Andrew H Moeller
Bacteria inhabiting the human body vary in genome size by over an order of magnitude, but the processes that generate this diversity are poorly understood. Here, we show that evolutionary forces drive divergence in genome size between bacterial lineages in the gut and their closest relatives in other body sites. Analyses of thousands of reference bacterial isolate genomes and metagenome-assembled genomes from the human microbiome indicated that transitions into the gut from other body sites have promoted genomic expansions, whereas the opposite transitions have promoted genomic contractions...
July 6, 2021: Genome Biology and Evolution
Dan Shen, Zhendong Guo, Kai Huang, Pengyuan Dai, Xiaoming Jin, Yansen Li, Chunmei Li
The particulate matter (PM) in livestock houses, one of the primary sources of atmospheric PM, is not only detrimental to the respiratory health of animals and farmworkers but also poses a threat to the public environment and public health and warrants increased attention. In this study, we investigated the variation in the pulmonary microbiome and metabolome in broiler chickens exposed to PM collected from a broiler house. We examined the pulmonary microbiome and metabolome in broilers, observing that PM induced a visible change in α and β diversity...
July 21, 2021: Journal of Hazardous Materials
Ali Akbari, Carolyn David, Arshath Abdul Rahim, Subhasis Ghoshal
Hydrocarbon and salt contamination of surface and groundwater resources often co-occur from oil production activities. However, salt is often considered as a potential inhibitor of microbial activity. The feasibility of microbiome-based biotechnologies to treat the hydrocarbon contamination is contingent on the ability of the indigenous community to adapt to saline conditions. Here, we demonstrate enhanced hydrocarbon biodegradation in soil slurries under saline conditions of up to ~1 M (5%) compared to non-saline systems and the underlying causes...
July 12, 2021: Water Research
Javier Edo Varg, Warren Kunce, David Outomuro, Richard Svanbäck, Frank Johansson
There is growing evidence of widespread contamination of freshwater ecosystems with microplastics. However, the effects of chronic microplastic ingestion and its interaction with other pollutants and stress factors on the life-history traits and the host-microbiome of aquatic invertebrates are not well understood. This study investigates the effects of exposure to sediment spiked with 1 μm polystyrene-based latex microplastic spheres, an environmentally realistic concentration of a pyrethroid pesticide (esfenvalerate), and a combination of both treatments on the life-history traits of the benthic-dwelling invertebrate, Chironomus riparius and its microbial community...
July 26, 2021: Environmental Pollution
Katherine A Overmyer, Timothy W Rhoads, Anna E Merrill, Zhan Ye, Michael S Westphall, Amit Acharya, Sanjay K Shukla, Joshua J Coon
Oral microbiome influences human health, specifically pre- and type 2 diabetes (Pre-DM/DM) and periodontal diseases (PD), through complex microbial interactions. To explore these relations, we performed 16S rDNA sequencing, metabolomics, lipidomics, and proteomics analyses on supragingival dental plaque collected from individuals with Pre-DM/DM (n=39), Pre-DM/DM and PD (n=37), PD alone (n=11), or neither (n=10). We identified on average 2,790 operational taxonomic units and 2,025 microbial and host proteins per sample and quantified 110 metabolites and 415 lipids...
July 28, 2021: Molecular & Cellular Proteomics: MCP
Akanksha Vishwakarma, Digvijay Verma
Global consumption of smokeless tobacco (SLT) reached 300 million users worldwide majorly from middle-income countries. More than 4000 chemical compounds represent it as one of the noxious consumable products by humans. Besides toxicants/carcinogens, the heavy microbial load on smokeless tobacco further keeps human health at higher risk. Several of these inhabitant microbes participate in biofilm formation and secrete endotoxin/mycotoxins and proinflammatory-like molecules, leading to several oral diseases...
July 31, 2021: Applied Microbiology and Biotechnology
Trent D Haydon, David J Suggett, Nachshon Siboni, Tim Kahlke, Emma F Camp, Justin R Seymour
Bacterial members of the coral holobiont play an important role in determining coral fitness. However, most knowledge of the coral microbiome has come from reef-building scleractinian corals, with far less known about the nature and importance of the microbiome of octocorals (subclass Octocorallia), which contribute significantly to reef biodiversity and functional complexity. We examined the diversity and structure of the bacterial component of octocoral microbiomes over summer and winter, with a focus on two temperate (Erythropodium hicksoni, Capnella gaboensis; Sydney Harbour) and two tropical (Sinularia sp...
