February 11, 2018

General microbiome

How the microbiome challenges our concept of self – Tobias Rees, PloS Biology

Human gut microbiome

Inflammatory bowel disease and Clostridium difficile infection: contrasting views of international clinical professionals – Andreas Stallmach, Zeitschrift für Gastroenterologie

Digestibility of sulfated polysaccharide from the brown seaweed Ascophyllum nodosum and its effect on the human gut microbiota in vitro – Ligen Chen, International Journal of Biological Macromolecules

Microbiome-based mechanisms hypothesized to initiate obesity-associated rheumatoid arthritis – Y. Luo, Obesity Reviews

Tissue macrophages as mediators of a healthy relationship with gut commensal microbiota – Brenda Naemi Nakagaki, Cellular Immunology

Fecal microbiota transplantation for recurrent Clostridium difficile infection in a patient with ulcerative colitis – Kosaku Nanki, Intestinal Research

Efficacy and safety of the adalimumab biosimilar Exemptia as induction therapy in moderate-to-severe ulcerative colitis – Vandana Midha, Intestinal Research

Sensing Bacterial-Induced DNA Damaging Effects via Natural Killer Group 2 Member D Immune Receptor: From Dysbiosis to Autoimmunity and Carcinogenesis – J. Luis Espinoza, Frontiers in Immunology

Environmental Exposures and Neuropsychiatric Disorders: What Role Does the Gut–Immune–Brain Axis Play? – Shannon Delaney, Current Environmental Health Reports

Human nearly-sterile sites

Identification and Characterization of Blood and Neutrophil-Associated Microbiomes in Patients with Severe Acute Pancreatitis Using Next-Generation Sequencing – Qiurong Li, Frontiers in Cellular and Infectious Microbiology

Animal experiments

Effects of levan-type fructan on growth performance, nutrient digestibility, diarrhoea scores, faecal shedding of total lactic acid bacteria and coliform bacteria, and faecal gas emission in weaning pigs – Xin Jian Lei, Journal of the Science of Food and Agriculture

Dietary proline supplementation alters colonic luminal microbiota and bacterial metabolite composition between days 45 and 70 of pregnancy in Huanjiang mini-pigs – Yujiao Ji, Journal of Animal Science and Biotechnology

Effects of the Artificial Sweetener Neotame on the Gut Microbiome and Fecal Metabolites in Mice – Liang Chi, Molecules

Animal microbiomes

Functional Transcripts Indicate Phylogenetically Diverse Active Ammonia-Scavenging Microbiota in Sympatric Sponges – Guofang Feng, Marine Biotechnology

Community structure, dispersal ability and functional profiling of microbiome existing in fat body and ovary of the brown planthopper, Nilaparvata lugens – Jian-Hua Zhang, Insect Science

Plant, root, and soil microbiome

Influence of biochar aged in acidic soil on ecosystem engineers and two tropical agricultural plants – Ihuoma N. Anyanwu, Ecotoxicology and Environmental Safety

Community Composition and Transcriptional Activity of Ammonia-Oxidizing Prokaryotes of Seagrass Thalassia hemprichii in Coral Reef Ecosystems –  Juan Ling, Frontiers in Microbiology

Dibutyl phthalate alters the metabolic pathways of microbes in black soils – Weihui Xu, Scientific Reports

Native soils with their microbiotas elicit a state of alert in tomato plants – Matteo Chialva, New Phytologist

Water and extremophile microbiome

A probabilistic approach to assess antibiotic resistance development risks in environmental compartments and its application to an intensive aquaculture production scenario – Andreu Rico, Environmental Pollution

Diversity patterns and isolation of Planctomycetes associated with metalliferous deposits from hydrothermal vent fields along the Valu Fa Ridge (SW Pacific) – Julia Endresen Storesund, Antonie van Leeuwenhoek

Enhancing methane production from lignocellulosic biomass by combined steam-explosion pretreatment and bioaugmentation with cellulolytic bacterium Caldicellulosiruptor bescii – Daniel Girma Mulat, Biotechnology for Biofuels

Microbial ecology

Kinetic analysis of a complete nitrifier reveals an oligotrophic lifestyle – K. Dimitri Kits, Nature Letters

Microbes in the news

Safety blunders expose lab staff to potentially lethal diseases in UK – The Guardian

This UV Lamp Could Prevent the Flu Virus From Spreading in Public Places –  Amanda Macmillan, Time

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January 19, 2018

Today’s digest features a review on gut microbial glycerol metabolism as a source of Acrolein, and an interesting article on the impact of climate cooling on ecosystem community structure and function in alpine soils. Happy reading!

