Today’s digest features a review on the major mechanisms by which the intestinal microbiota confers protection against infections, studies showing that depression alters gut microbiota while sleep restriction over several consecutive days does not overtly influence the composition of the microbiome.

General microbiome

Microbial communities change in an anaerobic digestion after application of microbial electrolysis cells – Beom Leea – Bioresource Technology

Perspective: Sharpening host defenses during infection: Proteases cut to the chase – Natalie C Marshall – Molecular and cellular proteomics

Review: Recent advances in genetic modification systems for Actinobacteria – Yu Deng – Applied Microbiology and Biotechnology

Preprint: Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica – Zhemin Zhou – bioRxiv

Preprint: In vivo structures of an intact type VI secretion system revealed by electron cryotomography – Yi-Wei Chang – bioRxiv

Eco-evolutionary feedbacks can rescue cooperation in microbial populations – Clara Moreno-Fenoll – Scientific Reports

Pregnancy and early life

Getting organized early in life – Andrea Du Toit – Nature Reviews Microbiology

Infant fungal communities: current knowledge and research opportunities – Tonya L. Ward – BMC Medicine

Human respiratory microbiome

IL-36γ is a crucial proximal component of protective type-1-mediated lung mucosal immunity in Gram-positive and -negative bacterial pneumonia – M A Kovach – MucosalImmunology

Longitudinal assessment of sputum microbiome by sequencing of the 16S rRNA gene in non-cystic fibrosis bronchiectasis patients – Michael J. Cox – PLoS ONE

Human skin microbiome

The Role of Cutaneous Microbiota Harmony in Maintaining a Functional Skin Barrier – Hilary E. Baldwin MD – Journal of Drugs in Dermatology

Preprint: Evolutionary and functional implications of hypervariable loci within the skin virome – Geoffrey D. Hannigan – PeerJ

Human vaginal microbiome

Diversity and composition of vaginal microbiota of pregnant women at risk for transmitting Group B Streptococcus treated with intrapartum penicillin – Luiz Fernando Wurdig Roesch – PLoS ONE

Influence of contraceptive choice on vaginal bacterial and fungal microflora – G. Donders – European Journal of Clinical Microbiology & Infectious Diseases

Human gut microbiome

Human and rat gut microbiome composition is maintained following sleep restriction – Shirley L. Zhang – PNAS

Reduction of Abeta amyloid pathology in APPPS1 transgenic mice in the absence of gut microbiota – T. Harach – Scientific Reports

Gut to Brain Dysbiosis: Mechanisms Linking Western Diet Consumption, the Microbiome, and Cognitive Impairment – Emily E. Noble – Frontiers in Behavioural Neuroscience

Parkinson’s disease and Parkinson’s disease medications have distinct signatures of the gut microbiome – Erin M. Hill-Burns – Movement Disorders

Persepctive: Diet-induced dysmotility and neuropathy in the gut precedes endotoxaemia and metabolic syndrome: the chicken and the egg revisited – Yvonne Elikplim – The Journal of Physiology

Editorial: Gut–brain axis, psychobiotics, and mental health – Arpit Parmar – Asian Journal of Psychiatry

Comparative study on the in vitro effects of Pseudomonas aeruginosa and seaweed alginates on human gut microbiota – Shaofeng Bai – PLoS ONE

Role of the Gut Microbiome in the Pathogenesis of Obesity and Obesity-Related Metabolic Dysfunction – Kristien E. Bouter – Gastroenterology

Variations in gut microbiota and fecal metabolic phenotype associated with depression by 16S rRNA gene sequencing and LC/MS-based metabolomics – Meng Yu – Journal of Pharmaceutical and Biomedical Analysis

Revised computational metagenomic processing uncovers hidden and biologically meaningful functional variation in the human microbiome – Ohad Manor – Microbiome

Review: Roles of the intestinal microbiota in pathogen protection – Carles Ubeda – Clinical & Translational Immunology

