February 24, 2018

100+ alerts today with interesting papers across every category. Some highlights include choosing FMT donors, viral insulin-like peptides, and 2 papers on detecting duplicated figures.

General microbiome
Review: The microbiome in precision medicine: the way forward. – Joseph F Petrosino – Genome Medicine

Motivations of participants in the citizen science of microbiomics: data from the British Gut Project. – Lorenzo Del Savio – Genetics In Medicine : Official Journal Of The American College Of Medical Genetics

Pregnancy and early life
The Role of the Genitourinary Microbiome in Pediatric Urology: a Review. – Daniel Gerber – Current Urology Reports

Review: Reproductive outcome of patients undergoing in vitro fertilization treatment and diagnosed with bacterial vaginosis or abnormal vaginal microbiota: a systematic PRISMA review and meta-analysis. – Thor Haahr – Bjog : An International Journal Of Obstetrics And Gynaecology

Multi-site human microbiome
Review: The Vagus Nerve at the Interface of the Microbiota-Gut-Brain Axis. – Bruno Bonaz – Frontiers In Neuroscience

Human vaginal microbiome
Protein Content of Cervicovaginal Fluid Is Altered During Bacterial Vaginosis. – Carolina Sanitá Tafner Ferreira – Journal Of Lower Genital Tract Disease

Human nearly-sterile sites
Microbiome-Host Interactions in Hematopoietic Stem-Cell Transplant Recipients. – Tessa Andermann – Biology Of Blood And Marrow Transplantation : Journal Of The American Society For Blood And Marrow Transplantation

Human gut microbiome
** Competitively Selected Donor Fecal Microbiota Transplantation: Butyrate Concentration and Diversity as Measures of Donor Quality. – Danielle Barnes – Journal Of Pediatric Gastroenterology And Nutrition

Metagenomic Characterization of the Human Intestinal Microbiota in Fecal Samples from STEC-Infected Patients. – Federica Gigliucci – Frontiers In Cellular And Infection Microbiology

ReviewHuman Gut Microbiota and Gastrointestinal Cancer. – Changting Meng – Genomics, Proteomics & Bioinformatics

Review: Impact of the Gut Microbiota on Intestinal Immunity Mediated by Tryptophan Metabolism. – Jing Gao – Frontiers In Cellular And Infection Microbiology

Microbial interactions
Competitive resource allocation to metabolic pathways contributes to overflow metabolisms and emergent properties in cross-feeding microbial consortia. – Ross P Carlson – Biochemical Society Transactions

Worlds Apart – Transcriptome Profiles of Key Oral Microbes in the Periodontal Pocket Compared to Single Laboratory Culture Reflect Synergistic Interactions. – Zhi-Luo Deng – Frontiers In Microbiology

Using niche breadth theory to explain generalization in mutualisms – Rebecca T. Batstone – Ecology

Metabolic division of labor in microbial systems – Ryan Tsoi – PNAS

Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle – Karthik Anantharaman – ISME

Review: Bacterial – Fungal Interactions: ecology, mechanisms and challenges. – A Deveau – Fems Microbiology Reviews

Role of extracellular polymeric substances in polymicrobial biofilm infections of Staphylococcus epidermidis and Candida albicans modelled in the nematode Caenorhabditis elegans. – Jillian E Holt – Pathogens And Disease (older, from July 2017)

Animal experiments
Acute and repeated exposure to social stress reduces gut microbiota diversity in Syrian hamsters. – Katherine A Partrick – Behavioural Brain Research

1H NMR based identification of intestinally-absorbed metabolites by Ussing chamber analysis of the rat cecum. – Meredith Dinges – Analytical Chemistry

Influence of gemcitabine chemotherapy on the microbiota of pancreatic cancer xenografted mice. – Concetta Panebianco – Cancer Chemotherapy And Pharmacology