 

Careers and Events

Research Fellow – National University of Singapore

Postdoctoral Fellow – Boston Children’s Hospital, Harvard Medical School

Scientific Officer/Senior Scientific Officer – The Cancer Research UK Beatson Institute

Staff Clinician – National Institutes of Health (NIH) National Heart, Blood and Lung Institute (NHLBI)

Human respiratory microbiome

Initial acquisition and succession of the cystic fibrosis lung microbiome is associated with disease progression in infants and preschool children – Marianne S. Muhlebach – Plos Pathogens

Human skin microbiome

Association of Disease Severity With Skin Microbiome and Filaggrin Gene Mutations in Adult Atopic Dermatitis – Maja-Lisa Clausen – JAMA Dermatology

Human gut microbiome

Review : Genetic and microbiome influence on lipid metabolism and dyslipidemia – Maria Matey Hernandez – Physiological Genomics

Review : Bile acids in glucose metabolism in health and disease – Hagit Shapiro – Journal of Experimental Microbiology

*Review: Gut Microbial Glycerol Metabolism as an Endogenous Acrolein Source – Jianbo Zhang – mBio

Review: How does ‘metabolic surgery’ work its magic? New evidence for gut microbiota – Peck Bailey C.E – Current Opinion in Endocrinology, Diabetes and Obesity

Multi-omics differentially classify disease state and treatment outcome in pediatric Crohn’s disease – Gavin M. Douglas – Microbiome

Genetic risk, dysbiosis, and treatment stratification using host genome and gut microbiome in inflammatory bowel disease – Ahmed Moustafa – Clinical and translational gastroenterology

Animal experiments

Flaxseed-enriched diets change milk concentration of the antimicrobial danofloxacin in sheep – Jon Andoni Otero – BMC Veterinary Research

Colonization of the cervicovaginal space with Gardnerella vaginalis leads to local inflammation and cervical remodeling in pregnant mice – Luz-Jeannette Sierra – Plos One

Kudingcha and Fuzhuan Brick Tea Prevent Obesity and Modulate Gut Microbiota in High-Fat Diet Fed Mice – Guijie Chen – Molecular Nutrition and Food Research

Plant, root, and soil microbiome

*Alpine soil carbon is vulnerable to rapid microbial decomposition under climate cooling – Linwei Wu – ISME Journal

Cultivable fungi present in Antarctic soils: taxonomy, phylogeny, diversity, and bioprospecting of antiparasitic and herbicidal metabolites – Eldon C. Q. Gomes – Extremophiles

Clearcutting alters decomposition processes and initiates complex restructuring of fungal communities in soil and tree roots – Petr Kohout – The ISME Journal

A large-scale field study of bacterial communities in cereal aphid populations across Morocco – Samir Fakhour – FEMS Microbiology Ecology

Microbial Mitigation-Exacerbation Continuum: A novel framework for microbiome effects on hosts in the face of stress – Aaron S. David – Ecology

Water and extremophile microbiome

Brief Report: Effects of grazing, phosphorus and light on the growth rates of major bacterioplankton taxa in the coastal NW Mediterranean – Olga Sánchez – Environmental Microbiology Reports

Development of a mediated whole cell-based electrochemical biosensor for joint toxicity assessment of multi-pollutants using a mixed microbial consortium – Guanyue Gao – Analytica Chimica Acta

The acute effects of erythromycin and oxytetracycline on enhanced biological phosphorus removal system: shift in bacterial community structure – Zhetai Hu – Environmental Science and Pollution Research

Probiotics / prebiotics

Valorization of Brewer’s spent grain to prebiotic oligosaccharide: production, xylanase catalyzed hydrolysis, in-vitro evaluation with probiotic strains and in a batch human fecal fermentation model – Mursalin Sajib – Journal of Biotechnology