Antibiotic-Induced Depletion of Anti-Inflammatory Clostridia is Associated with the Development of GVHD in Pediatric Stem Cell Transplant Patients – Tiffany R. Simms-Waldrip – Biology of Blood and Marrow Transplantation

Molecular analysis of the human faecal archaea in a southern Indian population – Sandya B Rani – Journal of Biosciences

Elimination diets’ efficacy and mechanisms in attention deficit hyperactivity disorder and autism spectrum disorder – Verena Ly – European Child & Adolescent Psychiatry

Differences in gut metabolites and microbial composition and functions between Egyptian and U.S. children are consistent with their diets – Shankar V – mSystems
also in the news by ASM

Animal experiments

Comparison of the microbial population in rabbits and guinea pigs by next generation sequencing – Edward J. Crowley – PLoS ONE

Development and validation of a new dynamic in vitro model of the piglet colon (PigutIVM): application to the study of probiotics – Mickaël Alain Fleury – Applied Microbiology and Biotechnology

Effects of dietary nutrient levels on microbial community composition and diversity in the ileal contents of pregnant Huanjiang mini-pigs – Yujiao Ji – PLoS ONE

Nopal feeding reduces adiposity, intestinal inflammation and shifts the cecal microbiota and metabolism in high-fat fed rats – Sofia Moran-Ramos – PLoS ONE
Animal microbiome

Comparative study of the gut microbiome potentially related to milk protein in Murrah buffaloes (Bubalus bubalis) and Chinese Holstein cattle – Jiachao Zhang – Scientific Reports

Meta-analysis to estimate the load of Leptospira excreted in urine: beyond rats as important sources of transmission in low-income rural communities – Veronica Barragan – BMC Research Notes

Plant, root, and soil microbiome

The microbe-secreted isopeptide poly-γ-glutamic acid induces stress tolerance in Brassica napus L. seedlings by activating crosstalk between H2O2 and Ca2+ – Peng Lei – Scientific Reports

Paenibacillus polymyxa NSY50 suppresses Fusarium wilt in cucumbers by regulating the rhizospheric microbial community – Lu Shi – Scientific Reports

Community-level physiological profiling analyses show potential to identify the copiotrophic bacteria present in soil environments – Salvador Lladó – PLoS ONE

Pseudomonas protegens CS1 from the lemon phyllosphere as a candidate for citrus canker biocontrol agent – G. Michavila – Plant biology

Role and Regulation of ACC Deaminase Gene in Sinorhizobium meliloti: Is It a Symbiotic, Rhizospheric or Endophytic Gene? – Alice Checcucci – Frontiers in Genetics

Use of endophytic and rhizosphere bacteria to improve phytoremediation of arsenic-contaminated industrial soils by autochthonous Betula celtiberica – Victoria Mesa – Applied and Environmental Microbiology

Bioaugmentation with bacteria selected from the microbiome enhances Arthrocnemum macrostachyum metal accumulation and tolerance – Salvadora Navarro-Torre – Marine Pollution Bulletin

Proteotyping of laboratory-scale biogas plants reveals multiple steady-states in community composition – F. Kohrs – Anaerobe

Soil microbial communities alter leaf chemistry and influence allelopathic potential among coexisting plant species – Scott J. Meiners – Oecologia

Review: Abiotic stress responses and microbe-mediated mitigation in plants: The omics strategies – Kamlesh K. Meena – Frontiers in Plant Science

Complete genome analysis of Serratia marcescens RSC-14: A plant growth-promoting bacterium that alleviates cadmium stress in host plants – Abdur Rahim Khan – PLoS ONE

Wildfire impact: Natural experiment reveals differential short-term changes in soil microbial communities – Miranda T. Prendergast-Miller – Soil Biology and Biochemistry

Diverse microbial communities in non-aerated compost teas suppress bacterial wilt – W. K. Mengesha – World Journal of Microbiology and Biotechnology

Fumigation with dazomet modifies soil microbiota in apple orchards affected by replant disease – Lidia Nicola – Applied Soil Ecology

