There were over 100 alerts today! Here are plenty of papers after the few light digests.

Events and jobs
Bioinformatics Scientist, Microbiome – Human Longevity, Inc, Greater San Diego Area

MSc position in Microbiology – Teagasc, London/Europe

General microbiome
Review: The multi-omics promise in context: from sequence to microbial isolate – Johanna Gutleben – Critical Reviews in Microbiology

Review: Symbiosis-inspired approaches to antibiotic discovery – Navid Adnani – Natural Product Reports

Pregnancy and early life
The Microbiome of Infants Recruited to a Randomised Placebo-controlled Probiotic Trial (PiPS Trial) – Michael Millar – EBioMedicine

Safety and tolerability of Bifidobacterium longum subspecies infantis EVC001 supplementation in healthy term breastfed infants: a phase I clinical trial – Jennifer T. Smilowitz – BMC Pediatrics

Human vaginal microbiome
Vaginal bacteria modify HIV tenofovir microbicide efficacy in African women – Nichole R. Klatt – Science

Changes in vaginal community state types reflect major shifts in the microbiome – J. Paul Brooks – Microbial Ecology in Health and Disease

Human gut microbiome
Chemoproteomic Profiling of Bile Acid Interacting Proteins – Shentian Zhuang – ACS Central Science

Fiber-utilizing capacity varies in Prevotella- versus Bacteroides-dominated gut microbiota – Tingting Chen – Scientific Reports

Vancomycin Taper and Risk of Failure of Fecal Microbiota Transplant in Patients With Recurrent Clostridium difficile Infection – Roberto L. Patron – Clinical Infectious Diseases

Surgically induced changes in gut microbiome and hedonic eating as related to weight loss: Preliminary findings in obese women undergoing bariatric surgery – Claudia P. Sanmiguel – Psychosomatic Medicine

Intestinal microbiota in patients with chronic hepatitis C with and without liver cirrhosis compared to healthy controls – Benjamin Heidrich – Liver International

Dimethyl fumarate reduces the risk of mycotoxins via improving intestinal barrier and microbiota – Ning Ma – Oncotarget

Optimized multiplex immunofluorescence single-cell analysis reveals tuft cell heterogeneity – Eliot T. McKinley – JCI Insight

Gut microbiota regulate hepatic von Willebrand Factor synthesis and arterial thrombus formation via Toll-like receptor-2 – Sven Jäckel – Blood

Review: Trust your gut – metformin and diabetes – Conor A. Bradley – Nature Reviews Endocrinology

Review: Gut microbiota: Inulin regulates endothelial function: a prebiotic smoking gun? – Francesca Fava – Nature Reviews Gastroenterology and Hepatology

Review: Gut Microbiota, Endocrine-Disrupting Chemicals, and the Diabetes Epidemic – Ganesan Velmurugan – Trends in Endocrinology and Metabolism

Review: Gut Microbiota and the Gut-Brain Axis: New Insights in the Pathophysiology of Metabolic Syndrome – de Clercq – Psychosomatic Medicine

Animal experiments
Genetic mouse models with intestinal-specific tight junction deletion resemble an ulcerative colitis phenotype – Wolfgang Stremmel – Journal of Crohn’s and Colitis

Deciphering the landscape of host barriers to Listeria monocytogenes infection – Ting Zhang – PNAS

Rifaximin exerts beneficial effects in PI-IBS mouse model beyond gut microbiota – Yu Jin – Journal of Gastroenterology and Hepatology

Farnesoid X Receptor Agonist Treatment Alters Bile Acid Metabolism but Exacerbates Liver Damage in a Piglet Model of Short-Bowel Syndrome – Prue M. Pereira-Fantini – Cellular and Molecular Gastroenterology and Hepatology

Faecal transplantation for the treatment of Clostridium difficile infection in a marmoset – Yumiko Yamazaki – BMC Veterinary Research

Effect of soybean husk supplementation on the fecal fermentation metabolites and microbiota of dogs – Htun Myint – Animal Science Journal

A diet change from dry food to beef induces reversible changes on the faecal microbiota in healthy, adult client-owned dogs – Kristin M. V. Herstad – BMC Veterinary Research