In vitro fermentation of gum acacia – impact on the faecal microbiota – Sehad Alarifi -International Journal of Food Sciences and Nutrition

A bioluminescent test system reveals valuable antioxidant properties of lactobacillus strains from human microbiota – Maria Marsova – World Journal of Microbiology and Biotechnology

Yeasts / Fungi

Review: Sequence-based classification and identification of Fungi – David Hibbett – Mycologia

Phages and viruses

Detection of bovine Deltapapillomavirus DNA in peripheral blood of healthy sheep (Ovis aries) – S. Roperto – Transboundary and Emerging Diseases

Metagenomics

In-depth resistome analysis by targeted metagenomics – Val F. Lanza – Microbiome

Metabolomics

Qualitative metabolomics profiling of serum and bile from dogs with gallbladder mucocele formation – Jody L. Gookin – Plos One

Bioinformatics

A distance-based approach for testing the mediation effect of the human microbiome -Jie Zhang – Bioinformatics

Anitha’s non-microbiology picks

NASA test proves pulsars can function as a celestial GPS

The dark side of light: how artificial lighting is harming the natural world

Ultrathin 2-D metals get their own periodic table

January 11, 2018

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

January 8, 2018

 

Today’s Microbiome Digest has many interesting articles. Read how microscope-based artificial intelligence could alleviate shortage of clinical microbiologists, the article by K. P. Smith. N. A. Kamennaya reports on “Pomacytosis”, a semi-extracellular phagocytosis of cyanobacteria, while M. F. Dias investigated the effect of different drinking waters on mouse gut microbiota.

Events

One-day Symposium (12 Jan 2018): Microbial symbiosis in the marine environment – live streamming

Jobs

Postdoctoral positions in evolutionary genomics, UT Austin

General microbiome

Dietary trehalose enhances virulence of epidemic Clostridium difficile – J. Collins – Nature

Transmission in the Origins of Bacterial Diversity, From Ecotypes to Phyla – Frederick M. Cohan – Microbiology Spectrum

How much do rRNA gene surveys underestimate extant bacterial diversity? – Luis M. Rodriguez-R – Applied and Environmental Microbiology

Vibrio cholerae genomic diversity within and between patients –  Inès Levade – Microbial Genomics

Automated Interpretation of Blood Culture Gram Stains using a Deep Convolutional Neural Network – Kenneth P. Smith – Applied and Environmental Microbiology

Regulated ploidy of Bacillus subtilis and three new isolates of Bacillus and Paenibacillus – Benjamin Böttinger – FEMS Microbiology Letters

Human respiratory microbiome

Heavy metal exposure and nasal Staphylococcus aureus colonization: analysis of the National Health and Nutrition Examination Survey (NHANES) – Shoshannah Eggers – Environmental Health

Oral microbiome

Microbial Analysis of Endodontic Infections in Root-filled Teeth with Apical Periodontitis before and after Irrigation Using Pyrosequencing – Homan Zandi – Journal of Endodontics

Human vaginal microbiome

Long-term Lactobacillus rhamnosus BMX 54 application to restore a balanced vaginal ecosystem: a promising solution against HPV-infection – Ettore Palma – BMC Infectious Diseases

Lactobacillus-deficient vaginal microbiota dominate post-partum women in rural Malawi – Ronan Doyle – Applied and Environmental Microbiology

Human nearly-sterile sites

Microbiota and the liver – Ting-Chin David Shen – Liver Transplatation

Human gut microbiome

Comparison of DNA extraction methods for human gut microbial community profiling – Mi Young Lim – Systematic and Applied Microbiology

Changes in Gut Microbiota–Related Metabolites and Long-term Successful Weight Loss in Response to Weight-Loss Diets: The POUNDS Lost Trial – Yoriko Heianza – Diabetes Care

Adaptation of human gut microbiota to bariatric surgeries in morbidly obese patients: A systematic review – Hanieh-Sadat Ejtahed – Microbial Pathogenesis