Arbuscular mycorrhiza enhance the rate of litter decomposition while inhibiting soil microbial community development – Heng Gui – Scientific Reports

Apple replant disorder of Pingyitiancha rootstock is closely associated with rhizosphere fungal community development – Jian Sun – Jounral of Phytopathology

Changes in soil bacterial communities in an evergreen broad-leaved forest in east China following 4 years of nitrogen addition – Jun Cui – Journal of Soils and Sediments

Distinct biogeographic patterns for archaea, bacteria, and fungi along the vegetation gradient at the continental scale in eastern China – Bin Ma – mSystems

Insight into the effects of different cropping systems on soil bacterial community and tobacco bacterial wilt rate – Jiaojio Niu – Journal of Basic Microbiology
Water and extremophile microbiome

Dimethylsulfoniopropionate biosynthesis in marine bacteria and identification of the key gene in this process – Andrew R. J. Curson – Nature Microbiology

Metagenomic survey of the taxonomic and functional microbial communities of seawater and sea ice from the Canadian Arctic – Etienne Yergeau – Scientific Reports

Response of deep subsurface microbial community to different carbon sources and electron acceptors during ~two months incubation in microcosms – Lotta Purkamo – Frontiers in Microbiology

Bacterial community dynamics are linked to patterns of coral heat tolerance – Maren Ziegler – Nature Communications

Preprint: Habitat generalists or specialists, insights from comparative genomic analyses of Thermosipho lineages – Thomas H.A. Haverkamp – bioRxiv

Culture scale-up and immobilisation of a mixed methanotrophic consortium for methane remediation in pilot-scale bio-filters – Obulisamy Parthiba Karthikeyan – Environmental technology

Effect of different enrichment strategies on microbial community structure in petroleum-contaminated marine sediment in Dalian, China – Chao Chen – Marine Pollution Bulletin

Microbial catabolic diversity in and beyond the rhizosphere of plant species and plant genotypes – Karst M. Brolsmaa – Pedobiologia

Preprint: Shifting microbial communities sustain multi-year iron reduction and methanogenesis in ferruginous sediment incubations – Marcus S Bray – bioRxiv

Bioinformatics

A multi-objective constraint-based approach for modeling genome-scale microbial ecosystems – Marko Budinich – PLoS ONE

Modelling functional resilience of microbial ecosystems: Analysis of governing processes – Sara König – Environmental Modelling & Software

An integrative Bayesian Dirichlet-multinomial regression model for the analysis of taxonomic abundances in microbiome data – W. Duncan Wadsworth – BMC Bioinformatics

Techniques

Metabolomics: A Primer – Xiaojing Liu – Trends in biochemical sciences

Fluorescence Lectin Bar-Coding of Glycoconjugates in the Extracellular Matrix of Biofilm and Bioaggregate Forming Microorganisms – Thomas R. Neu – Microorganisms

Microbes in the news

Experts reveal how the microbiome in your gut is linked to weight gain and health disorders – Leah Hardy – MailOnline
Will cities of the future embrace bacteria? – Starre Vartan- MNN.com

Microbes on the market

FDA Turmoil, Biology Mystery On List Of Hurdles For Microbiome Drugs – Ben Fidler – exome

Science, publishing, and career

FICUS JGI-NERSC Microbiome Data Science Call for Proposals (Open till 1st of March)

Events and jobs
Postdoctoral research fellow in Microbiome Research – Karolinska Institutet

Postdoctoral Scientist ( Microbiome, Mycobiome, Mucosal Immunology) – Jill Roberts Institute for Research in IBD at Weill Cornell Medicine, New York City

Senior Lecturer in Food Microbiology – RMIT Bundoora Campus

Junior Specialist in Environmental Microbiology – University of California, Santa Cruz

General microbiome
Uncharacterized bacterial structures revealed by electron cryotomography – Megan J Dobro – bioRxiv

Pregnancy and early life
Review: Infant fungal communities: current knowledge and research opportunities – Tonya L. Ward – BMC Medicine