Animal microbiome
Host-specific assembly of sponge-associated prokaryotes at high taxonomic ranks – Georg Steinert – Scientific Reports

The feline skin microbiota: The bacteria inhabiting the skin of healthy and allergic cats – Caitlin E. Older – PLoS One

Comparison of the fecal bacterial microbiota of healthy and diarrheic foals at two and four weeks of life – A. Schoster – BMC Veterinary Research

Cost-effective screening and isolation of xylano-cellulolytic positive microbes from termite gut and termitarium – Libin Mathew Varghese – 3 Biotech

Plant, root, and soil microbiome
Impact of metal stress on the production of secondary metabolites in Pteris vittata L. and associated rhizosphere bacterial communities – Hoang Nam Pham – Environmental Science and Pollution Research

High-throughput metagenomic analysis of petroleum-contaminated soil microbiome reveals the versatility in xenobiotic aromatics metabolism – Yun-Juan Bao – Journal of Environmental Sciences

Impact of microbial communities from tropical soils on the mobilization of trace metals during dissolution of cinnabar ore – Clarisse Balland-Bolou-Bi – Journal of Environmental Sciences

Divergent taxonomic and functional responses of microbial communities to field simulation of aeolian soil erosion and deposition – Xingyu Ma – Molecular Ecology

Anthropogenic protection alters the microbiome in intertidal mangrove wetlands in Hainan Island – Juanli Yun – Applied Microbiology and Biotechnology

Water and extremophile microbiome
Zooming in on the phycosphere: the ecological interface for phytoplankton-bacteria relationships – Justin R. Seymour – Nature Microbiology

Genetic characterization of periphyton communities associated with selenium bioconcentration and trophic transfer in a simple food chain – Vanessa Friesen – Environmental Science and Technology

Intraspecific differences in molecular stress responses and coral pathobiome contribute to mortality under bacterial challenge in Acropora millepora – Rachel M. Wright – Scientific Reports

Metabolic network analysis reveals microbial community interactions in anammox granules – Christopher E. Lawson – Nature Communications

Hot springs of Indian Himalayas: potential sources of microbial diversity and thermostable hydrolytic enzymes – Harmesh Sahay – 3 Biotech

High throughput sequencing of microbial eukaryotes in Lake Baikal reveals ecologically differentiated communities and novel evolutionary radiations – Zhenzhen Yi – FEMS Microbiology Ecology

Centralized Drinking Water Treatment Operations Shape Bacterial and Fungal Community Structure – Xiao Ma – Environmental Science and Technology

Built environment
Evolution of microbial communities growing with carbon monoxide, hydrogen and carbon dioxide – Sofia Esquivel-Elizondo – FEMS Microbiology Ecology

Adaptation of microbial community of the anode biofilm in microbial fuel cells to temperature – Xiaoxue Mei – Bioelectrochemistry

Structure and activity of thermophilic methanogenic microbial communities exposed to quaternary ammonium sanitizer – Jesus D. Fernandez-Bayo – Journal of Environmental Sciences

Bacterial community structure transformed after thermophilically composting human waste in Haiti – Yvette M. Piceno – PLoS One

Food microbiology
Characterization of the peptide fraction from digested Parmigiano Reggiano cheese and its effect on growth of lactobacilli and bifidobacteria – Benedetta Bottari – International Journal of Food Microbiology

Impact of food grade and nano-TiO2 particles on a human intestinal community – William Dudefoi – Food and Chemical Toxicology

Probiotics / prebiotics
Probiotic yogurt and acidified milk similarly reduce postprandial inflammation and both alter the gut microbiota of healthy, young men – Kathryn J. Burton – British Journal of Nutrition

Phages and viruses
Phylogenetic Diversity of T4-Type Phages in Sediments from the Subtropical Pearl River Estuary – Maoqiu He – Frontiers in Microbiology

Bacteriophage-prokaryote dynamics and interaction within anaerobic digestion processes across time and space – Junyu Zhang – Microbiome