The germ-organ theory of non-communicable diseases – Mariana X. Byndloss – Nature Reviews Microbiology

Evolution of a dominant natural isolate of Escherichia coli in the human gut over a year suggests a neutral evolution with reduced effective population size – Mohamed Ghalayini – Applied and Environmental Microbiology

Animal experiments

Changes in mouse gut bacterial community in response to different types of drinking water – Marcela F. Dias – Water Research

Plant, root, and soil microbiome

Microbial Communities of High-Elevation Fumaroles, Penitentes, and Dry Tephra “Soils” of the Puna de Atacama Volcanic Zone – Adam J. Solon – Microbial Ecology

Shifts in soil bacterial and archaeal communities during freeze-thaw cycles in a seasonal frozen marsh, Northeast China – Jiusheng Ren – Science of The Total Environment

The ‘Neglected’ Soil Virome – Potential Role and Impact – Akbar Adjie Pratama – Trends in Microbiology

Water and extremophile microbiome 

Study of marine bacteria inactivation by photochemical processes: disinfection kinetics and growth modeling after treatment – Javier Moreno-Andrés – Environmental Science and Pollution Research

Metabolic capability and in situ activity of microorganisms in an oil reservoir – Yi-Fan Liu – Microbiome

Phylogenetic distribution of roseobacticides in the Roseobacter group and their effect on microalgae – Eva C Sonnenschein – BioRxiv

“Pomacytosis”—Semi-extracellular phagocytosis of cyanobacteria by the smallest marine algae – Nina A. Kamennaya – PLOS Biology

The Green Berry Consortia of the Sippewissett Salt Marsh: Millimeter-Sized Aggregates of Diazotrophic Unicellular Cyanobacteria – Elizabeth G. Wilbanks – Frontiers in Microbiology

Dynamic changes in carbonate chemistry in the microenvironment around single marine phytoplankton cells – Abdul Chrachri – Nature Communications

Homogenization of lake cyanobacterial communities over a century of climate change and eutrophication – Marie-Eve Monchamp – Nature Ecology & Evolution

Bacterial Recycling of Archaeal Biomass as a New Strategy for Extreme Life in the Dead Sea Deep Sediment – Camille Thomas – EarthArXiv Preprints

Food microbiology

Seasonal variances in bacterial microbiota and volatile organic compounds in raw milk – Beata Nalepa – International Journal of Food Microbiology

Phages and viruses

Is weak CD4+ gain in the course of suppressive combination antiretroviral therapy for HIV infection a current clinical challenge? A case report and brief review of the literature – Camilla Tincati – BMC Infectious Diseases

Techniques

NanoAmpli-Seq: A workflow for amplicon sequencing from mixed microbial communities on the nanopore sequencing platform – Szymon T Calus – bioRxiv

Microbes in the news

Scientists engineer sound-reflecting bacteria

Experts: ‘Raw Water’ Offers Unfiltered Risk

 

December 20, 2017

A long but great digest today, with lots of diversity – a few studies of poultry gut microbiome and the effects food/probiotics have, a solid showing for human gut microbiome studies – covering its implications on a range of disorders, some news about biotech companies, studies on plants and from environmental sources, a promising analysis of techniques used for sampling for human gut studies, and my normal dosage of non-microbiology science.  Happy Holidays!

Events and jobs

ON-DEMAND WEBINAR How to Harness the Microbiome: Considerations and Implications of the Microbiome in Preclinical Research with Reproducible Results

Senior Biomedical Scientist (Microbiology) – Matchtech – Essex, England

Staff Research Associate 3, UCLA Department of Microbiology, Immunology and Molecular Genetics

Assistant (10782) – Clinical chemistry, microbiology and immunology – Ghent University

Pregnancy and early life

Early-Life Human Microbiota Associated With Childhood Allergy Promotes the T Helper 17 Axis in Mice – Dagbjort H. Petursdottir – Frontiers in Immunology

[Accepted Manuscript] – The neonatal window of opportunity – early priming for life – Harald Renz -Journal of Allergy and Clinical Immunology

Human oral microbiome

The Microbiome of Potentially Malignant Oral Leukoplakia Exhibits Enrichment for Fusobacterium, Leptotrichia, Campylobacter, and Rothia Species – Abdrazak Amer – Frontiers in Microbiology

