Today’s Microbiome Digest is quite long, since it contains alerts from two days. There are many interesting articles in Gut, Plant and Water Microbiome Sections. Interesting review to highlight is from L. Tipton about lung mycobiome and the one from D. Rose Ewald about human microbiota. Today we also have quite few articles about viruses, among which P.C. Hsu revails gene targets of Ebola virus microRNAs involved in the human skin microbiome, S. S. Jagdale reports on mutualistic interactions of viruses with lower eukaryotes and C. Winter explains how mixing alters the lytic activity of viruses in the dark ocean.
General microbiome
Complete genomic characterisation of two Escherichia coli lineages responsible for a cluster of carbapenem resistant infections in a Chinese hospital – Zhiyong Zong – bioRxiv
Geometrical Distribution of Cryptococcus neoformans Mediates Flower-Like Biofilm Development – William Lopes – Frontiers in Microbiology
Pregnancy and early life
Editorial: The Neonatal Immune System: A Unique Host-Microbial Interface – Joseph M. Bliss – Frontiers in Pediatrics
Modeling Metabolic Interactions in a Consortium of the Infant Gut Microbiome – Francisco Pinto – Frontiers in Microbiology
Gene-trait matching across the Bifidobacterium longum pan-genome reveals considerable diversity in carbohydrate catabolism among human infant strains – Silvia Arboleya – Genomics
Early-life gut microbiome and egg allergy – Mina Fazlollahi – Allergy
Human respiratory microbiome
Perspective: Fungal Microbiota in Chronic Airway Inflammatory Disease and Emerging Relationships with the Host Immune Response – Irene Zhang – Frontiers in Microbiology
Microbiome and asthma – Milena Sokolowska – Asthma Research and Practice
Review: The lung mycobiome in the next-generation sequencing era – Laura Tipton – Virulence
The lung tissue microbiota of mild and moderate chronic obstructive pulmonary disease – Alexa A. Pragman – Microbiome
Oral microbiome
Profiling of subgingival plaque biofilm microbiota in female adult patients with clear aligners: a three-month prospective study – Runzhi Guo – PeerJ
Ecological Approaches to Dental Caries Prevention: Paradigm Shift or Shibboleth? – Nebu Philip – Caries Research
Human skin microbiome
On revealing the gene targets of Ebola virus microRNAs involved in the human skin microbiome – Pei-Chun Hsu – PeerJ
Temporal Variation of the Skin Bacterial Community and Batrachochytrium dendrobatidis Infection in the Terrestrial Cryptic Frog Philoria loveridgei – Mariel Familiar López – Frontiers in Microbiology
Human vaginal microbiome
Microbiota-based analysis reveals specific bacterial traits and a novel strategy for the diagnosis of infectious infertility – Simon Graspeuntner – PLOS One
Human nearly-sterile sites
Culture-independent analysis of liver abscess using nanopore sequencing – Liang Gong – PLOS One
Human gut microbiome
The Gut Microbiome and Control of Weight Gain – Anita L. Kozyrskyj – Pediatric Obesity
Immunosuppressive effect of the gut microbiome altered by high-dose tacrolimus in mice – Z. Zhang – American Journal of Transplatation
Review: Human microbiota, blood group antigens, and disease – D. Rose Ewald – WIREs
Microbiome, Immunomodulation, and the Neuronal System – Eric Marietta – Neurotherapeutics
Editorial: Improve gut microbiome: a new horizon of cancer therapy – Hiroshi Fukui – Hepatobiliary Surgery and Nutrition
The Gut Microbiome and Multiple Sclerosis – Javier Ochoa-Repáraz – Cold Spring Harbor Perspectives in Medicine
Genomic diversity and distribution of Bifidobacterium longum subsp. longum across the human lifespan – Toshitaka Odamaki – Scientific Reports