Grape seed proanthocyanidins influence gut microbiota and enteroendocrine secretions in female rats. – Àngela Casanova-Martí – Food & Function

Combined Dietary Anthocyanins, Flavonols, and Stilbenoids Alleviate Inflammatory Bowel Disease Symptoms in Mice. – Aurelia Scarano – Frontiers In Nutrition

Ubc9 overexpression and SUMO1 deficiency blunt inflammation after intestinal ischemia/reperfusion. – Jörn Karhausen – Laboratory Investigation; A Journal Of Technical Methods And Pathology

Glucocorticosteroids and ciclosporin do not significantly impact canine cutaneous microbiota. – Giovanni Widmer – Bmc Veterinary Research

The effects of high dose of two manganese supplements (organic and inorganic) on the rumen microbial ecosystem. – Svetlana Kišidayová – Plos One

Hydrogen peroxide production by lactobacilli promotes epithelial restitution during colitis. – Ashish K Singh – Redox Biology

Neuroprotective effects of fecal microbiota transplantation on MPTP-induced Parkinson’s disease mice: gut microbiota, glial reaction and TLR4/TNF-α signaling pathway. – Meng-Fei Sun – Brain, Behavior, And Immunity

Rotenone induces gastrointestinal pathology and microbiota alterations in a rat model of Parkinson’s disease. – Michaela E Johnson – Neurotoxicology

Prenatal Androgen Exposure Causes Hypertension and Gut Microbiota Dysbiosis. – Shermel Sherman – Gut Microbes

Dominance of Endozoicomonas bacteria throughout coral bleaching and mortality suggests structural inflexibility of the Pocillopora verrucosa microbiome – Claudia Pogoreutz – Ecology And Evolution

Gut microbiota modulates adoptive cell therapy via CD8α dendritic cells and IL-12. – Mireia Uribe-Herranz – Jci Insight

Animal microbiome
Spatial Heterogeneity and Co-occurrence of Mucosal and Luminal Microbiome across Swine Intestinal Tract. – Li Zhang – Frontiers In Microbiology

Characterization of gut bacterial flora of Apis mellifera from north-west Pakistan – Syed Ishtiaq Anjum – Saudi Journal Of Biological Sciences

A Member of the Roseobacter Clade, Octadecabacter sp., is the Dominant Symbiont in the Brittle Star Amphipholis squamata. – Kathleen M Morrow – Fems Microbiology Ecology

Alimentary microbes of winter-form Drosophila suzukii. – M T Fountain – Insect Molecular Biology

The development of gut microbiota in ostriches and its association with juvenile growth – Elin Videvall – bioRxiv

Review: Regulation of intestinal health by branched-chain amino acids. – Hua Zhou – Animal Science Journal = Nihon Chikusan Gakkaiho

Book chapter: Termite Gut Microbiome – Navodita Maurice – Sustainability in Plant and Crop Protection

Plant, root, and soil microbiome
Compositional shifts in root-associated bacterial and archaeal microbiota track the plant life cycle in field-grown rice. – Joseph A Edwards – Plos Biology

Quantitative Genetic Analysis of the Maize Leaf Microbiome – Jason G. Wallace – bioRxiv

 

Variable response of nirK and nirS containing denitrifier communities to long term pH manipulation and cultivation. – Miriam B Herold – Fems Microbiology Letters

Landscape topography structures the soil microbiome in arctic polygonal tundra. – Neslihan Taş – Nature Communications

Effects of soil depth and plant-soil interaction on microbial community in temperate grasslands of northern China. – Xiaodong Yao – The Science Of The Total Environment

Seasonal dynamics in the community structure and trophic structure of testate amoebae inhabiting the Sanjiang peatlands, Northeast China. – Lihong Song – European Journal Of Protistology

Investigation of rhizospheric microbial communities in wheat, barley and two rice varieties at the seedling stage. – Tao Lu – Journal Of Agricultural And Food Chemistry