July 31, 2021: Microbial Ecology
Tongda Li, Ross Mann, Jatinder Kaur, German Spangenberg, Timothy Sawbridge
Paenibacillus species are Gram-positive bacteria that have been isolated from a diverse array of plant species and soils, with some species exhibiting plant growth-promoting (PGP) activities. Here we report two strains (S02 and S25) of a novel Paenibacillus sp. that were isolated from perennial ryegrass (Lolium perenne) seeds. Comparative genomics analyses showed this novel species was closely related to P. polymyxa. Genomic analyses revealed that strains S02 and S25 possess PGP genes associated with biological nitrogen fixation, phosphate solubilisation and assimilation, as well as auxin production and transportation...
July 30, 2021: Scientific Reports
Kontham Kulangara Varsha, Arun Padmakumar Maheshwari, Kesavan Madhavan Nampoothiri
It is a well-established fact that the microbiome harboring the human body plays a critical role in maintaining human health and can influence treatments against various ailments. Human microbiome-based research contemplates the possibility of selecting and administering specific commensal bacterial strains to modulate the gut microbiota to attain favorable outcomes to the therapies. Consumption of probiotics and probiotic-based dietary supplements as functional foods has been a promising treatment strategy against various diseases...
August 2021: Clinical Nutrition ESPEN
Pranvera Hiseni, Knut Rudi, Robert C Wilson, Finn Terje Hegge, Lars Snipen
BACKGROUND: A major bottleneck in the use of metagenome sequencing for human gut microbiome studies has been the lack of a comprehensive genome collection to be used as a reference database. Several recent efforts have been made to re-construct genomes from human gut metagenome data, resulting in a huge increase in the number of relevant genomes. In this work, we aimed to create a collection of the most prevalent healthy human gut prokaryotic genomes, to be used as a reference database, including both MAGs from the human gut and ordinary RefSeq genomes...
July 31, 2021: Microbiome
Ramón Cacabelos, Iván Carrera, Olaia Martínez-Iglesias, Natalia Cacabelos, Vinogran Naidoo
INTRODUCTION: . Alzheimer's disease models (ADMs) are currently used for drug development (DD). More than 20,000 molecules were screened for AD treatment over decades, with only one drug (Aducanumab)FDA-approved over the past 18 years. A revision of pathogenic concepts and ADMs are needed. AREAS COVERED: The authors discuss herein preclinical models including: (i) in vitro models (cell lines, primary neuron cell cultures, iPSC-derived brain cells), (ii) ex vivo models, and (iii) in vivo models (artificial, transgenic, non-transgenic and induced)...
July 30, 2021: Expert Opinion on Drug Discovery
Tim Avis, Francis X Wilson, Nawaz Khan, Clive S Mason, David J Powell
A factor in our inability to meet the challenge of clinical antibiotic resistance has been the low productivity of research and development (R&D) efforts, with only incremental improvements on existing broad-spectrum classes coming into clinical use recently. The disappointing returns from this approach have focussed attention on narrower-spectrum antibiotics; such new agents are directed against the pathogen of relevance with the additional benefit of preserving the human microbiome(s). Our knowledge of the gut microbiome and its contribution to health homeostasis increases yearly and suggests that broad-spectrum treatments incur health costs beyond the initial infection...
July 27, 2021: Drug Discovery Today
Gertrude Ecklu-Mensah, Jack Gilbert, Suzanne Devkota
The human gut microbiota harbors a heterogenous and dynamic community of microorganisms which coexist with the host to exert a marked influence on human physiology and health. Throughout the lifespan, diet can shape the composition and diversity of the members of the gut microbiota by determining the microorganisms that will colonize, persist, or become extinct. This is no more pronounced than during early-life succession of the gut microbiome when food type and source changes relatively often and food preferences are established, which is largely determined by geographic location and the customs and cultural practices of that environment...
July 27, 2021: Cellular and Molecular Gastroenterology and Hepatology
Yujin Lee, Andrew HyoungJin Kim, Eunwoo Kim, SeungHwan Lee, Kyung-Sang Yu, In-Jin Jang, Jae-Yong Chung, Joo-Youn Cho
AIMS: Although metformin has been reported to affect the gut microbiome, the mechanism has not been fully determined. We explained the potential underlying mechanisms of metformin through a multiomics approach. METHODS: An open-label and single-arm clinical trial involving 20 healthy Korean was conducted. Serum glucose and insulin concentrations were measured, and stool samples were collected to analyze the microbiome. Untargeted metabolomic profiling of plasma, urine, and stool samples was performed by GC-TOF-MS...
