Todays picks include nice reviews on microbiome engineering, and one on skin microbiomes in humans and animals. Biodegredation of mononitrophenol isomers by a tailor-made microbial consortium.  Quite a lot of microbiome news – from autism to inflammatory bowel disease.

Events and jobs

Microbiome Scientist Job – Merck – Cambridge, MA

General microbiome

Review: Microbiome engineering: Current applications and its future – Jee Loon Foo – Biotechnology Journal

Simultaneous biodegradation of three mononitrophenol isomers by a tailor-made microbial consortium immobilized in sequential batch reactors – H. Fu – Letters in Applied Microbiology

Human skin microbiome

Review: The cutaneous ecosystem: the roles of the skin microbiome in health and its association with inflammatory skin conditions in humans and animals – Aline Rodrigues Hoffmann – Veterinary Dermatology

Animal experiments

A metagenomic study of the preventive effect of Lactobacillus rhamnosus GG on intestinal polyp formation in ApcMin/+ mice – Y. Ni – Journal of Applied Microbiology

Water and extremophile microbiome

Biofilms for Monitoring Presence of Microsporidia in Environmental Water – Joseph A. Moss – Journal of Eukaryotic Microbiology

Haptophyte Diversity and Vertical Distribution Explored by 18S and 28S Ribosomal RNA Gene Metabarcoding and Scanning Electron Microscopy – Sandra Gran-Stadniczeñko – Journal of Eukaryotic Microbiology

Bioinformatics

Preprint: In-Depth Resistome Analysis by Targeted Metagenomics – Val F Lanza – bioRxiv

Microbes in the news

Could Fecal Microbiota Transplant Benefit Autistic Children? – MPR

Premature birth risk linked to bacteria in vagina and cervix – Catharine Paddock – MNT

New evidence of how gut microbes affect Inflammatory Bowel Disease – Kate Sweeney – BuisnessWeekly

Boost your immunity with foods that are alive – Rachel Yan – 9News

Rebalancing gut microbiome lengthens survival in mouse model of ALS – ScienceDaily

Carbohydrate That Promotes Biofilm May Be Key to Treating Pseudomonas Infections – Magdalena Kegel – CysticFibrosisNewsToday

General microbiome
Commentary: The AGA’s Fecal Microbiota Transplantation National Registry: An important step toward understanding risks and benefits of microbiota therapeutics – Colleen R. Kelly – Gastroenterology

Review: Microbes and Mental Health: A Review – Ryan Rieder – Brain, Behavior, and Immunity

Review: The role of divalent metals for infectious diseases susceptibility and outcome – Guenter Weiss – Clinical Microbiology and Infection

Human gut microbiome
Effects of Acarbose on the Gut Microbiota of Prediabetic Patients: A Randomized, Double-blind, Controlled Crossover Trial – Xiuying Zhang – Diabetes Therapy

Clinical Commentary: More Than a Gut Feeling: The Implications of the Gut Microbiota in Psychiatry – Pochu Ho – Biological Psychiatry

Animal experiments
Target Intestinal Microbiota to Alleviate Disease Progression in Amyotrophic Lateral Sclerosis – Yong-guo Zhang – Clinical Therapeutics

Commensal Bacteria at the Crossroad between Cholestrol Homeostasis and Chronic Inflammation in Atherosclerosis – Kazuyuki Kasahara – Journal of Lipid Research

Bovine milk oligosaccharides decrease gut permeability and improve inflammation and microbial dysbiosis in diet-induced obese mice – Gaelle Boudry – Journal of Dairy Science

Broad spectrum antibiotic enrofloxacin modulates contact sensitivity through gut microbiota in a murine model – Anna Strzepa – Journal of Allergy and Clinical Immunology

Effects of subchronic oral toxic metal exposure on the intestinal microbiota of mice -Qixiao Zhai – Science Bulletin

In vitro fermentation of key dietary compounds with rumen fluid: A genome-centric perspective – Stefano Campanaro – Science of the Total Environment

Cow, yak, and camel milk diets differentially modulated the systemic immunity and fecal microbiota of rats – Wen Yongping – Science Bulletin

Animal microbiome
The oral microbiota of domestic cats harbors a wide variety of Staphylococcus species with zoonotic potential – Ciro Cesar Rossi – Veterinary Microbiology

Effects of daidzein on performance, serum metabolites, nutrient digestibility, and fecal bacterial community in bull calves – X.H. Zhao – Animal Feed Science and Technology