Dynamics of metatranscription in the inflammatory bowel disease gut microbiome – Melanie Schirmer – Nature Microbiology
Links between Dietary Protein Sources, the Gut Microbiota, and Obesity – Lise Madsen – Frontiers in Physiology
Ceftriaxone promotes the emergence of AmpC-overproducing Enterobacteriaceae in gut microbiota from hospitalized patients – Victoire de Lastours – European Journal of Clinical Microbiology & Infectious Diseases
Functional analysis of arginine decarboxylase gene speA of Bacteroides dorei by markerless gene deletion – Mikiyasu Sakanaka – FEMS Microbiology Letters
SadA-Expressing Staphylococci in the Human Gut Show Increased Cell Adherence and Internalization – Arif Luqman – Cell Reports
Gut microbiome populations are associated with structure-specific changes in white matter architecture – Irene M. Ong – Translational Psychiatry
Spatiotemporally Heterogeneous Population Dynamics of Gut Bacteria Inferred from Fecal Time Series Data – Hidetoshi Inaminea – mBio
Animal experiments
Identification of a protective B-cell epitope of the Staphylococcus aureus GapC protein by screening a phage-displayed random peptide library – Mengyao Wang – PLOS One
Lactobacillus plantarum CCFM10 alleviating oxidative stress and restoring the gut microbiota in D-galactose-induced aging mice – Jichun Zhao – Food and Function
Effect of dark sweet cherry powder consumption on the gut microbiota, short-chain fatty acids, and biomarkers of gut health in obese db/db mice – Jose F. Garcia-Mazcorro – PeerJ
Dietary Corn Bran Fermented by Bacillus subtilis MA139 Decreased Gut Cellulolytic Bacteria and Microbiota Diversity in Finishing Pigs – Ping Liu – Frontiers in Cellular and Infection Microbiology
Intestinal and Systemic Immune Responses upon Multi-drug Resistant Pseudomonas aeruginosa Colonization of Mice Harboring a Human Gut Microbiota – Eliane von Klitzing – Frontiers in Microbiology
Modulation of Intestinal Microbiome Prevents Intestinal Ischemic Injury – Alessandra Bertacco – Frontiers in Physiology
Animal microbiome
Influence of fruit and invertebrate consumption on the gut microbiota of wild white-faced capuchins (Cebus capucinus) – Elizabeth K. Mallott – American Journal of Physical Anthropology
Differential Ecological Specificity of Protist and Bacterial Microbiomes across a Set of Termite Species – Lena Waidele – Frontiers in Microbiology
Molecular identification and phylogenetic analysis of Bothrops insularis bacterial and fungal microbiota – Lidiane Nunes Barbosa – Journal of Toxicology and Environmental Health
Plant, root, and soil microbiome
Diazotroph abundance and community composition in an acidic soil in response to aluminum-tolerant and aluminum-sensitive maize (Zea mays L.) cultivars under two nitrogen fertilizer forms – Chao Wang – Plant and Soil
The influence of microbial communities for triadimefon enantiomerization in soils with different pH values – Khaled Mohamed Ahmed Talab – Chirality
Antimony Redox Biotransformation in the Subsurface: Effect of Indigenous Sb(V) Respiring Microbiota – Liying Wang – Encironmental Science and Technology
Biostimulant Action of Protein Hydrolysates: Unraveling Their Effects on Plant Physiology and Microbiome – Giuseppe Colla – Frontiers in Plant Science
Inner Plant Values: Diversity, Colonization and Benefits from Endophytic Bacteria – Hongwei Liu – Frontiers in Microbiology
Bacillus amyloliquefaciens L-S60 Reforms the Rhizosphere Bacterial Community and Improves Growth Conditions in Cucumber Plug Seedling – Yuxuan Qin – Frontiers in Microbiology
Exploring the Microbiota of Faba Bean: Functional Characterization of Lactic Acid Bacteria – Michela Verni – Frontiers in Microbiology
Contribution of Zinc Solubilizing Bacteria in Growth Promotion and Zinc Content of Wheat – Sana Kamran – Frontiers in Microbiology