Bioinformatics
Evaluating the accuracy of amplicon-based microbiome computational pipelines on simulated human gut microbial communities – Jonathan L. Golob – BMC Bioinformatics

Techniques
Review: Capturing the genetic makeup of the active microbiome in situ – Esther Singer – ISME

Novel Co-Culture Plate Enables Growth Dynamic-Based Assessment Of Contact-Independent Microbial Interactions – Thomas J. Moutinho Jr. – bioRxiv

Optimization of high-yielding protocol for DNA extraction from the forest rhizosphere microbes – Sadam D. V. Satyanarayana – 3 Biotech

DNA metabarcoding to assess indoor fungal communities: Electrostatic dust collectors and Illumina sequencing – Steffi Rocchi – Journal of Microbiological Methods

Differentiation of Bifidobacterium longum subspecies longum and infantis by quantitative PCR using functional gene targets – Blair Lawley – PeerJ

Microbes in the news
Unhealthy vagina microbiome can make HIV drugs less effective – Bob Roehr – New Scientist
Article featured above!

Gut microbiota and melanoma treatment responses – Caroline Robert and Franck Carbonnel – OUPblog

Biologists examine biofilm as part of port field studies – Sandor Gyarmati – Delta Optimist

Bacteria used as factories to produce cancer drugs – Phys.Org

Boffins find evidence of strange uranium-producing bacteria lurking underground – Katyanna Quach – The Reigster

Man dies from flesh-eating bacteria after swimming with new tattoo – MSN

Microbes on the market
Why Should we be Excited about the Emerging Microbiome Field? – Antonio – LabBioTech

A bit of a late night Digest today! Still here though, quite a few articles about rhizosphere, a hot topic at the moment; some genome sequences from ASM Genome Announcements, and a few methods & bioinformatics papers. Enjoy!

Multi-site human microbiome

Bacterial Composition and Diversity in Breast Milk Samples from Mothers Living in Taiwan and Mainland China
Shiao-Wen Li et al. – Frontiers in Microbiology

Review: Recent advances in dental biofilm: impacts of microbial interactions on the biofilm ecology and pathogenesis
Yung-Hua Li et al. – AIMS Bioengineering

The Evolving Cystic Fibrosis Microbiome: A Comparative Cohort Study Spanning Sixteen Years
Nicole Acosta et al. – Annals of the American Thoracic Society

Human epitelial microbiome

A tale of two risks: smoking, diabetes and the subgingival microbiome
Sukirth M. Ganesan et al. – The ISME Journal

Quantitative proteomic analysis of host epithelial cells infected by Salmonella enterica serovar Typhimurium
Linlu Qi et al. – Proteomics

Human gut microbiome

Distinctive microbiomes and metabolites linked with weight loss after gastric bypass, but not gastric banding
Zehra Esra Ilhan et al. – The ISME Journal

Microbe Profile: Akkermansia muciniphila: a conserved intestinal symbiont that acts as the gatekeeper of our mucosa
Willem M de Vos – Microbiology

Fecal Microbiota Transplantation: From Clostridium difficile to Inflammatory Bowel Disease
Robert J. Gianotti & Alan C. Moss – Gastroenterology & Hepatology

Bacteriophage transfer during faecal microbiota transplantation in Clostridium difficile infection is associated with treatment outcome
Tao Zuo et al. – Gut

Microbial diseases

Review: ‘Omic’ Approaches to Study Uropathogenic Escherichia coli Virulence
Alvin W. Lo et al. – Trends in Microbiology

Case report: Ecthyma Gangrenosum: Escherichia coli or Pseudomonas aeruginosa?
Mohamed Abbas et al. – Frontiers in Microbiology

General environmental microbiology

Successive range expansion promotes diversity and accelerates evolution in spatially structured microbial populations
Felix Goldschmidt et al. – The ISME Journal

Animal microbiome

Thesis: Biotic and Abiotic Factors Influence Formation and Ontogenic Dynamics of Molecularly Defined Gastro-Intestinal Microbial Communities in Lake Sturgeon (Acipenser Fulvescens) and Channel Catfish (Ictalurus Punctatus)
Abdul Razak – Michigan State University