Plant microbiome
Marchantia liverworts as a proxy to plants basal microbiomes – Luis David Alcaraz – bioRxiv

Water and extremophile microbiome
Microbial succession in biofilms growing on artificial substratum in subtropical freshwater aquaculture ponds  – Zhifei Li – FEMS Microbiology Letters

Model communities hint to promiscuous metabolic linkages between ubiquitous free-living freshwater bacteria – Sarahi L Garcia – bioRxiv

Metagenomic identification of active methanogens and methanotrophs in serpentinite springs of the Voltri Massif, Italy – William J. Brazelton – PeerJ

Food microbiology
Beneficial effects of legumes in gut health – Alfonso Clemente – Current Opinion in Food Science

Probiotics / prebiotics
Impact of ageing and a synbiotic on the immune response to seasonal influenza vaccination; a randomised controlled trial – Sumaia Enani – Clinical Nutrition

Antivirulence Properties of Probiotics in Combating Microbial Pathogenesis – M. Surendran Nair – Advances in Applied Microbiology

Bioinformatics
MetaShot: an accurate workflow for taxon classification of host-associated microbiome from shotgun metagenomic data  – B Fosso – Bioinformatics

Linclust: clustering protein sequences in linear time – Martin Steinegger – bioRxiv

Techniques
Chapter 3: Best practices for germ-free derivation and gnotobiotic zebrafish husbandry – E. Melancon – Methods in Cell Biology

Chapter 10: Modeling intestinal disorders using zebrafish – X. Zhao – Methods in Cell Biology

A novel LCMSMS method for quantitative measurement of short-chain fatty acids in human stool derivatized with 12C- and 13C-labelled aniline – James Chun Yip Chan – Journal of Pharmaceutical and Biomedical Analysis

Newly Isolated Strains
Actinomyces bouchesdurhonensis sp. nov. and Actinomyces mediterranea sp. nov., isolated from Human Stomach and Duodenum – Morgane Mailhe – Human Microbiome Journal

Peptoniphilus duodeni sp. nov., a new bacterial species identified in human duodenum – Morgane Mailhe – Human Microbiome Journal

Bacteroides bouchesdurhonensis sp. nov., a new bacterium isolated from the human gut – Sokhna Ndongo – Human Microbiome Journal

Microbes in the news
What Even is Kombucha, Anyway? – Anthony Rivas – BuzzFeed

Preventing Biofilm and Bacteria in Dental Operatory Tubing – Tech Featured

Non-Microbiology picks
The State of Systems Genetics in 2017 – Nitin S. Baliga – Cell Systems

Trump’s Immigration Ban Is Already Harming American Science – Ed Yong – The Atlantic

Geneticist launches bid for US Senate – Sara Reardon – Nature

Among todays picks; Microbiota Transfer Therapy improves gastrointestinal and autism symptoms. Primate microbiota is linked to degree of host sociality. Identifying microbial community changes in space and time opens a door to predicting ecosystem level functioning. Native soil microbes help native plants compete with exotics. Metal toxicity and stress response adaptations represent an important selective force for influencing diversity within marine Synechococcus populations.

Events and jobs

Postdoctoral fellowships in microbiome/neuroscience – Northwestern University

Medical Lab Technician in Microbiology – Medical University of South Carolina

Microbiology Technologist – CK Group, Surrey

General microbiome

Predicting the structure and function of coalesced microbial communities –Pawel Sierocinski – bioRxiv

Multi-site human microbiome

Frozen: Thawing and Its Effect on the Postmortem Microbiome in Two Pediatric Cases – Jennifer L. Pechal – Journal of Forensic Sciences

Human vaginal microbiome

Appreciable uncertainty regarding benefits and risks in the treatment of bacterial vaginosis to prevent preterm birth – Thor Haahr -Acta Obstetricia et Gynecologica Scandinavica

Human gut microbiome

Microbiota Transfer Therapy alters gut ecosystem and improves gastrointestinal and autism symptoms: an open-label study – Dae-Wook Kang – Microbiome

Dysregulation of Systemic and Mucosal Humoral Responses to Microbial and Food Antigens as a Factor Contributing to Microbial Translocation and Chronic Inflammation in HIV-1 Infection. – Zdenek Hel – PLOS PATHOGENS

Impact of the Microbiota and Gastric Disease Development by Helicobacter pylori. – Teresa Alarcón –  Current Topics in Microbiology and Immunology