Human gut microbiome
A prominent glycyl radical enzyme in human gut microbiomes metabolizes trans-4-hydroxy-l-proline – B.J. Levin – Science
Also described in this short article: New tool can help researchers identify enzymes—and their abundance—in microbiomes – Phys.org

Dynamics of the human gut microbiome in inflammatory bowel disease – Jonas Halfvarson – Nature Microbiology

Inediibacterium massiliense gen. nov., sp. nov., a new bacterial species isolated from the gut microbiota of a severely malnourished infant – Maryam Tidjani Alou – Antonie van Leewenhoek

Animal microbiome
The microbiome of bulk tank milk: Characterization and associations with somatic cell count and bacterial count – M.X. Rodrigues – Journal of Dairy Science

Dynamics of the microbiota found in the vaginas of dairy cows during the transition period: Associations with uterine diseases and reproductive outcome – M.L.S. Bicalho – Journal of Dairy Science

Prophylactic use of a standardized botanical extract for the prevention of naturally occurring diarrhea in newborn Holstein calves – A.G.V. Teixeira – Journal of Dairy Science

Plant, root, and soil microbiome
Four years of experimental warming do not modify the interaction between subalpine shrub species – Alba Anadon-Rosell – Oecologia

Response to nitrogen addition reveals metabolic and ecological strategies of soil bacteria – Md Sainur Samad – bioRxiv

Water and extremophile microbiome
Dimethylsulfoniopropionate biosynthesis in marine bacteria and identification of the key gene in this process – Andrew R.J. Curson – Nature Microbiology
This is summed up in the short article: Marine bacteria produce an environmentally important molecule with links to climate – Phys.org

Structural dynamics of microbial communities in polycyclic aromatic hydrocarbon-contaminated tropical estuarine sediments undergoing simulated aerobic biotreatment – Chioma C. Obi – Applied Microbiology and Biotechnology

Diversity and community composition of particle-associated and free-living bacteria in mesopelagic and bathypelagic Southern Ocean water masses: Evidence of dispersal limitation in the Bransfield Strait – Mathias Milici – Limnology and Oceanography

Proteotyping of biogas plant microbiomes separates biogas plants according to process temperature and reactor type – R. Heyer – Biotechnology for Biofuels

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

Reclamation of Chinese herb residues using probiotics and evaluation of their beneficial effect on pathogen infection – Fanjing Meng – Journal of Infection and Public Health

Probiotic dietary supplementation in Nile tilapia as prophylaxis against streptococcosis – M.M. Yamashita – Aquaculture Nutrition

Phages and viruses
Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families – Jemma L. Geoghegan – PLoS Pathogens

Plaques formed by mutagenized viral populations have elevated co-infection frequencies – Elizabeth R. Aguilera – bioRxiv

Bioinformatics
dRep: A tool for fast and accurate genome de-replication that enables tracking of microbial genotypes and improved genome recovery from metagenomes – Matthew R Olm – bioRxiv

ROCker: accurate detection and quantification of target genes in short-read metagenomic data sets by modeling sliding-window bitscores – Luis H. Orellana – Nucleic Acids Research

Techniques
A real-time PCR assay for accurate quantification of the individual members of the Altered Schaedler Flora microbiota in gnotobiotic mice – Joao Carlos Gomes-Neto – Journal of Microbiological Methods

Neutral and niche dynamics in a synthetic microbial community – NJ Cira – bioRxiv

Microbes in the news
“Archaea” unites University on sesquicentennial – Tess O’Brien – The Daily Illini (student newspaper at University of Illinois)

How to quickly identify sepsis-causing bacteria – melt it down – Lisa-Ann Lee – New Atlas
The paper referenced is Nested Machine Learning Facilitates Increased Sequence Content for Large-Scale Automated High Resolution Melt Genotyping – Stephanie I. Fraley – Scientific Reports

Chemical engineers boost bacteria’s productivity – phys.org
The paper referenced is Dynamic regulation of metabolic flux in engineered bacteria using a pathway-independent quorum-sensing circuit – Apoorv Gupta – Nature Biotechnology