Application of Endophytic Pseudomonas fluorescens and a Bacterial Consortium to Brassica napus Can Increase Plant Height and Biomass under Greenhouse and Field Conditions – Richard D. Lally – Frontiers in Microbiology
Exploiting rhizosphere microbial cooperation for developing sustainable agriculture strategies – Yoann Besset-Manzoni – Environmental Science and Pollution Research
Dynamics of oxygen and carbon dioxide in rhizospheres of Lobelia dortmanna – a planar optode study of belowground gas exchange between plants and sediment – Nikola Lenzewski – New Phytologist
Characterization of Microbial Communities in Acidified, Sulfur Containing Soils – Grzegorz Czerwonka – Polish Journal of Microbiology
Comparison of Microbial Communities Associated with Halophyte (Salsola stocksii) and Non-Halophyte (Triticum aestivum) Using Culture-Independent Approaches – Salma Mukhtar – Polish Journal of Microbiology
Water and extremophile microbiome
Data-mining of Antibiotic Resistance Genes Provides Insight into the Community Structure of Ocean Microbiome – Shiguang Hao – bioRxiv
Mixing alters the lytic activity of viruses in the dark ocean – Christian Winter – Ecology
Biological Characterization of Microenvironments in a Hypersaline Cold Spring Mars Analog – Haley M. Sapers – Frontiers in Microbiology
Patterns and Drivers of Vertical Distribution of the Ciliate Community from the Surface to the Abyssopelagic Zone in the Western Pacific Ocean – Feng Zhao – Frontiers in Microbiology
Aerobic and Anaerobic Methanotrophic Communities Associated with Methane Hydrates Exposed on the Seafloor: A High-Pressure Sampling and Stable Isotope-Incubation Experiment – David H. Case – Frontiers in Microbiology
A Multi-season Investigation of Microbial Extracellular Enzyme Activities in Two Temperate Coastal North Carolina Rivers: Evidence of Spatial but Not Seasonal Patterns – Avery Bullock – Frontiers in Microbiology
Functional Stability and Community Dynamics during Spring and Autumn Seasons Over 3 Years in Camargue Microbial Mats – Mercedes Berlanga – Frontiers in Microbiology
Oxygenation of Hypoxic Coastal Baltic Sea Sediments Impacts on Chemistry, Microbial Community Composition, and Metabolism – Elias Broman – Frontiers in Microbiology
Exploring the Cultivable Ectocarpus Microbiome – Hetty KleinJan – Frontiers in Microbiology
Phylogenetic Structure and Metabolic Properties of Microbial Communities in Arsenic-Rich Waters of Geothermal Origin – Simona Crognale – Frontiers in Microbiology
Prokaryotic Community Composition in Arctic Kongsfjorden and Sub-Arctic Northern Bering Sea Sediments As Revealed by 454 Pyrosequencing – Yin-Xin Zeng – Frontiers in Microbiology
Comparative Metagenomics Reveals the Distinctive Adaptive Features of the Spongia officinalis Endosymbiotic Consortium – Elham Karimi – Frontiers in Microbiology
Comparative genomics highlights symbiotic capacities and high metabolic flexibility of the marine genus Pseudovibrio – Dennis Versluis – GBE Genome BIology and Evolution
Geobacteraceae are important members of mercury-methylating microbial communities of sediments impacted by waste water releases – Andrea G. Bravo – ISME
Dynamics of phytoplankton and heterotrophic bacterioplankton in the western tropical South Pacific Ocean along a gradient of diversity and activity of diazotrophs – France Van Wambeke – Biogeosciences
Microbial methanogenesis in the sulfate-reducing zone of sediments in the Eckernförde Bay, SW Baltic Sea – Johanna Maltby – Biogeosciences
Built environment
Control of corrosive bacterial community by bronopol in industrial water system – Jayaraman Narenkumar – 3 Biotech