July 27, 2021: Diabetes Research and Clinical Practice
Stephen L Shiao, Kathleen M Kershaw, Jose J Limon, Sungyong You, Junhee Yoon, Emily Y Ko, Jlenia Guarnerio, Alka A Potdar, Dermot P B McGovern, Shikha Bose, Tahir B Dar, Paul Noe, Jung Lee, Yuzu Kubota, Viviana I Maymi, Madison J Davis, Regina M Henson, Rachel Y Choi, Wensha Yang, Jie Tang, Matthew Gargus, Alexander D Prince, Zachary S Zumsteg, David M Underhill
Studies suggest that the efficacy of cancer chemotherapy and immunotherapy is influenced by intestinal bacteria. However, the influence of the microbiome on radiation therapy is not as well understood, and the microbiome comprises more than bacteria. Here, we find that intestinal fungi regulate antitumor immune responses following radiation in mouse models of breast cancer and melanoma and that fungi and bacteria have opposite influences on these responses. Antibiotic-mediated depletion or gnotobiotic exclusion of fungi enhances responsiveness to radiation, whereas antibiotic-mediated depletion of bacteria reduces responsiveness and is associated with overgrowth of commensal fungi...
July 29, 2021: Cancer Cell
Qing Wu, Xianyi Liang, Kai Wang, Jun Lin, Xuemei Wang, Pengcheng Wang, Yangming Zhang, Qixing Nie, Huiying Liu, Zhipeng Zhang, Junhui Liu, Yanli Pang, Changtao Jiang
Accumulating evidence suggests that the gut microbiota regulates obesity through metabolite-host interactions. However, the mechanisms underlying such interactions have been unclear. Here, we found that intestinal hypoxia-inducible factor 2α (HIF-2α) positively regulates gut lactate by controlling the expression of intestinal Ldha. Intestine-specific HIF-2α ablation in mice resulted in lower lactate levels, and less Bacteroides vulgatus and greater Ruminococcus torques abundance, respectively. Together, these changes resulted in elevated taurine-conjugated cholic acid (TCA) and deoxycholic acid (DCA) levels and activation of the adipose G-protein-coupled bile acid receptor, GPBAR1 (TGR5)...
July 26, 2021: Cell Metabolism
Kanika Sehgal, Sahil Khanna
INTRODUCTION: : Obesity is a major public health concern with an increasing prevalence. Recent studies suggest an influence of gastrointestinal microbiota on obesity. Consequently, microbiota restoration therapies are being considered as potential management. We present data on microbiome markers and the future of microbiota therapeutics for obesity. AREAS COVERED: : We summarize the pathogenesis of obesity, relationship between gut microbiota and obesity, use of microbiota-based therapies...
July 30, 2021: Expert Review of Gastroenterology & Hepatology
Young-Joon Ko, Sangsoo Kim, Cheol-Ho Pan, Keunwan Park
As the microbiome is composed of a variety of microbial interactions, it is imperative in microbiome research to identify a microbial sub-community that collectively conducts a specific function. However, current methodologies have been highly limited to analyzing conditional abundance changes of individual microorganisms without considering group-wise collective microbial features. To overcome this limitation, we developed a network-based method using nonnegative matrix factorization (NMF) to identify functional meta-microbial features (MMFs) that, as a group, better discriminate specific environmental conditions of samples using microbiome data...
July 30, 2021: IEEE/ACM Transactions on Computational Biology and Bioinformatics
Zheng-Hao Li, Li Yuan, Wei Shao, Guo-Ping Sheng
Earthworms have shown their effectiveness in reducing the abundances of antibiotic resistance genes (ARGs) from solid waste. However, the mechanisms of the reduced ARGs by earthworm and whether the solid waste would affect the ARGs profile in earthworm gut were poorly understood. Herein, the patterns of ARGs and microbial communities in digested sludge-amended soil and earthworm gut after 80-day cultivation were investigated. Results show that the enrichment of ARGs (e.g., tetA, tetQ, and sulII) in soil caused by digested sludge-amendment was temporary and would recover to their original levels before amendment...
July 17, 2021: Journal of Hazardous Materials
K B Arun, Aravind Madhavan, Raveendran Sindhu, Shibitha Emmanual, Parameswaran Binod, Arivalagan Pugazhendhi, Ranjna Sirohi, R Reshmy, Mukesh Kumar Awasthi, Edgard Gnansounou, Ashok Pandey
The gut microbiome, often referred to as "super organ", comprises up to a hundred trillion microorganisms, and the species diversity may vary from person to person. They perform a decisive role in diverse biological functions related to metabolism, immunity and neurological responses. However, the microbiome is sensitive to environmental pollutants, especially heavy metals. There is continuous interaction between heavy metals and the microbiome. Heavy metal exposure retards the growth and changes the structure of the phyla involved in the gut microbiome...
July 17, 2021: Journal of Hazardous Materials
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