Helicobacter pylori-Induced Changes in Gastric Acid Secretion and Upper Gastrointestinal Disease. – Adam J. Smolka –  Current Topics in Microbiology and Immunology

Sleepy, circadian disrupted and sick: Could intestinal microbiota play an important role in shift worker health? – Amy C. Reynolds – Molecular Metabolism

Oxidation During Digestion of Meat: Interactions with the Diet and Helicobacter pylori Gastritis, and Implications on Human Health – Thomas Van Hecke – Comprehensive Reviews in Food Science and Food Safety

Glucosinolate and Desulfo-glucosinolate Metabolism by a Selection of Human Gut Bacteria. – Vijitra Luang-In – Current Microbiology

Animal experiments

Species-specific immunity to Helicobacter suis – Iris Bosschem – Helicobacter

Animal microbiome 

The Association of Specific Constituents of the Fecal Microbiota with Immune-Mediated Brain Disease in Dogs. – Nick D. Jeffery – PLOS ONE

Patterns in Gut Microbiota Similarity Associated with Degree of Sociality among Sex Classes of a Neotropical Primate. – Katherine R. Amato – Microbial Ecology

Plant, root, and soil microbiome

Antimicrobial Activities of Some Actinomycetes Isolated from Different Rhizospheric Soils in Tunisia. – Ines Trabelsi – Current Microbiology

Native plants fare better against an introduced competitor with native microbes and lower nitrogen availability. – W. Gaya Shivega – AoB PLANTS

Identity of biocrust species and microbial communities drive the response of soil multifunctionality to simulated global change – Yu-Rong Liu – Soil Biology and Biochemistry

Distinct roles for soil fungal and bacterial communities associated with the suppression of vanilla Fusarium wilt disease – Wu Xiong – Soil Biology and Biochemistry

Prolonged exposure does not increase soil microbial community response to warming along geothermal gradients – Dajana Radujkovic – bioRxiv

Water and extremophile microbiome

Coupling Spatiotemporal Community Assembly Processes to Changes in Microbial Metabolism – Emily B. Graham – Frontiers in Microbiology 

Copper toxicity response influences mesotrophic Synechococcus community structure – Rhona K. Stuart – Environmental Microbiology

Identification and bioactive potential of marine microorganisms from selected Florida coastal areas – Anna Christensen – MicrobiologyOpen

Diversity and mineral substrate preference in endolithic microbial communities from marine intertidal outcrops (Isla de Mona, Puerto Rico) – Estelle Couradeau –
Biogeosciences

Techniques

Review: Mining for CRISPR–Cas – Ashley York – Nature Reviews Microbiology

Data Mining Techniques Applied to Hydrogen Lactose Breath Test – Cristina Rubio-Escudero – PLOS ONE

Profiling Living Bacteria Informs Preparation of Fecal Microbiota Transplantations – Nathaniel D. Chu – PLOS ONE

Statistical test for tolerability of effects of an antifungal biocontrol strain on fungal communities in three arable soils – Kai Antweiler – Microbial Biotechnology

Molecular beacons to identify gifted microbes for genome mining – Richard H Baltz – The Journal of Antibiotics

Phages and viruses

Fecal virome of healthy chickens reveals a large diversity of the eukaryote viral community, including novel circular single-stranded DNA viruses –  Diane Lima – Journal of General Virology

Studies on the Virome of the Entomopathogenic Fungus Beauveria bassiana Reveal Novel dsRNA Elements and Mild Hypervirulence – Ioly Kotta-Loizou – PLOS PATHOGENS

Microbes in the news 

Microbiome Science Could Bring a Revolution in Medical Care –  Lois Parshley – NBC NEWS

Is showering everyday bad for you? New research says yes  – Sarah Young – The INDEPENDENT

Rapidly identifying life-threatening bacteria in hospitals – Phys.org

Bacteria May Be Altering Your Brain To Suppress Your Appetite When You’re Sick – Josh Davis – IFL Science

Stanford Medicine and uBiome Investigate Relationship Between Gut Bacteria and Diabetes – Julie Taylor – Prweb

Microbes in the news

*Pathogen-Mediated Inhibition of Anorexia Promotes Host Survival and Transmission – Sheila Rao – Cell

• Media: Why salmonella doesn’t want you to poop out – Helen Thompson – ScienceNews

Microbes on the market 

Global Human Microbiome Market Is Expected to Witness a Steady Growth By 2020 – MedGadget

Daily Dog Diet Significantly Influences Canine Gut Microbiome, Report Says – Kalyan Kumar – Tech Times