Exploring the Association between Alzheimer’s Disease, Oral Health, Microbial Endocrinology and Nutrition – Alice Harding – Frontiers in Aging Neuroscience

Admission to the Intensive Care Unit is Associated With Changes in the Oral Mycobiome – Richard R. Watkins – Journal of Intensive Care Medicine

Human nearly-sterile sites

Metagenomics in pooled plasma, with identification of potential emerging infectious pathogens – Min Xu – Transfusion

Human gut microbiome

** High-resolution profiling of the gut microbiome reveals the extent of Clostridium difficile burden – Ninalynn Daquigan – npj Biofilms and Microbiomes

Unravelling the specificity and mechanism of sialic acid recognition by the gut symbiont Ruminococcus gnavus – C. David Owen – Nature Communication

[Editorial] Is gut microbiome a predictive marker to response to immune checkpoint inhibitors? – Khalil Saleh – Immunotherapy

Microbiota Modulate Anxiety-Like Behavior and Endocrine Abnormalities in Hypothalamic-Pituitary-Adrenal Axis – Ran Huo – Front. Cell. Infect. Microbiology

Possible role of the gut microbiota–brain axis in the antidepressant effects of (R)-ketamine in a social defeat stress model – Chun Yang – Translational Psychiatry

Microbial antigen encounter during a preweaning interval is critical for tolerance to gut bacteria – Kathryn A. Knoop – Science Immunology

Stool Donor Body Mass Index Does Not Affect Recipient Weight After a Single Fecal Microbiota Transplantation for C. difficile Infection – Monika Fischer – Clinical Gastroenterology and Hepatology

The role of microbiota in the pathogenesis of schizophrenia and major depressive disorder and the possibility of targeting microbiota as a treatment option – Fengli Lv – Oncotarget

Characterization of the urinary microbiota of elderly women and the effects of type 2 diabetes and urinary tract infections on the microbiota – Fengping Liu – Oncotarget

Animal experiments 

Food-grade cationic antimicrobial ε-polylysine transiently alters the gut microbial community and predicted metagenome function in CD-1 mice – Xiaomeng You – npj Science of Food

Significant improvement of intestinal microbiota of gibel carp (Carassius auratus gibelio) after traditional Chinese medicine feeding – Zhenbing Wu – Journal of Applied Microbiology

* The gastrointestinal microbiome and its association with the control of pathogens in broiler chicken production: A review – Viviana Clavijo – Poultry Science

Influence of dietary avilamycin on ileal and cecal microbiota in broiler chickens – J-H Choi – Poultry Science

Plant, root, and soil microbiome

* Geometagenomics illuminates the impact of agriculture on the distribution and prevalence of plant viruses at the ecosystem scale – Pauline Bernardo – The ISME Journal

Dispersal alters bacterial diversity and composition in a natural community – Michaeline B N Albright – The ISME Journal

** Genomic features of bacterial adaptation to plants – Asaf Levy – Nature Genetics

Soil Bacterial Community Structure and Co-occurrence Pattern during Vegetation Restoration in Karst Rocky Desertification Area – Liang Xue – Frontiers in Microbiology

First insight into microbial community composition in a phosphogypsum waste heap soil – Sylwia Zielińska – ABP

Harnessing the microbiomes of Brassica vegetables for health issues – Birgit Wassermann – Scientific Reports

Water and extremophile microbiome 

Microdiversification in genome-streamlined ubiquitous freshwater Actinobacteria – Stefan M Neuenschwander – The ISME Journal

Recurrent patterns of microdiversity in a temperate coastal marine environment – Meghan Chafee – The ISME Journal

Microcystin-LR does not induce alterations to transcriptomic or metabolomic profiles of a model heterotrophic bacterium – Robbie M. Martin – PLOS One

Pre-treatment and inoculum affect the microbial community structure and enhance the biogas reactor performance in a pilot-scale biodigestion of municipal solid waste – Valeria Ventorino – Waste Management

Food microbiology

* Inner Workings: Companies seek food safety using a microbiome approach – Carolyn Beans – PNAS