Microbes on the market
Human Microbiome Market is Expecting Worldwide Growth by 2020 – Persistence Market Research Study

Ritter Pharmaceuticals Announces Collaboration with University of British Columbia to Explore Development of Microbiome Therapeutics in Environmental Enteropathy – Yahoo Finance

Science, publishing, and career
The Troll Taunter – Andrew McMillen – BackChannel
This is an amazing piece: “But on that Friday night, Temple-Wood had an idea. For every harassing email, death threat, or request for nude photos that she received, she resolved to create a Wikipedia biography on a notable woman scientist who was previously unknown to the free online encyclopedia.”

Do’s and don’ts for scientists who want to shape policy – Erik Stokstad – Science

Scientists should be political but not partisan – Angela de Pace – Medium

Today ‘s digest features a roundworm as a new model of host-microbiota interactions, a new theory on apple replant disease, and a double-blinded, placebo-controlled, crossover-designed probiotic trial on Japanese medical students. Also, an interesting study on how an active lifestyle promotes growth of Faecalibacterium prausnitzii, Roseburia hominis and Akkermansia muciniphila commensals in women when compared to a sedentary lifestyle. Stay active!

General microbiome

C. elegans and its bacterial diet as a model for systems-level understanding of host–microbiota interactions – Jingyan Zhang – Current Opinion in Biotechnology

Microbial Respiration and Formate Oxidation as Metabolic Signatures of Inflammation-Associated Dysbiosis – Elizabeth R. Hughes – Cell Host & Microbe

Metagenomic and metatranscriptomic analyses reveal structure and dynamics of a dechlorinating community containing Dehalococcoides mccartyi and corrinoid-providing microorganisms under cobalamin-limited condition – Yujie Men – Applied and Environmental Microbiology

Human respiratory microbiome

Sputum DNA sequencing in cystic fibrosis: non-invasive access to the lung microbiome and to pathogen details – Rounak Feigelman – Microbiome

Human gut microbiome

Review: Role of the Gut Microbiome in the Pathogenesis of Obesity and Obesity-Related Metabolic Dysfunction – Kristien E. Bouter – Gastroenterology

*Differences in gut microbiota profile between women with active lifestyle and sedentary women. – Carlo Bressa – PLoS One

Animal experiments

Secondary bile acid-induced dysbiosis promotes intestinal carcinogenesis – Hailong Cao – International Journal of Cancer

Enteric helminth-induced type-I interferon signalling protects against pulmonary virus infection through interaction with the microbiota – Amanda J. McFarlane – Journal of Allergy and Clinical Immunology

Berberine-induced bioactive metabolites of the gut microbiota improve energy metabolism – Yan Wang – Metabolism

Plant, root, and soil microbiome

Use of endophytic and rhizosphere bacteria to improve phytoremediation of arsenic-contaminated industrial soils by autochthonous Betula celtiberica. – Victoria Mesa – Applied and Environmental Microbiology

Fumigation with dazomet modifies soil microbiota in apple orchards affected by replant disease – Lidia Nicola – Applied Soil Ecology

Food microbiology

Review: Non-dairy Based Probiotics: A Healthy Treat for Intestine. – Sangita Bansal –
Critical Reviews in Food Science and Nutrition

Probiotics / prebiotics

Daily intake of Lactobacillus gasseri CP2305 improves mental, physical, and sleep quality among Japanese medical students enrolled in a cadaver dissection course – Daisuke Sawada – Journal of Functional Foods

Bioinformatics

Recovery of genomes from metagenomes via a dereplication, aggregation, and scoring strategy – Christian M.K. Sieber – bioRxiv

Being Sunday there aren’t that many publications to talk about. However the study by Zheng and colleagues makes up for it and is a must read! A bit like BCG for bladder cancer they engineered bacteria to induce an effective antitumor immune response, successfully treating tumors in several different mouse models with no evidence of toxicity. In another interesting study, Harach et al demonstrate microbial involvement in the development of Abeta amyloid pathology, and suggest that microbiota may contribute to the development of neurodegenerative diseases.