Pete’s non-microbiology picks

Terrestrial discharges mediate trophic shifts and enhance methylmercury accumulation in estuarine biota – Sofi Jonsson – Science Advances

• Media: New mercury threat to oceans from climate change – Matt McGrath – BBC News

Events and jobs

Head Of Bioinformatics – Commense Health

Postdoctoral Research Assistant in Structural Cell Biology of Bacterial Biofilm Formation – University of Oxford – Apply by February 3, 2017

Postdoctoral Research Position in Experimental Microbiome Research – The Ohio State University

General microbiome

*Review Life history and eco-evolutionary dynamics in light of the gut microbiota – Emilie Macke – OIKOS

Pregnancy and early life

Maturation of the infant microbiome community structure and function across multiple body sites and in relation to mode of delivery – Derrick M Chu – Nature Medicine

Method of birth does not effect microbiome composition – Dipali Pathak – Baylor College of Medicine  

Human gut microbiome

*Review The gut-brain axis: is intestinal inflammation a silent driver of Parkinson’s disease pathogenesis? – Madelyn C. Houser – npj Parkinson’s Disease

Animal microbiome

Structure, and culture and predicted function of the gut microbiome of the Mormon cricket Anabrus simplex (Orthoptera: Tettigoniidae)  – Chad C Smith – bioRxiv

Composition of Gut Microbiota in the Gibel Carp (Carassius auratus gibelio) Varies with Host Development – Xinghao Li – Microbial Ecology

Variation in Metabolite Profiles of Amphibian Skin Bacterial Communities Across Elevations in the Neotropics – Daniel Medina – Microbial Ecology

Plant, root, and soil microbiome

Soil microbial communities and elk foraging intensity: implications for soil biogeochemical cycling in the sagebrush steppe – Lauren C. Cline – Ecology Letters

Shared and host-specific microbiome diversity and functioning of grapevine and accompanying weed plants – Abdul Samad – Environmental Microbiology

Soil microbial communities in cucumber monoculture and rotation systems and their feedback effects on cucumber seedling growth – Xingang Zhou – Plant and Soil

Soil bacterial communities and ecosystem functioning change more strongly with season than habitat in a restored floodplain – Emanuela Samaritani – Applied Soil Ecology

Water and extremophile microbiome

Bringing microbial diversity into focus: high-resolution analysis of iron mats from the Lō‘ihi Seamount – Jarrod J. Scott – Environmental Microbiology

Diversity and Distribution of Thermophilic Bacteria in Hot Springs of Pakistan – Arshia Amin – Microbial Ecology

*Editorial Editorial: Geomicrobes: life in terrestrial deep subsurface – Malin Bomberg – Frontiers in Microbiology

Phages and viruses

Newly isolated Nodularia phage influences cyanobacterial community dynamics – S. E. Coloma – Environmental Microbiology

Bioinformatics

MetaSort untangles metagenome assembly by reducing microbial community complexity – Peifeng Ji – Nature Communications

A Dirichlet-tree multinomial regression model for associating dietary nutrients with gut microorganisms – Tao Wang – Biometrics

Bayesian latent variable models for hierarchical clustered count outcomes with repeated measures in microbiome studies – Lizhen Xu – Genetic Epidemiology  

Viral Phylogenomics Using an Alignment-Free Method: A Three-Step Approach to Determine Optimal Length of k-mer – Qian Zhang – Scientific Reports

VirusSeeker, a computational pipeline for virus discovery and virome composition analysis – Guoyan Zhao – Virology  

Quantitative Comparison of Abundance Structures of Generalized Communities: From B-Cell Receptor Repertoires to Microbiomes – Mohammadkarim Saeedghalati – PLoS Computational Biology

Techniques

Optimisation of methods for bacterial skin microbiome investigation: primer selection and comparison of the 454 versus MiSeq platform – Madhura Castelino – BMC Microbiology

Towards long-read metagenomics: complete assembly of three novel genomes from bacteria dependent on a diazotrophic cyanobacterium in a freshwater lake co-culture – Connor B. Driscoll – Standards in Genomic Sciences

*Review Metaproteomics as a Complementary Approach to Gut Microbiota in Health and Disease – Bernando Petriz – Frontiers in Chemistry

Microbes in the news

Uncultivated microbes reveal new CRISPR–Cas systems – Ross Cloney – Nature Reviews Genetics

The Cervicovaginal Microbiome May Wield Influence Against HIV Acquisition – Charles B. Hicks, MD –  NEJM Journal Watch