A metaproteomics method to determine carbon sources and assimilation pathways of species in microbial communities – Manuel Kleiner – bioRxiv
Uncovering the Potential of Termite Gut Microbiome for Lignocellulose Bioconversion in Anaerobic Batch Bioreactors – Lucas Auer – Frontiers in Microbiology
Microbial Communities Shaped by Treatment Processes in a Drinking Water Treatment Plant and Their Contribution and Threat to Drinking Water Safety – Qi Li – Frontiers in Microbiology
Food microbiology
Development of novel quinoa-based yoghurt fermented with dextran producer Weissella cibaria MG1 – Emanuele Zannini – International Journal of Food Microbiology
Bacterial Community and Spoilage Profiles Shift in Response to Packaging in Yellow-Feather Broiler, a Highly Popular Meat in Asia – Huhu Wang – Frontiers in Microbiology
Metagenomic Profiling of the Bacterial Community Changes from Koji to Mash Stage in the Brewing of Soy Sauce – Hongbin Wang – Polish Journal of Microbiology
Probiotics / prebiotics
Probiotics or Pro-healers the Role of Beneficial Bacteria in Tissue Repair – Jovanka Lukic – Wound Reparation and Regeneration
Probiotic Lactobacillus sp. inhibit growth, biofilm formation and gene expression of caries-inducing Streptococcus mutans – Reham Wasfi – Journal of Cellular and Molecular Medicine
A mixture of Lactobacillus species isolated from traditional fermented foods promote recovery from antibiotic-induced intestinal disruption in mice – Ying Shi – Journal of Applied Microbiology
Beneficial changes in rumen bacterial community profile in sheep and dairy calves as a result of feeding the probiotic Bacillus amyloliquefaciens H57 – Benjamin J Schofield – Journal of Applied Microbiology
Phages and viruses
Enemies with benefits: mutualistic interactions of viruses with lower eukaryotes – Shounak S. Jagdale – Archives of Virology
Biogeography & environmental conditions shape bacteriophage-bacteria networks across the human microbiome – Geoffrey D. Hannigan – bioRxiv
Investigation of prevalence of free Shiga toxin-producing Escherichia coli (STEC)-specific bacteriophages and its correlation with STEC bacterial hosts in a produce-growing area in Salinas, California – Yen-Te Liao – PLOS One
Component tree analysis of cystovirus φ6 nucleocapsid Cryo-EM single particle reconstructions – Lucas M. Oliveira – PLOS One
Bioinformatics
HTSSIP: An R package for analysis of high throughput sequencing data from nucleic acid stable isotope probing (SIP) experiments – Nicholas D. Youngblut – PLOS One
Biotechnology
Cyanobacterial diversity held in microbial biological resource centers as a biotechnological asset: the case study of the newly established LEGE culture collection – Vitor Ramos – Journal of Applied Phycology
Rapidly moving new bacteria to model-organism status – Hualan Liu – Current Opinion in Biotechnology
Techniques
Development of a biosensor protein bullet as a fluorescent method for fast detection of Escherichia coli in drinking water – Ignacio Gutiérrez-del-Río – PLOS One
Research Note: Methods for detecting Gemmata spp. bacteremia in the microbiology laboratory – Jacques-Robert Christen – BMS Genomics
A metaproteomics method to determine carbon sources and assimilation pathways of species in microbial communities – Manuel Kleiner – bioRxiv
Microbes in the news
Gene/cell connection provides new insight into how our gut microbiome stays healthy
A powerful new weapon against drug-resistant bacteria was inspired by the human body
ASU developing biodegradable plastics made from bacteria
Pharmaceutical Pollution Drives Microbial Resistance in Urban Streams
Microbes and Art
This scientist creates ephemeral works of art with bioluminescent bacteria
Microbiome Digest - Bik's Picks 