Phages and viruses

* Temporal dynamics of uncultured viruses: a new dimension in viral diversity – Ksenia Arkhipova – The ISME Journal

Bioinformatics

A confidence interval analysis of sampling effort, sequencing depth, and taxonomic resolution of fungal community ecology in the era of high-throughput sequencing – Ryoko Oono – PLOS One

Techniques

Performance of DNA metabarcoding, standard barcoding, and morphological approach in the identification of host–parasitoid interactions – Martin Šigut – PLOS One

** Successful collection of stool samples for microbiome analyses from a large community-based population of elderly men – Melanie Abrahamson – Contemporary Clinical Trials Communications

Microbes on the market 

BiomX Acquires RondinX to Boost Microbiome Discovery and Development Capabilities

Vanterra Capital Backs BIOHM Health, A Total Microbiome Company

Second Genome Advances Lead, Oral Small Molecule SGM-1019, Toward Clinical Investigation in NASH After Demonstrating Safety and Tolerability in Phase 1 Study

Ed’s non-microbiology picks 

Cannabidiol (CBD) as an Adjunctive Therapy in Schizophrenia: A Multicenter Randomized Controlled Trial – Philip McGuire – The American Journal of Psychiatry

Effects of Legal Access to Cannabis on Scheduled II–V Drug Prescriptions – Sarah S. Stith – JAMDA

Ticks parasitised feathered dinosaurs as revealed by Cretaceous amber assemblages – Enrique Peñalver – Nature Communications

Induced and controlled dietary ketosis as a regulator of obesity and metabolic syndrome pathologies – Madeline K. Gibas – Diabetes & Metabolic Syndrome: Clinical Research & Reviews

The effect of vitamin D supplement on the score and quality of sleep in 20-50 year-old people with sleep disorders compared with control group – Mohammad Shahi Majid – Nutritional Neuroscience

Engineers create plants that glow – MIT

December 15, 2017

The leaders of ten research universities/institutes pledge to report student and postdoc outcomes in biomedical research as the Coalition for Next Generation Life Science initiative, commensal fungi and their cell-wall mannans can functionally replace benefits of intestinal bacteria, a new cheese starter system with improved bacteriophage resistance and antimicrobial activity.

Events and jobs

Postdoctoral Fellow, Functional Microbiome – Claesen Group, Department of Cellular and Molecular Medicine, Cleveland Clinic (also looking for interested graduate students)

Human nearly-sterile sites

Microorganisms in the human placenta are associated with altered CpG methylation of immune and inflammation-related genes – Martha Scott Tomlinson – PLOS ONE

Human gut microbiome

Faecal microbiota transplantation for Clostridium difficile infection using a lyophilized inoculum from non-related donors: A case series involving 19 patients – Vigvári Szabolcs – Acta Microbiologica et Immunologica Hungarica

Animal experiments

Commensal Fungi Recapitulate the Protective Benefits of Intestinal Bacteria – Tony T Jiang – Cell Host & Microbe

CCL28-Deficient Mice Have Reduced IgA Antibody–Secreting Cells and an Altered Microbiota in the Colon – Kazuhiko Matsuo – The Journal of Immunology

Animal microbiome

Behavior of bacteriome symbionts during transovarial transmission and development of the Asian citrus psyllid – Hiroki Dan – PLOS ONE

Plant, root, and soil microbiome

Root-derived carbon and nitrogen from beech and ash trees differentially fuel soil animal food webs of deciduous forests – Sarah L Zieger – PLOS ONE

Historical and recent land use affects ecosystem functions in subtropical grasslands in Brazil – Jan L G Leidinger – Ecosphere

Mechanisms of arsenic sequestration by Prosopis juliflora during phytostabilization of metalliferous mine tailings – Corin M Hammond

Transfer Mechanism, Uptake Kinetic Process and Bioavailability of P, Cu, Cd, Pb and Zn in Macrophyte Rhizosphere Using DGT – Shengrui Wang – Environmental Science & Technology