Microbes on the market

RondinX Expands its Microbiome Computational Platform for Drug Development with a Unified Reference Range of Bacterial Dynamics Based on Database of 1,400 Healthy Individuals – Business Wire

Microbiome modeling with Gusto – Juliet Preston – MedCity News

Jobs and Grants
Assistant Research Professor in Microbiome Bioinformatics – University of Oklahoma – Apply by January 31

Assistant Professor of Horticulture (Plant Microbiome Research) – University of Kentucky

Michael Davidson and Roger Tsien Commemorative Travel Awards – Apply by January 31 – Open to masters/PhD students and postdocs traveling to an academic conference in 2017 who can demonstrate that fluorescent proteins have/will have an impact on their research

American Public Health Laboratories (APHL)-CDC Fellowships
Infectious Diseases – Due February 17
Bioinformatics – Due February 28
Antimicrobial Resistance – Due February 28

General microbiome
*Opinion: Host–microbiota interactions: epigenomic regulation – Vivienne Woo – Current Opinion in Immunology

Human gut microbiome
Discovery of Reactive Microbiota-Derived Metabolites that Inhibit Host Proteases – Chun-Jun Guo – Cell

A case of pyometrocolpos with Bifidobacterium species – Maanasa M. Bhaskar – Anaerobe

*Review: Gut microbiota: A player in aging and a target for anti-aging intervention – Alexander M. Vaiserman – Ageing Research Reviews

Microbiome remodeling via the montmorillonite adsorption-excretion axis prevents obesity-related metabolic disorders – Pengfei Xu – EBioMedicine

Animal experiments
The Bactericidal Lectin RegIIIβ Prolongs Gut Colonization and Enteropathy in the Streptomycin Mouse Model for Salmonella Diarrhea – Tsuyoshi Miki – Cell Host and Microbe

Composition of Gut Microbiota in the Gibel Carp (Carassius auratus gibelio) Varies with Host Development – Xinghao Li – Microbial Ecology

Effects of gut microbiota on the microRNA and mRNA expression in the hippocampus of mice – Jian-jun Chen – Behavioural Brain Research

Plant, root, and soil microbiome
From Microhabitat of Floral Nectar Up to Biogeographic Scale: Novel Insights on Neutral and Niche Bacterial Assemblies – Yana Aizenberg-Gershtein – Environmental Microbiology

Microbial changes linked to the accelerated degradation of the herbicide atrazine in a range of temperate soils – R.L. Yale – Environmental Science and Pollution Research

Microbial siderophores and root exudates enhanced goethite dissolution and Fe/As uptake by As-hyperaccumulator Pteris vittata – Xue Liu – Environmental Pollution

Water and extremophile microbiome
Influence of silver nanoparticles on benthic oxygen consumption of microbial communities in freshwater sediments determined by microelectrodes – Lingzhan Miao – Environmental Pollution

Built environment
Heterogenic response of prokaryotes toward silver nanoparticles and ions is facilitated by phenotypes and attachment of silver aggregates to cell surfaces – Yuting Guo – Cytometry

Phages and viruses
The use of bacteriophages to biocontrol oral biofilms – Szymon P. Szafrański – Journal of Biotechnology

Bioinformatics
A portable system for metagenomic analyses using nanopore-based sequencer and laptop computers can realize rapid on-site determination of bacterial compositions – Satomi Mitsuhashi – bioRxiv

A fast and robust protocol for metataxonomic analysis using RNAseq data – Jeremy W. Cox – Microbiome

Microbes in the news
Scientists have caught viruses talking to each other—and that could be the key to a new age of anti-viral drugs – Akshat Rathi – Quartz

Bacteria powered battery built on sheet of paper – Tim Sandle – Digital Journal

Molecule shows ability to thwart pathogens’ genetic resistance to antibiotic – Oregon State University
The original paper is here: Peptide-conjugated phosphorodiamidate morpholino oligomer (PPMO) restores carbapenem susceptibility to NDM-1-positive pathogens in vitro and in vivo – Erin K. Sully – Journal of Antimicrobial Chemotherapy

Andrew Wakefield appearance at Trump inaugural ball triggers social media backlash – Casey Ross – STAT News

Science, publishing, and career
Gates Foundation research can’t be published in top journals – Richard Van Noorden – Nature

Non-microbiology picks
Could a Neuroscientist Understand a Microprocessor? – Eric Jonas – PLoS Computational Biology
Interesting to consider since there are parallels in microbiome analyses!