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Human gut

Nazarii Kobyliak, Ludovico Abenavoli, Galyna Mykhalchyshyn, Liudmyla Kononenko, Luigi Boccuto, Dmytro Kyriienko, Oleg Dynnyk
BACKGROUND: Probiotics have a beneficial effect on nonalcoholic fatty liver disease (NAFLD) in animal models. Randomized placebo-controlled trials (RCTs) in NAFLD are still lacking in humans despite a large number of data from animal research. AIM: We performed a double-blind single center RCT of live multi-strain probiotic vs. placebo in type 2 diabetes patients with NAFLD. METHODS: A total of 58 patients met the criteria for inclusion. They were randomly assigned to receive the multi-probiotic "Symbiter" (concentrated biomass of 14 probiotic bacteria genera Bifidobacterium, Lactobacillus, Lactococcus, Propionibacterium) or placebo for 8-weeks administered as a sachet formulation in double-blind treatment...
March 2018: Journal of Gastrointestinal and Liver Diseases: JGLD
Marina Ezcurra
High-throughput molecular studies are greatly advancing our knowledge of the human microbiome and its specific role in governing health and disease states. A myriad of ongoing studies aim at identifying links between microbial community disequilibria (dysbiosis) and human diseases. However, due to the inherent complexity and heterogeneity of the human microbiome we need robust experimental models that allow the systematic manipulation of variables to test the multitude of hypotheses arisen from large-scale 'meta-omic' projects...
March 19, 2018: Biogerontology
Vikas C Ghattargi, Yogesh S Nimonkar, Shaunak A Burse, Dimple Davray, Shreyas V Kumbhare, Sudarshan A Shetty, Meghana A Gaikwad, Mangesh V Suryavanshi, Swapnil P Doijad, Bhimashankar Utage, Om Prakash Sharma, Yogesh S Shouche, Bharati S Meti, Shrikant P Pawar
The human gut microbiome plays a crucial role in human health and efforts need to be done for cultivation and characterisation of bacteria with potential health benefits. Here, we isolated a bacterium from a healthy Indian adult faeces and investigated its potential as probiotic. The cultured bacterial strain 17OM39 was identified as Enterococcus faecium by 16S rRNA gene sequencing. The strain 17OM39 exhibited tolerance to acidic pH, showed antimicrobial activity and displayed strong cell surface traits such as hydrophobicity and autoaggregation capacity...
March 19, 2018: Functional & Integrative Genomics
Casey M Theriot
Over the past 10 years, microbiome research has focused on defining the structures associated with different disease states in multiple systems, but has fallen short on showing causation. Prior omic studies have generated many new hypotheses, but moving forward we need to start dissecting the function of each bacterium alone and in concert with complex bacterial communities in well-characterized systems. Over the next 5 years, we need a merging of new omic technologies for exploratory studies with classical bacterial genetics, bacterial physiology, protein engineering, and biochemistry to further define the biochemical mechanisms of the gut microbiota...
March 2018: MSystems
Isabelle Laforest-Lapointe, Marie-Claire Arrieta
Human-associated microbial communities include prokaryotic and eukaryotic organisms across high-level clades of the tree of life. While advances in high-throughput sequencing technology allow for the study of diverse lineages, the vast majority of studies are limited to bacteria, and very little is known on how eukaryote microbes fit in the overall microbial ecology of the human gut. As recent studies consider eukaryotes in their surveys, it is becoming increasingly clear that eukaryotes play important ecological roles in the microbiome as well as in host health...
March 2018: MSystems
N Dione, I I Ngom, C Valles, F Cadoret, P E Fournier, D Raoult, J C Lagier
We report here the main characteristics of 'Collinsella provencensis' strain Marseille-P3740 (CSUR P3740), 'Parabacteroides bouchesdurhonensis' strain Marseille-P3763 (CSUR P3763) and 'Sutterella seckii' strain Marseille-P3660 (CSUR P3660), which were isolated using culturomics from the human gut microbiota of healthy individuals living in Marseille.
May 2018: New Microbes and New Infections
Bastian Hornung, Vitor A P Martins Dos Santos, Hauke Smidt, Peter J Schaap
Humans are not autonomous entities. We are all living in a complex environment, interacting not only with our peers, but as true holobionts; we are also very much in interaction with our coexisting microbial ecosystems living on and especially within us, in the intestine. Intestinal microorganisms, often collectively referred to as intestinal microbiota, contribute significantly to our daily energy uptake by breaking down complex carbohydrates into simple sugars, which are fermented to short-chain fatty acids and subsequently absorbed by human cells...
2018: Genes & Nutrition
Carmen Losasso, Ester M Eckert, Eleonora Mastrorilli, Jorg Villiger, Marzia Mancin, Ilaria Patuzzi, Andrea Di Cesare, Veronica Cibin, Federica Barrucci, Jakob Pernthaler, Gianluca Corno, Antonia Ricci
Diet and lifestyle have a strong influence on gut microbiota, which in turn has important implications on a variety of health-related aspects. Despite great advances in the field, it remains unclear to which extent the composition of the gut microbiota is modulated by the intake of animal derived products, compared to a vegetable based diet. Here the specific impact of vegan, vegetarian, and omnivore feeding type on the composition of gut microbiota of 101 adults was investigated among groups homogeneous for variables known to have a role in modulating gut microbial composition such as age, anthropometric variables, ethnicity, and geographic area...