Plant, root, and soil microbiome

Interactive effects of seasonal drought and elevated atmospheric carbon dioxide concentration on prokaryotic rhizosphere communities
Barbara Drigo et al. – Environmental Microbiology

The biogeographic pattern of microbial functional genes along an altitudinal gradient of the Tibetan pasture
Qi Qi et al. – Frontiers in Microbiology

Communication: Microbial functionality as affected by experimental warming of a temperate mountain forest soil—A metaproteomics survey
Dong Liu et al. – Applied Soil Ecology

Letter: Leaf bacterial diversity mediates plant diversity and ecosystem function relationships
Isabelle Laforest-Lapointe et al. – Nature

Soil amendments influence Pratylenchus penetrans populations, beneficial rhizosphere microorganisms, and growth of newly planted sweet cherry
Tristan T. Watson et al. – Applied Soil Ecology

Comparative analysis of bacterial community structure in the rhizosphere of maize by high-throughput pyrosequencing
Yi Yang et al. – PLoS One

Soil Warming Increases Arsenic Availability in the Rice Rhizosphere
Rebecca B. Neumann et al. – Agricultural & Environmental Letters

Secondary metabolite genes encoded by potato rhizosphere microbiomes in the Andean highlands are diverse and vary with sampling site and vegetation stage
Gajender Aleti et al. – Scientific Reports

Metagenomic-based impact study of transgenic grapevine rootstock on its associated virome and soil bacteriome
Jean-Michel Hilly et al. – Plant Biotechnology Journal

A Small Number of Low-abundance Bacteria Dominate Plant Species-specific Responses during Rhizosphere Colonization
Wayne Dawson et al. – Frontiers in Microbiology

Alpine soil carbon is vulnerable to rapid microbial decomposition under climate cooling
Linwei Wu et al. – The ISME Journal

Book chapter: Cannabis Endophytes and Their Application in Breeding and Physiological Fitness
Parijat Kusari et al. – Cannabis sativa L. – Botany and Biotechnology

Water, estuarine and sediment microbiome

Nutrient Stoichiometry Shapes Microbial Community Structure in an Evaporitic Shallow Pond
Zarraz M.-P. Lee et al. – Frontiers in Microbiology

Microbes influence the biogeochemical and optical properties of maritime Antarctic snow
Hodson, AJ et al. – Journal of Geophysical Research

Bacterial diversity in Shahu lake, northwest China is significantly affected by nutrient composition rather than location
Jing-Yu Li et al. – Annals of Microbiology

Built environment

Effects of triclosan on bacterial community composition and Vibrio populations in natural seawater microcosms
Keri Ann Lydon et al. – Elementa Science

Thesis: Characterization of Microbial Contaminants Associated with Floor Material Types
Mridula Gupta – The Ohio State University

Microbial biotechnology

Magnetotactic Coccus Strain SHHC-1 Affiliated to Alphaproteobacteria Forms Octahedral Magnetite Magnetosomes
Heng Zhang et al. – Frontiers in Microbiology

Abundance and diversity of ammonia-oxidizing archaea in a biological aerated filter process
Hongyi Chen et al. – Annals of Microbiology

Biochemical Mechanisms and Catabolic Enzymes Involved in Bacterial Estrogen Degradation Pathways
Yi-Lung Chen et al. – Cell Chemical Biology

An environment friendly engineered Azotobacter can replace substantial amount of urea fertilizer and yet sustain same wheat yield
Umesh K. Bageshwar et al. – Applied and Environmental Microbiology

Biofertilizers and sustainable agriculture: exploring arbuscular mycorrhizal fungi
Nicholas O. Igiehon & Olubukola O. Babalola – Applied Microbiology and Biotechnology

Food microbiology

Removal of foodborne pathogen biofilms by acidic electrolyzed water
Qiao Han et al. – Frontiers in Microbiology

General microbiology and evolution

Systematics of haloarchaea and biotechnological potential of their hydrolytic enzymes
Amoozegar MA et al. – Microbiology

Surface sensing for flagellar gene expression on solid media in Paenibacillus sp. NAIST15-1
Kazuo Kobayashi et al. – Applied and Environmental Microbiology

