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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
Ramesh J Pandit, Ankit T Hinsu, Shriram H Patel, Subhash J Jakhesara, Prakash G Koringa, Fosso Bruno, Androniki Psifidi, S V Shah, Chaitanya G Joshi
Zebu (Bos indicus) is a domestic cattle species originating from the Indian subcontinent and now widely domesticated on several continents. In this study, we were particularly interested in understanding the functionally active rumen microbiota of an important Zebu breed, the Gir, under different dietary regimes. Metagenomic and metatranscriptomic data were compared at various taxonomic levels to elucidate the differential microbial population and its functional dynamics in Gir cattle rumen under different roughage dietary regimes...
March 9, 2018: Systematic and Applied Microbiology
Dong Yan, Tao Zhang, Jing Su, Li-Li Zhao, Hao Wang, Xiao-Mei Fang, Yu-Qin Zhang, Hong-Yu Liu, Li-Yan Yu
The structural variation of the bacterial community associated with particulate matter (PM) was assessed in an urban area of Beijing during haze and non-haze days. Sampling for different PM fractions (PM2.5, PM10, and total suspended particulate) was conducted using three portable air samplers from September 2014 to February 2015. The airborne bacterial community in these samples was analyzed using the Illumina MiSeq platform with bacteria-specific primers targeting the 16S rRNA gene. A total of 1,707,072 reads belonging to 6009 operational taxonomic units were observed...
March 16, 2018: Applied and Environmental Microbiology
Diego Javier Jiménez, Maryam Chaib De Mares, Joana Falcão Salles
Plant biomass (PB) is an important source of sugars useful for biofuel production, whose degradation efficiency depends on synergistic and dynamic interactions of different enzymes. Here, using a metatranscriptomics-based approach, we explored the expression of PB-degrading enzymes in a five-species synthetic bacterial consortium during cultivation on sugarcane bagasse as a unique carbon source. By analyzing the temporal expression dynamics of a selection of enzymes we revealed the functional role of each consortium member and disentangled the potential interactions between them...
2018: Frontiers in Microbiology
Paula M Tribelli, Nancy I López
It is well known that cold environments are predominant over the Earth and there are a great number of reports analyzing bacterial adaptations to cold. Most of these works are focused on characteristics traditionally involved in cold adaptation, such as the structural adjustment of enzymes, maintenance of membrane fluidity, expression of cold shock proteins and presence of compatible solutes. Recent works based mainly on novel "omic" technologies have presented evidence of the presence of other important features to thrive in cold...
March 13, 2018: Life
J Solbiati, J Frias-Lopez
The last few decades have witnessed an increasing interest in studying the human microbiome and its role in health and disease. The focus of those studies was mainly the characterization of changes in the composition of the microbial communities under different conditions. As a result of those studies, we now know that imbalance in the composition of the microbiome, also referred to as microbial dysbiosis, is directly linked to developing certain conditions. Dysbiosis of the oral microbiome is a prime example of how this imbalance leads to disease in the case of periodontal disease...
March 1, 2018: Journal of Dental Research
Bridget Hegarty, Karen Dannemiller, Jordan Peccia
Dampness and visible mold growth in homes is associated with negative human health outcomes but causal relationships between fungal exposure and health are not well established. The purpose of this study was to determine if dampness in buildings impacts fungal community gene expression and how, in turn, gene expression may modulate human health impacts. A metatranscriptomic study was performed on house dust fungal communities to investigate the expression of genes and metabolic processes in chamber experiments at water activity levels of 0...
March 3, 2018: Indoor Air
Karel Schoonvaere, Guy Smagghe, Frédéric Francis, Dirk C de Graaf
Bees are associated with a remarkable diversity of microorganisms, including unicellular parasites, bacteria, fungi, and viruses. The application of next-generation sequencing approaches enables the identification of this rich species composition as well as the discovery of previously unknown associations. Using high-throughput polyadenylated ribonucleic acid (RNA) sequencing, we investigated the metatranscriptome of eight wild bee species ( Andrena cineraria, Andrena fulva, Andrena haemorrhoa, Bombus terrestris, Bombus cryptarum, Bombus pascuorum, Osmia bicornis , and Osmia cornuta ) sampled from four different localities in Belgium...
2018: Frontiers in Microbiology
Thomas Reid, Subba Rao Chaganti, Ian G Droppo, Christopher G Weisener
Baseline biogeochemical surveys of natural environments is an often overlooked field of environmental studies. Too often research begins once contamination has occurred, with a knowledge gap as to how the affected area behaved prior to outside (often anthropogenic) influences. These baseline characterizations can provide insight into proposed bioremediation strategies crucial in cleaning up chemical spill sites or heavily mined regions. Hence, this study was conducted to survey the in-situ microbial activity within freshwater hydrocarbon-rich environments cutting through the McMurray formation - the geologic strata constituting the oil sands...
February 19, 2018: Water Research
Yu Xia, Chao Yang, Tong Zhang
Background: Part-stream low-frequency ultrasound (LFUS) was one of the common practices for sludge disintegration in full-scale anaerobic digestion (AD) facilities. However, the effectiveness of part-stream LFUS treatment and its effect on AD microbiome have not been fully elucidated. Methods: Here we testified the effectiveness of part-stream LFUS pretreatment by treating only a fraction of feed sludge (23% and 33% total solid of the feed sludge) with 20 Hz LFUS for 70 s...
2018: Biotechnology for Biofuels
Sheng-Yong Niu, Jinyu Yang, Adam McDermaid, Jing Zhao, Yu Kang, Qin Ma
No abstract text is available yet for this article.