2018: Frontiers in Microbiology
Melanie Tramontano, Sergej Andrejev, Mihaela Pruteanu, Martina Klünemann, Michael Kuhn, Marco Galardini, Paula Jouhten, Aleksej Zelezniak, Georg Zeller, Peer Bork, Athanasios Typas, Kiran Raosaheb Patil
Bacterial metabolism plays a fundamental role in gut microbiota ecology and host-microbiome interactions. Yet the metabolic capabilities of most gut bacteria have remained unknown. Here we report growth characteristics of 96 phylogenetically diverse gut bacterial strains across 4 rich and 15 defined media. The vast majority of strains (76) grow in at least one defined medium, enabling accurate assessment of their biosynthetic capabilities. These do not necessarily match phylogenetic similarity, thus indicating a complex evolution of nutritional preferences...
March 19, 2018: Nature Microbiology
Lisa Maier, Mihaela Pruteanu, Michael Kuhn, Georg Zeller, Anja Telzerow, Exene Erin Anderson, Ana Rita Brochado, Keith Conrad Fernandez, Hitomi Dose, Hirotada Mori, Kiran Raosaheb Patil, Peer Bork, Athanasios Typas
A few commonly used non-antibiotic drugs have recently been associated with changes in gut microbiome composition, but the extent of this phenomenon is unknown. Here, we screened more than 1,000 marketed drugs against 40 representative gut bacterial strains, and found that 24% of the drugs with human targets, including members of all therapeutic classes, inhibited the growth of at least one strain in vitro. Particular classes, such as the chemically diverse antipsychotics, were overrepresented in this group...
March 19, 2018: Nature
Xiaole Tong, Mujeeb Ur Rehman, Shucheng Huang, Xiong Jiang, Hui Zhang, Jia KuiLi
Tibial dyschondroplasia (TD) is a common skeletal problem of avian species. The cause and etiology of this disorder is still not clear. The intestinal bacterial community is a complex ecosystem and plays very important role in healthy life of human and animals. Many researchers have made the connection between diseases and alteration of gut microbiota. However, little is know about the role of gut microbiota in TD. The objective of this study was to explore the diversity and composition of small and large intestinal bacterial communities of TD chickens...
March 16, 2018: Microbial Pathogenesis
Renata N Florindo, Valquiria P Souza, Lívia R Manzine, Cesar M Camilo, Sandro R Marana, Igor Polikarpov, Alessandro S Nascimento
Bifidobacterium is an important genus of probiotic bacteria colonizing the human gut. These bacteria can uptake oligosaccharides for the fermentative metabolism of hexoses and pentoses, producing lactate, acetate as well as short-chain fatty acids and propionate. These end-products are known to have important effects on human health. β-glucosidases (EC are pivotal enzymes for the metabolism and homeostasis of Bifidobacterium, since they hydrolyze small and soluble saccharides, typically producing glucose...
March 16, 2018: Biochimie
Nevena Kardum, Maria Glibetic
Regular and optimal intake of polyphenols associates with numerous health-promoting effects. Bioavailability and activity of polyphenols depend on foods' structure and interactions with other food constituents, especially proteins, lipids, and carbohydrates. Polyphenols-proteins interactions can result in various biological effects, such as sense of astringency. So far, polyphenols interactions with food lipids have not been of special importance, except in case of plant oils. Polyphenols-carbohydrates interactions can influence the organoleptic properties, while interactions with dietary fibers are particularly significant...
2018: Advances in Food and Nutrition Research
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
Ricardo Carrasco-Garcia, Patricia Barroso, Javier Perez-Olivares, Vidal Montoro, Joaquín Vicente
Understanding the role that facultative scavenger species may play in spreading infectious pathogens, and even becoming reservoirs for humans, domestic and wild ungulates or, on the contrary, preventing the spread of disease, requires a prior understanding of the pattern of carrion scavenging in specific scenarios. The objectives of this paper are (i) to describe the guild of vertebrate scavengers and (ii) to study the species-specific, habitat, and management-related factors involved in the usage of gut piles in South Central Spain (SCS), a tuberculosis (TB) endemic area...
2018: Frontiers in Veterinary Science
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
Heidi Doden, Lina A Sallam, Saravanan Devendran, Lindsey Ly, Greta Doden, Steven L Daniel, João M P Alves, Jason M Ridlon
Bile acids are important cholesterol-derived nutrient signaling hormones, synthesized in the liver, that act as detergents to solubilize dietary lipids. Bile acid 7α-dehydroxylating gut bacteria generate the toxic bile acids deoxycholic acid and lithocholic acid from host bile acids. The ability of these bacteria to remove the 7-hydroxyl group is partially dependent on 7α-hydroxysteroid dehydrogenase (HSDH) activity which reduces 7-oxo-bile acids generated by other gut bacteria. 3α-HSDH is an important enzymatic activity in the bile acid 7α-dehydroxylation pathway...
March 16, 2018: Applied and Environmental Microbiology
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