July 9, 2018

Today’s Digest features new insights into the microbial communities associated with shisha (water pipe), microbial mats, and tropical marine ecosystems. In addition, there are some new techniques and benchmarks to read about, including domain intelligible models for mining ‘omics data and the potential of giant viruses to introduce errors into metagenomic binning. I also highlighted some non-microbiology picks about the potential role for robots in autism therapies and photographs of a brand new planet taken at the Max Planck Institute for Astronomy!

Human gut microbiome
Faecal microbiota transplantation alters gut microbiota in patients with irritable bowel syndrome: results from a randomised, double-blind placebo-controlled study – Sofie Ingdam Halkjær – Gut

Animal experiments
Early-life sickness may predispose Siberian hamsters to behavioral changes following alterations of the gut microbiome in adulthood – Kristyn E. Sylvia – Brain, Behavior, and Immunity

Deficiency in class III PI3-kinase confers postnatal lethality with IBD-like features in zebrafish – Shaoyang Zhao – Nature Communications

Plant, root, and soil microbiome
Shisha microbiota: the good, the bad and the not so ugly – Julia Hani – BMC Research Notes

Disentangling the drivers of functional complexity at the metagenomic level in Shark Bay microbial mat microbiomes – Hon Lun Wong – The ISME Journal

Water and extremophile microbiome
A long-standing complex tropical dipole shapes marine microbial biogeography – Wei Yan – Applied and Environmental Microbiology

Probiotics / prebiotics
Probiotic Lactobacillus paracasei HII01 protects rats against obese-insulin resistance-induced kidney injury and impaired renal organic anion transporter 3 (Oat3) function – Keerati Wanchai – Clinical Science

Bioinformatics
Domain Intelligible Models – Sultan Imangaliyev – Methods

Techniques
Metagenomic binning reconstruction coupled with automatic pipeline annotation and giant viruses: a potential source of mistake in annotations – Julien Andreani – Virus Research

Does universal 16S rRNA gene amplicon sequencing of environmental communities provide an accurate description of nitrifying guilds? – Vaibhav Diwan – Journal of Microbiological Methods

Linking uncultivated microbial populations with benthic carbon turnover using quantitative stable isotope probing – Ömer K. Coskun – Applied and Environmental Microbiology

Determining lineage-specific bacterial growth curves with a novel approach based on amplicon reads normalization using internal standard (ARNIS) – Kasia Piwosz – The ISME Journal

Alyson’s non-microbiology picks
Personalized machine learning for robot perception of affect and engagement in autism therapy – Ognjen Rudovic – Science Robotics

Scientists Capture First Birth Of A Planet – M. Keppler – via NPR

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June 25, 2018

Today’s Microbiome Digest features the sea turtle microbiome, the bacteria responsible for degrading bioplastics, a new clinical center for phage therapy, the gut-microbiome-brain axis in an Alzheimer’s Disease model, and a preprint about image duplication in scientific publishing.

Pregnancy and early life

Late-onset Sepsis in Preterm Infants Can Be Detected Preclinically by Fecal Volatile Organic Compound Analysis: A Prospective, Multicenter Cohort Study. – Daniel J C Berkhout- Clinical Infectious Diseases

Human vaginal microbiome

Abnormal vaginal microbioma is associated with severity of localized provoked vulvodynia. Role of aerobic vaginitis and Candida in the pathogenesis of vulvodynia. – Gilbert G. G. Donders- European Journal of Clinical Microbiology & Infectious Diseases

Human gut microbiome

* Gut microbiota regulates maturation of the adult enteric nervous system via enteric serotonin networks – Filipe De Vadder – PNAS

Linking the Gut Microbiota to a Brain Neurotransmitter – Kelly G. Jameson – Trends in Neurosciences

Can epilepsy be treated by antibiotics? – Hilde M. H. Braakman – Journal of Neurology

* Changes in intestinal microbiota in HIV-1-infected subjects following cART initiation: influence of CD4+ T cell count – Yongjia Ji – Emerging Microbes & Infections

Review: Human gut microbiome: hopes, threats and promises – Patrice D Cani – Gut

Review: New treatments and therapeutic targets for IBS and other functional bowel disorders – Magnus Simrén – Nature Reviews Gastroenterology & Hepatology

Animal experiments

Effects of chronic noise exposure on the microbiome-gut-brain axis in senescence-accelerated prone mice: implications for Alzheimer’s disease – Bo Cui – Journal of Neuroinflammation

Bacterial methionine metabolism genes influence Drosophila melanogaster starvation resistance – Alec M. Judd – Applied and Environmental Microbiology

The benign helminth Hymenolepis diminuta ameliorates chemically induced colitis in a rat model system – Kateřina Jirků Pomajbíková – Parasitology

Protective role of commensal bacteria in Sjögren Syndrome – Mahira Zaheer – Journal of Autoimmunity

Lactobacillus murinus HF12 colonizes neonatal gut and protects rats from necrotizing enterocolitis. – Mubina Isani – PLOS One

Animal microbiome

Identification of bacteria present in ulcerative stomatitis lesions of captive sea turtles Chelonia mydas – D. X. Vega-Manriquez – Veterinary Research Communications

Characterization of the Microbiota of Oyster Larvae (Crassostrea virginica) and Tank Water from an Aquaculture System with High and Low Larval Survival Rates – Padmini Ramachandran – Genome Announcements

Early colonisation and temporal dynamics of the gut microbial ecosystem in Standardbred foals – S. Quercia – Equine Veterinary Journal

Plant, root, and soil microbiome

Microbial communities responsible for the degradation of poly(lactic acid)/poly(3-hydroxybutyrate) blend mulches in soil burial respirometric tests – Lenka Jeszeová – World Journal of Microbiology and Biotechnology

Phylogenetic diversity and investigation of plant growth-promoting traits of actinobacteria in coastal salt marsh plant rhizospheres from Jiangsu, China – Yuan Gong – Systematic and Applied Microbiology

Dynamics of soil microbial recovery from cropland to orchard along a 20-year chronosequence in a degraded karst ecosystem. – Hongkai Liao – Science of The Total Environment

Investigation of viable taxa in the deep terrestrial biosphere suggests high rates of nutrient recycling. – Margarita Lopez-Fernandez – FEMS Microbial Ecology

Distinct impacts of reductive soil disinfestation and chemical soil disinfestation on soil fungal communities and memberships. – Jun Zhao – Applied Microbiology and Biotechnology

* Dispersal-competition tradeoff in microbiomes in the quest for land colonization – Francisco Dini-Andreote – Scientific Reports

Water and extremophile microbiome

Linking patterns of net community production and marine microbial community structure in the western North Atlantic. – Seaver Wang – The ISME Journal

Probiotics/Prebiotics

Composition and metabolism of fecal microbiota from normal and overweight children are differentially affected by melibiose, raffinose and raffinose-derived fructans. – Kaarel Adamberg – Anaerobe

Review: Nutraceuticals in Colorectal Cancer: A Mechanistic Approach – Marco Rossi – European Journal of Pharmacology

Science, publishing, and career

* Analysis and Correction of Inappropriate Image Duplication: The Molecular and Cellular Biology Experience – Arturo Casadevall – bioRxiv

Microbes in the news

U.S. center will fight infections with viruses – Kelly Servick – Science

Alyson’s non-microbiology pick

Neanderthal brain organoids come to life – Jon Cohen – Science