Food microbiology

A Multibacteriocin Cheese Starter System, Comprising Nisin and Lacticin 3147 in Lactococcus lactis, in Combination with Plantaricin from Lactobacillus plantarum – S Mills – Applied and Environmental Microbiology

Bioinformatics

Colonic Butyrate-Producing Communities in Humans: an Overview Using Omics Data – Marius Vital – mSystems

Discovery of carbamate degrading enzymes by functional metagenomics – Lisa Ufarté – PLOS ONE

Science, career, and publishing

A new data effort to inform career choices in biomedicine – Rebecca Blank – Science

News Feature: The science that’s never been cited – Richard Van Noorden – Nature

December 14, 2017

Two interesting articles on pregnancy and early life: the placentobiome, and the cervical microbiome, as well as articles on the circadian rhythms of the saliva microbiome, the microbiome of exposed rock,  and new techniques to sequence single bacterial and archaeal cells.

Events and jobs

Postdoctoral Research Scientist – Genomics and Metagenomics – Quadram Institute Bioscience – Norwich UK

Assistant Professor, Cell Biology, Molecular Biology or Microbiology – Albany College of Pharmacy and Health Sciences

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Pregnancy and early life

*Mother-to-newborn transmission of mycobacterial L-forms and Vδ2 T-cell response in placentobiome of BCG-vaccinated pregnant women – T. Dimova – Scientific Reports*

*Analysis of the cervical microbiome and potential biomarkers from postpartum HIV-positive women displaying cervical intraepithelial lesions – Gislaine Curty – Scientific Reports

Multi-site human microbiome

Microbiome in PTEN hamartoma tumor syndrome – Victoria Byrd – Society for Endrocrinology

Human respiratory microbiome

The Alteration of Nasopharyngeal and Oropharyngeal Microbiota in Children with MPP and Non-MPP – Zhiwei Lu – Genes

Human skin microbiome

Review: Staphylococcus aureus and Atopic Dermatitis: A Complex and Evolving Relationship – Joan A. Geoghegan – Trends in Microbiology

Human oral microbiome

*Timing of food intake impacts daily rhythms of human salivary microbiota: a randomized, crossover study – María Carmen Collado – The FASEB Journal

Human vaginal microbiome

Influence of Orally Administered Probiotic Lactobacillus Strains on Vaginal Microbiota in Women with Breast Cancer during Chemotherapy: A Randomized Placebo-Controlled Double-Blinded Pilot Study – J Marschalek – Breast Care

Human gut microbiome

A Metagenomic and in Silico Functional Prediction of Gut Microbiota Profiles May Concur in Discovering New Cystic Fibrosis Patient-Targeted Probiotics – Pamela Vernocchi – Nutrients

Entamoeba Species in South Africa: Correlations With the Host Microbiome, Parasite Burdens, and First Description of Entamoeba bangladeshi Outside of Asia – Renay Ngobeni – Journal of Infectious Diseases

Mutual interaction of phenolic compounds and microbiota: Metabolism of complex phenolic apigenin C- and kaempferol O-derivatives by human fecal samples – Maren Vollmer – Journal of Agricultural and Food Chemistry

Estimation of the bioaccessibility and bioavailability of Fe, Mn, Cu, and Zn in Chinese vegetables using the in vitro digestion/Caco-2 cell model: the influence of gut microbiota – Xiaolin Cai – Food and Function

Food-Associated Lactobacillus plantarum and Yeasts Inhibit the Genotoxic Effect of 4-Nitroquinoline-1-Oxide – Roberta Prete – Frontiers in Microbiology

Butyrate suppresses motility of colorectal cancer cells via deactivating Akt/ERK signaling in histone deacetylase dependent manner – Qingran Li – Journal of Pharmacological Sciences

Review: Exercise has the guts: How physical activity may positively modulate gut microbiota in chronic and immune-based diseases – Roberto Codella – Digestive and Liver Disease

Review: Alzheimer’s disease and gut microbiota modifications: The long way between preclinical studies and clinical evidence – Cesare Mancuso – Pharmacological Research

Adjuvant Probiotics and the Intestinal Microbiome: Enhancing Vaccines and Immunotherapy Outcomes – Luis Vitetta – Vaccines

