Today’s digest is about metaproteomics in microbial communities, infant and child microbiome and association with diseases, coral ecosphere, microbial biospherics and updates on new techniques to analyze microbiome sequencing data.
General microbiome
Metaproteomics: Much More than Measuring Gene Expression in Microbial Communities – Manuel Kleiner – mSystems
Associational effects in the microbial neighborhood – Anja Worrich – ISME Journal
Uncovering complex molecular networks in host–pathogen interactions using systems biology – Joshua M. Peters – Emerging Topics in Life Sciences
Human microbiome
The skin microbiome of vertebrates – Ashley A. Ross – Microbiome
Patterns in the longitudinal oropharyngeal microbiome evolution related to ventilator-associated pneumonia – Rami Sommerstein – Antimicrobial Resistance & Infection Control
Microbial composition of the human nasopharynx varies according to influenza virus type and vaccination status – Tao Ding -BioRxiv
Cytometric fingerprints of gut microbiota predict Crohn’s disease state – Peter Rubbens – BioRxiv
Dynamic colonization of microbes and their functions after fecal microbiota transplantation for inflammatory bowel disease – Nathaniel D. Chu – BioRxiv
Pregnancy and infant microbiome
Paediatrician’s perspective of infant gut microbiome research: current status and challenges – Paul MacDaragh Ryan – Archives of Disease in Childhood
The Salivary Microbiome Is Altered in Children With Eosinophilic Esophagitis and Correlates With Disease Activity – Hiremath Girish – Clinical and Translational Gastroenterology
Influence of own mother’s milk and different proportions of formula on intestinal microbiota of very preterm newborns – Adriana Zanella – PlosOne
Influence of a Serratia marcescens outbreak on the gut microbiota establishment process in low-weight preterm neonates – Esperanza Escribano – PlosOne
Reviewing the evidence on breast milk composition and immunological outcomes – Alba Boix-Amorós – Nutrition Reviews
Characterization of Stool Virome in Children Newly Diagnosed With Moderate to Severe Ulcerative Colitis – Rafal Tokarz – Inflammatory Bowel Diseases
Animal experiments
Effect of intestinal tapeworms on the gut microbiota of the common carp, Cyprinus carpio – Pei P. Fu – Parasites and Vectors
Comparison of Bacterial Populations in the Ceca of Swine at Two Different Stages and their Functional Annotations – Himanshu Kumar – Genes
Toll‐like receptor 2 and toll‐like receptor 4 responses regulate neutrophil infiltration into the junctional epithelium and significantly contribute to the composition of the oral microbiota – Ana M. Chang – Journal of Periodontology
Plant, root, soil microbiome
Mediterranean grassland soil C–N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms – Spencer Diamond – Nature Microbiology
Rhizosphere microbiomes diverge among Populus trichocarpa plant-host genotypes and chemotypes, but it depends on soil origin – Allison M. Veach – Microbiome
Microbial community drivers of PK/NRP gene diversity in selected global soils – Chiara Borsetto – Microbiome
Decreased temporary turnover of bacterial communities along soil depth gradient during a 35-year grazing exclusion period in a semiarid grassland – Chao Zhang – Geoderma
Soil bacterial community dynamics following surfactant addition and bioaugmentation in pyrene-contaminated soils – D.C.Wolf – Chemosphere
Structural and Functional Responses of Soil Microbial Communities to Biodegradable Plastic Film Mulching in Two Agroecosystems – Sreejata Bandopadhyay – BioRxiv
Ecological and genomic attributes of novel bacterial taxa that thrive in subsurface soil horizons – Tess E. Brewer – BioRxiv
Water microbiome and extremophiles
The coral ecosphere: A unique coral reef habitat that fosters coral–microbial interactions – Laura Weber – Limnology and Oceanography
Tide driven microbial dynamics through virus-host interactions in the estuarine ecosystem – Xiaowei Chen – Water Research
Microbial biofilm formation and community structure on low-density polyethylene microparticles in lake water microcosms – Mengting Gong – Environmental Pollution
Diversity and relative abundance of ammonia- and nitrite-oxidizing microorganisms in the offshore Namibian hypoxic zone – Evan Lau – PlosOne
Consistent metagenome-derived metrics verify and define bacterial species boundaries – Matthew R. Olm – BioRxiv
Techniques
Competitive interaction with keystone taxa induced negative priming under biochar amendments – Lijun Chen – Microbiome
Strengthening Insights in Microbial Ecological Networks from Theory to Applications – Xiaofei Lv – mSystems
Microbial biospherics: The experimental study of ecosystem function and evolution – Matthias C. Rillig – PNAS
NUFEB: A Massively Parallel Simulator for Individual-based Modelling of Microbial Communities – Bowen Li – BioRxiv
Detecting interaction networks in the human microbiome with conditional Granger causality – Kumar Mainali – Plos Computational Biology
M1CR0B1AL1Z3R—a user-friendly web server for the analysis of large-scale microbial genomics data – Oren Avram – Nucleic Acids Research
End-to-end assessment of fecal bacteriome analysis: from sample processing to DNA sequencing and bioinformatics results – Ana Paula Christoff – BioRxiv
Microbiome in news
Antibiotics may help curb Alzheimer’s symptoms – Medical News Today
SANISCALP®, to preserve the Microbiome for a soothed and healthy scalp! – Cosmetics desgin.com – Mamamia
Mother Dirt Expands Biome-Friendly Skincare Range With New Body Care Line – Mid Daily News
Microbes and the market
Global Microbiome Drugs Market Forecast 2019-2025: MaaT Pharma, Pfizer, Second Genome, Seres Therapeutics – Technology Market
Global Human Microbiome Modulators Market Report 2019: Trends and Opportunities for the Business Prediction over 2024 – Current News Magazine
Microbiome Sequencing Services Market 2019 Report Shows the Competitive Situation Among the Top Manufacturers, With Sales, Revenue and Share – Augusta Observer
Microbiome Digest - Bik's Picks 