General microbiome

*Two-step enhanced cancer immunotherapy with engineered Salmonella typhimurium secreting heterologous flagellin – Jin Hai Zheng – Science Translational Medicine

Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica –  Zhemin Zhou – bioRxiv

A target-specific assay for rapid and quantitative detection of Mycobacterium chimaera DNA in environmental and clinical specimens – Enrique Zozaya-Valdes – bioRxiv

Human gut microbiome

*Reduction of Abeta amyloid pathology in APPPS1 transgenic mice in the absence of gut microbiota – T. Harach –  Scientific Reports

Gut bacteria may play a role in Alzheimer’s disease –  Science Daily

Water and extremophile microbiome 

A survey of microparasites present in adult migrating Chinook salmon (Oncorhynchus tshawytscha) in south-western British Columbia determined by high-throughput quantitative polymerase chain reaction – A L Bass – Journal of Fish Disease

Distinct Biogeographic Patterns for Archaea, Bacteria, and Fungi along the Vegetation Gradient at the Continental Scale in Eastern China – B Ma – mSystems

Bioinformatics

OptiClust: Improved method for assigning amplicon-based sequence data to operational taxonomic units – Sarah L Westcott – bioRxiv

 Microbes in the news 

Gut Microbiota Improved when Eating Whole Grains – Council Chronicle

Feeding probiotics to rats before stressing them out reduces disruption of gut microbiota – The Indian Express

Researchers develop new method that can rapidly profile resistome of gut microbial communities – News Medical

Changes in the gut microbiota during aging is associated with increased gut permeability and peripheral inflammation and may mediate cognitive decline. An overview of the gut microbiome in Crohn’s Disease and insight into how extremophiles might maintain protein folding. 

General microbiome

Whole genome sequence of lactic acid bacterium Pediococcus acidilactici strain S1 – Gun-Seok Park – Brazilian Journal of Microbiology

‘Pygmaiobacter massiliensis’ sp. nov., a new bacterium isolated from the human gut of a Pygmy woman – M. Bilen – NMNI

Human and rat gut microbiome composition is maintained following sleep restriction – Zhang SL – PNAS

Palaeogeographic variation in the Permian−Triassic boundary microbialites: A discussion of microbial and ocean processes after the end-Permian mass extinction – Stephen Kershaw – Journal of Palaeogeography

Assessment of bacterial profiles in aged, home-made Sichuan paocai brine with varying titratable acidity by PacBio SMRT sequencing technology – Jialu Cao – Food Control

Human gut microbiome

Differences in Gut Metabolites and Microbial Composition and Functions between Egyptian and U.S. Children Are Consistent with Their Diets  – V. Shankar – mSystems

*PrePrint:  Postmortem succession of gut microbial communities in human cadavers – Jennifer M DeBruyn – PeerJ Preprints

Substituting whole grains for refined grains in a 6-wk randomized trial has a modest effect on gut microbiota and immune and inflammatory markers of healthy adults – Vanegas SM – American Journal of Clinical Nutrition

Altered molecular signature of intestinal microbiota in irritable bowel syndrome patients compared with healthy controls: A systematic review and meta-analysis – Hai-Ning Liu – Digestive and Liver Disease

Animal experiments 

Revisiting Metchnikoff: Age-related Alterations in Microbiota-Gut-Brain Axis in the Mouse – Karen A. Scott – Brain, Behavior, and Immunity

Animal microbiome 

Immune system stimulation by the native gut microbiota of honey bees – Waldan K. Kwong – Royal Society for Open Science

Deep Sequencing Reveals Highly Variable Gut Microbial Composition of Invasive Fish Mossambicus Tilapia (Oreochromis mossambicus) Collected from Two Different Habitats – Swapnil Sopan Gaikwad – Indian Journal of Microbiology