February 22, 2018: Briefings in Bioinformatics
Bela Hausmann, Claus Pelikan, Craig W Herbold, Stephan Köstlbacher, Mads Albertsen, Stephanie A Eichorst, Tijana Glavina Del Rio, Martin Huemer, Per H Nielsen, Thomas Rattei, Ulrich Stingl, Susannah G Tringe, Daniela Trojan, Cecilia Wentrup, Dagmar Woebken, Michael Pester, Alexander Loy
Sulfur-cycling microorganisms impact organic matter decomposition in wetlands and consequently greenhouse gas emissions from these globally relevant environments. However, their identities and physiological properties are largely unknown. By applying a functional metagenomics approach to an acidic peatland, we recovered draft genomes of seven novel Acidobacteria species with the potential for dissimilatory sulfite (dsrAB, dsrC, dsrD, dsrN, dsrT, dsrMKJOP) or sulfate respiration (sat, aprBA, qmoABC plus dsr genes)...
February 23, 2018: ISME Journal
Zhuolin Yi, Yang Fang, Kaize He, Dayu Liu, Huibo Luo, Dong Zhao, Hui He, Yanling Jin, Hai Zhao
BACKGROUND: Chinese Nong-flavor (NF) liquor is continuously and stably produced by solid-state fermentation technology for 1000 years, resulting in enrichment of special microbial community and enzymes system in its starter. Based on traditional culture-dependent methods, these functional enzymes are hardly obtained. According to our previous metatranscriptomic analysis, which identifies plenty of thermostable carbohydrate-active enzymes in NF liquor starter, the aim of this study is to provide a direct and efficient way to mine these thermostable enzymes...
February 22, 2018: Microbial Cell Factories
Aonghus Lavelle, Harry Sokol
No abstract text is available yet for this article.
February 21, 2018: Nature Reviews. Gastroenterology & Hepatology
Loo Wee Chia, Bastian V H Hornung, Steven Aalvink, Peter J Schaap, Willem M de Vos, Jan Knol, Clara Belzer
Host glycans are paramount in regulating the symbiotic relationship between humans and their gut bacteria. The constant flux of host-secreted mucin at the mucosal layer creates a steady niche for bacterial colonization. Mucin degradation by keystone species subsequently shapes the microbial community. This study investigated the transcriptional response during mucin-driven trophic interaction between the specialised mucin-degrader Akkermansia muciniphila and a butyrogenic gut commensal Anaerostipes caccae. A...
February 19, 2018: Antonie Van Leeuwenhoek
M Schären, J Frahm, S Kersten, U Meyer, J Hummel, G Breves, S Dänicke
Different studies have shown a strong correlation between the rumen microbiome and a range of production traits (e.g., feed efficiency, milk yield and components) in dairy cows. Underlying dynamics concerning cause and effect are, however, still widely unknown and warrant further investigation. The aim of the current study was to describe possible functional interrelations and pathways using a large set of variables describing the production, the metabolic and immunological state, as well as the rumen microbiome and fermentation characteristics of dairy cows in early lactation (n = 36, 56 ± 3 d in milk)...
February 14, 2018: Journal of Dairy Science
Yong-Wei Yan, Qiu-Yue Jiang, Jian-Gong Wang, Ting Zhu, Bin Zou, Qiong-Fen Qiu, Zhe-Xue Quan
Intertidal mudflats are land-sea interaction areas and play important roles in global nutrient cycles. However, a comprehensive understanding of microbial communities in these mudflats remains elusive. In this study, mudflat sediment samples from the Dongtan wetland of Chongming Island, the largest alluvial island in the world, were collected. Using a modified metatranscriptomic method, the depth-wise distributions of potentially active microbial communities were investigated based on small subunit ribosomal RNA (SSU rRNA) sequences...
2018: Frontiers in Microbiology
Christian F Edwardson, James T Hollibaugh
We compared the composition of microbial communities obtained by sequencing 16S rRNA gene amplicons with taxonomy derived from metatranscriptomes from the same samples. Samples were collected from alkaline, hypersaline Mono Lake, California, USA at five depths that captured the major redox zones of the lake during the onset of meromixis. The prokaryotic community was dominated by bacteria from the phyla Proteobacteria, Firmicutes, and Bacteroidetes, while the picoeukaryotic chlorophyte Picocystis dominated the eukaryotes...
2018: Frontiers in Microbiology
M Q Wang, Y Li, C H Sun
The human gastro-intestinal tract is not only the habitat of gut microbiota, but also the main place that the body gets available nutrients. Therefore, the gut microbiota of human can be inseparable associated with the human nutrition. The common technologies used among gut microbiota research included metageonomic, metatranscriptomics, metaproteomics, and metabolomics. The research of gut microbiota based on above omics methods confirmed that diets were the main factors influencing the composition and expression of gut microbiota...
February 6, 2018: Zhonghua Yu Fang Yi Xue za Zhi [Chinese Journal of Preventive Medicine]
Mamoru Oshiki, Takahiro Segawa, Satoshi Ishii
Various microorganisms play key roles in the Nitrogen (N) cycle. Quantitative PCR (qPCR) and PCR-amplicon sequencing of the N cycle functional genes allow us to analyze the abundance and diversity of microbes responsible in the N transforming reactions in various environmental samples. However, analysis of multiple target genes can be cumbersome and expensive. PCR-independent analysis, such as metagenomics and metatranscriptomics, is useful but expensive especially when we analyze multiple samples and try to detect N cycle functional genes present at relatively low abundance...
February 2, 2018: Applied and Environmental Microbiology
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