Complete genome sequence of a denitrifying bacterium, Pseudomonas sp. CC6-YY-74, isolated from Arctic Ocean sediment
Xuenzheng Lin et al. – Marine Genomics

Draft Genome Sequence of Acidihalobacter ferrooxidans DSM 14175 (Strain V8), a New Iron- and Sulfur-Oxidizing, Halotolerant, Acidophilic Species
Himel N. Khaleque et al. – Genome Announcements

Draft Genome Sequence of Saccharomonospora sp. Strain LRS4.154, a Moderately Halophilic Actinobacterium with the Biotechnologically Relevant Polyketide Synthase and Nonribosomal Peptide Synthetase Systems
Scarlett Alonso-Carmona et al. – Genome Announcements

Genome-Wide Analyses Reveal Genes Subject to Positive Selection in Pasteurella multocida
Peili Cao et al. – Frontiers in Microbiology

Phages and viruses

Review: Metagenomic Approaches to Assess Bacteriophages in Various Environmental Niches
Stephen Hayes et al. – Viruses

Bioinformatics and statistics

Predicting microbial interactions from time series data with network information
Yan Wang et al. – International Journal of Data Mining and Bioinformatics

Commentary: Bioinformatics can boost metabolomics research
René Meier et al. – Journal of Biotechnology

Techniques and methods

Thesis: Carbon dioxide titration method for soil respiration measurements
Luis Martín Rubio – Tampere University of Applied Sciences

Protocol: Harnessing the Power of PCR Molecular Fingerprinting Methods and Next Generation Sequencing for Understanding Structure and Function in Microbial Communities
Sujal Phadke et al. – PCR

An optimized extraction method to remove humic acids interferences from soil samples prior to microbial proteome measurements
Chen Qian & Robert L. Hettich – Journal of Proteome Research

Microbes in the news

Gene Drives Could Wipe Out Insect-Borne Disease — But What’s the Price?
Shelly Fan – Ontological Design

Non-microbiology picks

Application of mass spectrometry-based metabolomics approaches for food safety, quality and traceability
María Castro-Puyana et al. – Trends in Analytical Chemistry

Hunting for Nature’s Treasures or Learning from Nature?: The Narrative Ambivalence of the Ecotechnological Turn
Sanne van der Hout & Martin Drenthen – Berghahn Journals

What if you can workout while keeping cool with a pleasant smell ? In today’s post, read about researchers from MIT who have developed a ‘breathable workout suit’ using humidity-sensitive E.coli that can take care of cooling you down as you sweat.

Human vaginal microbiome

Early pregnancy vaginal microbiome trends and preterm birth – Stout MJ – Am J Obstet Gynecol.

Human gut microbiome

Chronic consequences on human health induced by microbial pathogens: Growth faltering among children in developing countries – Nataro JP – Vaccine

The gut-brain axis in Parkinson’s disease: Possibilities for food-based therapies – Perez-Pardo P – Eur J Pharmacol.

Animal experiments

Influence of Dietary Avocado on Gut Health in Rats – Paturi G – Plant Foods Hum Nutr.

Review:
Transcriptional networks in rodent models support a role for gut-brain communication in neurogenic hypertension: A review of the evidence – Zubcevic J – Physiol Genomics

Plant, root, and soil microbiome

Review: Let the Core Microbiota Be Functional – Lemanceau P – Trends Plant Sci.

An environment friendly engineered Azotobacter can replace substantial amount of urea fertilizer and yet sustain same wheat yield – Umesh K. Bageshwar – Appl Environ Microbiol.
High-resolution analyses reveal structural diversity patterns of microbial communities in Chromite Ore Processing Residue (COPR) contaminated soils – Min X – Chemosphere

Built environment
Pathways in bacterial and archaeal communities dictated by ammonium stress in a high solid anaerobic digester with dewatered sludge – Li N – Bioresour Technol.

Microbes in the news
Experimental athletic shirt uses bacteria to keep you cool during workouts – eParisExtra
Gut Bacteria Changes After Some Weight-Loss Surgeries – tucson.com