals. C. glabrata displays high resistance to common azole antifungals, which necessitates new treatments. In this investigation, we identified five C. glabrata deletion mutants ( Δada2 , Δbas1 , Δhir3, Δino2 and Δmet31 ) from a library of 196 transcription factor mutants that were unable to grow and activate an immune response in Drosophila larvae...
March 13, 2018: G3: Genes—Genomes—Genetics
Yi Lyu, Lei Wu, Fang Wang, Xinchun Shen, Dingbo Lin
Dysbiosis, a broad spectrum of imbalance of the gut microbiota, may progress to microbiota dysfunction. Dysbiosis is linked to some human diseases, such as inflammation-related disorders and metabolic syndromes. However, the underlying mechanisms of the pathogenesis of dysbiosis remain elusive. Recent findings suggest that the microbiome and gut immune responses, like immunoglobulin A production, play critical roles in the gut homeostasis and function, and the progression of dysbiosis. In the past two decades, much progress has been made in better understanding of production of immunoglobulin A and its association with commensal microbiota...
January 1, 2018: Experimental Biology and Medicine
Markus Arnoldini, Jonas Cremer, Terence Hwa
The human gut microbiota is highly dynamic, and the host has a strong influence on its composition. In our recent study, we integrated new quantitative measurements on bacterial growth physiology with a reanalysis of published data on human physiology to build a comprehensive modeling framework to generate predictions of how changes in different host factors influence microbiota composition. We show that hydrodynamics forces in the colon, along with colonic water absorption that manifests as transit time, exert a major impact on microbiota density and composition through their effect on colonic pH which directly affects microbiota competition for food...
March 13, 2018: Gut Microbes
Shabana, Saleem U Shahid, Uzma Irfan
The human GI tract harbors a diverse and dynamic microbial community comprising bacteria, archaea, viruses and eukaryotic microbes, which varies in composition from individual to individual. A healthy microbiota metabolizes various indigestible dietary components of the host, maintains host immune homeostasis and nutrient intake, but, an imbalanced microbiota has been reported to be associated with many diseases, including obesity. Rodent studies have produced evidence in support of the causal role of the gut microbiota in the development of obesity, however, such causal relationship is lacking in humans...
March 13, 2018: Future Microbiology
Joseph M Awika, Devin J Rose, Senay Simsek
Cereal grains and grain pulses are primary staples often consumed together, and contribute a major portion of daily human calorie and protein intake globally. Protective effects of consuming whole grain cereals and grain pulses against various inflammation-related chronic diseases are well documented. However, potential benefits of combined intake of whole cereals and pulses beyond their complementary amino acid nutrition is rarely considered in literature. There is ample evidence that key bioactive components of whole grain cereals and pulses are structurally different and thus may be optimized to provide synergistic/complementary health benefits...
March 13, 2018: Food & Function
Jocelyn Sietsma Penington, Megan A S Penno, Katrina M Ngui, Nadim J Ajami, Alexandra J Roth-Schulze, Stephen A Wilcox, Esther Bandala-Sanchez, John M Wentworth, Simon C Barry, Cheryl Y Brown, Jennifer J Couper, Joseph F Petrosino, Anthony T Papenfuss, Leonard C Harrison
To optimise fecal sampling for reproducible analysis of the gut microbiome, we compared different methods of sample collection and sequencing of 16S rRNA genes at two centers. Samples collected from six individuals on three consecutive days were placed in commercial collection tubes (OMNIgeneGut OMR-200) or in sterile screw-top tubes in a home fridge or home freezer for 6-24 h, before transfer and storage at -80 °C. Replicate samples were shipped to centers in Australia and the USA for DNA extraction and sequencing by their respective PCR protocols, and analysed with the same bioinformatic pipeline...
March 12, 2018: Scientific Reports
Sophie A Poeker, Annelies Geirnaert, Laura Berchtold, Anna Greppi, Lukasz Krych, Robert E Steinert, Tomas de Wouters, Christophe Lacroix
Consumption of fermentable dietary fibers (DFs), which can induce growth and/or activity of specific beneficial populations, is suggested a promising strategy to modulate the gut microbiota and restore health in microbiota-linked diseases. Until today, inulin and fructo-oligosaccharides (FOS) are the best studied DFs, while little is known about the gut microbiota-modulating effects of β-glucan, α-galactooligosaccharide (α-GOS) and xylo-oligosaccharide (XOS). Here, we used three continuous in vitro fermentation PolyFermS model to study the modulating effect of these DFs on two distinct human adult proximal colon microbiota, independently from the host...
March 12, 2018: Scientific Reports
Ziyu Jiang, Joe Antony Jacob, Jianyue Li, Xiahui Wu, Guoli Wei, Vimalanathan ArunPrasanna, Rajesh Mani, Prasannabalaji Nainangu, Uma Maheshwari Rajadurai, Baoan Chen
Human gut comprises of a huge mixture of microorganisms as they had co-existed for millions of years. The change in co-existence of microbial genera leads to dysbiosis, which creates several disorders in humans. Diet and diet associated agents can have a considerable influence on host health by regulating the gut microbiome, which can thereby maintain the homeostasis of the gut. Analysis of the gut microbiome and the agents that can have an influence on the gut need a profound understanding, which is the need of the hour...
March 9, 2018: Microbial Pathogenesis
Liang Lu, Zhiqin Wan, Ting Luo, Zhengwei Fu, Yuanxiang Jin
Microplastic (MP) has become a concerning global environmental problem. It is toxic to aquatic organisms and can spread through the food chain to ultimately pose a threat to humans. In the environment, MP can interact with microbes and act as a microbial habitat. However, effects of polystyrene MP on the gut microbiota in mammals remain unclear. Here, male mice were exposed to two different sizes of polystyrene MP for 5 weeks to explore its effect. We observed that oral exposure to 1000 μg/L of 0.5 and 50 μm polystyrene MP decreased the body, liver and lipid weights in mice...
March 9, 2018: Science of the Total Environment
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