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Animal experiments

Fecal short-chain fatty acids at different time points after ceftriaxone administration in rats – Yu. V. Holota – The Ukrainian Biochemical Journal

1H NMR-Based Metabonomic Study of Functional Dyspepsia in Stressed Rats Treated with Chinese Medicine Weikangning – Yu Guo – Evidence-Based Complementary and Alternative Medicine

A Novel Prebiotic Blend Product Prevents Irritable Bowel Syndrome in Mice by Improving Gut Microbiota and Modulating Immune Response – Qian Chen – Nutrients

Animal microbiome

Diversification of Type VI Secretion System Toxins Reveals Ancient Antagonism among Bee Gut Microbes – Margaret I. Steele – mBio

Differential Microbial Diversity in Drosophila melanogaster: Are Fruit Flies Potential Vectors of Opportunistic Pathogens? – Luis A. Ramírez-Camejo – International Journal of Microbiology

Archaeal community structure and underlying ecological processes in swine manure slurry – Priyanka Kumari – bioRxiv

Genetic adaptation of microbial populations present in high-intensity catfish production systems with therapeutic oxytetracycline treatment – Qifan Zeng – Scientific Reports

Altered Gut Microbiota Profiles in Sows and Neonatal Piglets Associated with Porcine Epidemic Diarrhea Virus Infection – Deping Song – Scientific Reports

Plant, root, and soil microbiome

*Tales from the tomb: the microbial ecology of exposed rock surfaces
Authors – Tess E Brewer – Environmental Microbiology

Long-term nitrogen addition affects the phylogenetic turnover of soil microbial community responding to moisture pulse – Chi Liu – Scientific Reports

Impact of Glyphosate on the Rhizosphere Microbial Communities of An EPSPS-Transgenic Soybean Line ZUTS31 by Metagenome Sequencing – Gui-Hua Lu – Current Genomics

Microbial communities in natural rubber coagula during maturation: impacts on technological properties of dry natural rubber – Mélanie Salomez – Journal of Applied Microbiology

Manure and mineral fertilization change enzyme activity and bacterial community in millet rhizosphere soils – Lixia Xu – World Journal of Microbiology and Biotechnology

Resistome

Drivers of dissolved organic carbon export in a subarctic catchment: Importance of microbial decomposition, sorption-desorption, peatland and lateral flow – Itziar Lekunberri – Environmental Pollution

Food microbiology

Conference Proceedings: The microbial community and free amino acid composition in salted and fermented squid products – Daisuke Ouchi- The JSFS 85th Anniversary-Commemorative International Symposium

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Waste and Pollution

Anaerobic Baffled Reactor in Treatment of Natural Rubber Processing Wastewater: Reactor Performance and Analysis of Microbial Community – Phuong Thao Tran – Journal of Water and Environment Technology

Microbial Community Structure and Enumeration of Bacillus species in Activated Sludge – Masashi Hatamoto – Journal of Water and Environment Technology

Techniques

Sampling, Extraction, and High-Throughput Sequencing Methods for Environmental Microbial and Viral Communities – Pedro J. Torres – In: Next Generation Sequencing. Methods in Molecular Biology, vol 1712. Humana Press

*Sequencing of Genomes from Environmental Single Cells – Robert Bowers – In: Methods in Molecular Biology, vol 1712. Humana Press

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Microbes in the news

Why Probiotic Skin Care Is (Actually) Worth It, According to Experts – Lauren Valenti – – Vogue

Celebrating a decade of interdisciplinary microbiology – Raleigh McElvery – MIT News

Plant pathologists discover unusual evolutionary transition in common bacteria – Chris Branam – Phys.org

Efforts of bacteria to defend against predators is so great that few resources left for offspring – Science Daily

Specially designed protein fights several species of bacteria – EurekaAlert

Reprogramming bacteria instead of killing them could be the answer to antibiotic resistance – Yu-Hsuan Tsai – Phys.org

Bacteria and Art

Shout Out: Hunter Cole, biology lecturer and artist – Genevieve Bookwalter- Chicago Tribune

Kathy High with Sadie R. Starnes, Gut Love: You are my future – Esther Klein – The Brooklyn Rail