The gastrointestinal tract microbiota of the Japanese quail, Coturnix japonica –  Ngare Wilkinson – Environmental Biotechnology

Plant, root, and soil microbiome

Hydrogen Peroxide and Strigolactones Signaling Are Involved in Alleviation of Salt Stress Induced by Arbuscular Mycorrhizal Fungus in Sesbania cannabina Seedlings – Cun-Cui Kong – Journal of Plant Growth Regulation

Potential Role of Plant-Associated Bacteria in Plant Metal Uptake and Implications in Phytotechnologies – Petra S. Kidd – Advances in Botanical Research

Application of bacteria from non-cultivated plants to promote growth, alter root architecture and alleviate salt stress of cotton – Ivelisse Irizarry – Journal of Applied Microbiology

Water and extremophile microbiome 

Molecular determinant of the effects of hydrostatic pressure on protein folding stability – Calvin R. Chen – Nature Communications

Microarray analysis of the benthic bacterium Shewanella piezotolerans WP3 at low temperature – Huahua Jian – Marine Genomics

Metagenomic exploration of microbial community in mine tailings of Malanjkhand copper project, India – Abhishek Gupta – Genomics Data

Illumina sequencing-based analysis of sediment bacteria community in different trophic status freshwater lakes – Yu Wan – Microbiology Open

Variations in airborne bacterial communities at high altitudes over the Noto Peninsula (Japan) in response to Asian dust events – Teruya Maki – Atmospheric Chemistry and Physics Discussions

Phages and viruses

Viruses comprise an extensive pool of mobile genetic elements in eukaryote cell cultures and human clinical samples – Thannesberger J – The FASEB Journal

Techniques

Community-level physiological profiling analyses show potential to identify the copiotrophic bacteria present in soil environments – Salvador Llado – PLOS one

Cultivation-Free Raman Spectroscopic Investigations of Bacteria – Björn Lorenz – Trends in Microbiology

*Review:  Proteomics Tracing the Footsteps of Infectious Disease – Todd M Greco – Molecular and Cellular Proteomics

Metabolomics as a Challenging Approach for Medicinal Chemistry and Personalized Medicine – Michel Fredérich – Journal of Medical Chemistry

An integrative Bayesian Dirichlet-multinomial regression model for the analysis of taxonomic abundances in microbiome data – Wadsworth WD – BMC Bioinformatics

Microbes on the market 

General microbiome

*Review: Gut microbiota and acute coronary syndromes: ready for use in the emergency room? – Trøseid M. – Eur Heart J

Review: Fecal Microbiota Transplant versus Oral Vancomycin Taper: Important Undiscussed Limitations. – Jansen JW – Clin Infect Dis

Review: Fecal Microbiota Transplantation: do we need harmonization? – Galpérine T – Clin Infect Dis

Fecal microbiota transplantation in patients with slow-transit constipation: A randomized, clinical trial. – Tian H – PLoS One

Listeriolysin S: a bacteriocin from epidemic Listeria monocytogenes strains that targets the microbiota. – Quereda-Torres JJ – Gut Microbes

*Possible Alternative Predictors of Failure of Fecal Microbiota Transplant for Therapy of Recurrent C difficile Infection. – Bodiwala V – Am J Gastroenterol

Repeated fecal microbiota transplantations attenuate diarrhea and lead to sustained changes in the fecal microbiota in acute, refractory gastrointestinal graft-versus-host-disease. – Spindelboeck W – Haematologica

Review: Gastrointestinal Immune and Microbiome Changes During Parenteral Nutrition. – Pierre JF –  Am J Physiol Gastrointest Liver Physiol.

Microbiome sharing between children, livestock and household surfaces in western Kenya. – Mosites E – PLoS One

Pregnancy and early life

Oral yeast colonization throughout pregnancy. – Rio R – Med Oral Patol Oral Cir Bucal

Review: Human Milk Oligosaccharides and the Preterm Infant: A Journey in Sickness and in Health. – Moukarzel S – Clin Perinatol

Loss of cutaneous microbial diversity during first three weeks of life in very low birth weight infants. – Salava A – Exp Dermatol

The Fecal Microbial Community of Breast-fed Infants from Armenia and Georgia. – Lewis ZT – Sci Rep

Antibiotic resistance potential of the healthy preterm infant gut microbiome. – Rose G – PeerJ

Multi-site human microbiome

Review: From Evolutionary Advantage to Disease Agents: Forensic Reevaluation of Host-Microbe Interactions and Pathogenicity. – Rivera-Pérez JI – Microbiol Spectr

Human respiratory microbiome

*Microbes Associate with Host Innate Immune Response in Idiopathic Pulmonary Fibrosis. – Huang Y – Am J Respir Crit Care Med

Human gut microbiome

Review: The Enigmatic Gut in Cystic Fibrosis: Linking Inflammation, Dysbiosis, and the Increased Risk of Malignancy. – Garg M – Curr Gastroenterol Rep

Involvement of gut microbiota in the association between GLP-1/GLP-1 receptor expression and gastrointestinal motility. – Yang M – Am J Physiol Gastrointest Liver Physiol

*Novel insight into the role of microbiota in colorectal surgery. – Bachmann R – Gut

*Race-dependent association of sulfidogenic bacteria with colorectal cancer. –  Yazici C – Gut

Review: The “gut microbiota” hypothesis in primary sclerosing cholangitis. – Pontecorvi V – Ann Transl Med

Review: The development and role of microbial-host interactions in gut mucosal immune development. – Stokes CR – J Anim Sci Biotechnol

Yogurt Containing Lactobacillus gasseri Mitigates Aspirin-Induced Small Bowel Injuries: A Prospective, Randomized, Double-Blind, Placebo-Controlled Trial. – Suzuki T – Digestion

Animal experiments 

Dietary fibres modulate the composition and activity of butyrate-producing bacteria in the large intestine of suckling piglets – Mu C – Antonie Van Leeuwenhoek

Drunk Bugs: Chronic Vapour Alcohol Exposure Induces Marked Changes in the Gut Microbiome in Mice. – Peterson VL – Behav Brain Res

Microscopic Evaluation of the Effect of Oral Microbiota on the Development of Bisphosphonate-Related Osteonecrosis of the Jaws in Rats. – Silveira FM – J Oral Maxillofac Res

Animal microbiome

The bovine colostrum microbiome and its association with clinical mastitis. – Lima SF – J Dairy Sci

Bacterial bile salt hydrolase: an intestinal microbiome target for enhanced animal health. – Geng W – Anim Health Res Rev

Functional analysis for gut microbes of the brown tree frog (Polypedates megacephalus) in artificial hibernation. – Weng FC – BMC Genomics

Plant, root, and soil microbiome

Dairy propionibacteria prevent the proliferative effect of plant lectins on SW480 cells and protect the metabolic activity of the intestinal microbiota in vitro. – Zárate G – Anaerobe

Probiotics / prebiotics

Review: Potential Beneficial Effects of Probiotics on Human Migraine Headache: A Literature Review. – Dai YJ – Pain Physician

Bioinformatics

Robust Inference of Genetic Exchange Communities from Microbial Genomes Using TF-IDF. – Cong Y – Front Microbiol

Techniques

A quantitative SMRT cell sequencing method for ribosomal amplicons. – Jones BM – J Microbiol Methods

RiboTagger: fast and unbiased 16S/18S profiling using whole community shotgun metagenomic or metatranscriptome surveys. – Xie C – BMC Bioinformatics

Survey of (Meta)genomic Approaches for Understanding Microbial Community Dynamics. – Sharma A – Indian J Microbiol

Microbe in the news

Malin takes 33% Stake in Start-Up Microbiome Targeting Firm Artizan – Genetic Engineering & Biotechnology News (blog)

A Pilot Study Assessing Intestinal Microbiota Diversification and Changes After Travel to South(East) Asia From the US – Satellite PR News (press release)