Increasing N deposition impacts neither diversity nor functions of deadwood-inhabiting fungal communities, but adaptation and functional redundancy warrants ecosystem function. – Witoon Purahong – Environmental Microbiology

Belowground Interactions Impact the Soil Bacterial Community, Soil Fertility, and Crop Yield in Maize/Peanut Intercropping Systems. – Qisong Li – International Journal Of Molecular Sciences

Lost in diversity: the interactions between soil-borne fungi, biodiversity and plant productivity. – Liesje Mommer – The New Phytologist

Isolation and characterization of N2 -fixing bacteria from giant reed and switchgrass for plant growth promotion and nutrient uptake – Jia Xu – Journal of Basic Microbiology

Structural diversity across arbuscular mycorrhizal, ectomycorrhizal, and endophytic plant-fungus networks – Hirokazu Toju – bioRxiv

Water and extremophile microbiome
Seasonal variability in the persistence of dissolved environmental DNA (eDNA) in a marine system: The role of microbial nutrient limitation. – Ian Salter – Plos One

Elevated temperature drives kelp microbiome dysbiosis, while elevated carbon dioxide induces water microbiome disruption. – Jeremiah J Minich – Plos One

Elevated seawater temperature disrupts the microbiome of an ecologically important bioeroding sponge. – Blake D Ramsby – Molecular Ecology

Microbial Diversity and Mineralogical-Mechanical Properties of Calcitic Cave Speleothems – Navdeep K Dhami – Frontiers In Microbiology

Microbial Community Structure and Function Indicate the Severity of Chromium Contamination of the Yellow River. – Yaxin Pei – Frontiers In Microbiology

Assessing the microbial communities inhabiting drinking water networks and nitrifying enrichments with special respect on nitrifying microorganisms. – Zsuzsanna Nagymáté – Acta Microbiologica Et Immunologica Hungarica

Microbial community composition along a 50,000 year lacustrine sediment sequence. – Aurèle Vuillemin – Fems Microbiology Ecology

Diversity of Rare and Abundant Prokaryotic Phylotypes in the Prony Hydrothermal Field and Comparison with Other Serpentinite-Hosted Ecosystems. – Eléonore Frouin – Frontiers In Microbiology

Sediment bacteria in an urban stream: Spatiotemporal patterns in community composition – Alescia A. Roberto – Water Research

Built environment
Dog introduction alters the home dust microbiota. – Alexandra Sitarik – Indoor Air

Urbanization Reduces Transfer of Diverse Environmental Microbiota Indoors. – Anirudra Parajuli – Frontiers In Microbiology

Removal of artificial sweeteners and their effects on microbial communities in sequencing batch reactors. – Shaoli Li – Scientific Reports

Microbes in space
Soil microbial habitats in an extreme desert Mars-analogue environment – Kimberley Warren-Rhodes – bioRxiv

Food microbiology
** Editorial: Microbiome Yarns: human milk oligosaccharides, Bifidobacterium and immunopowergames. – Kenneth Timmis – Microbial Biotechnology

Detection of Bacterial DNA During the Process of Sake Production Using Sokujo-Moto. – Momoka Terasaki – Current Microbiology

A Walnut-Enriched Diet Affects Gut Microbiome in Healthy Caucasian Subjects: A Randomized, Controlled Trial. – Charlotte Bamberger – Nutrients

Impact of Chemical and Biological Fungicides Applied to Grapevine on Grape Biofilm, Must, and Wine Microbial Diversity. – Rocío Escribano-Viana – Frontiers In Microbiology

Review: The Promising Pharmacological Effects and Therapeutic/Medicinal applications of Punica Granatum L. (Pomegranate) as a Functional Food in Humans and Animals. – Kuldeep Dhama – Recent Patents On Inflammation & Allergy Drug Discovery

Probiotics / prebiotics / antibiotics
Bile-Salt-Hydrolases from the Probiotic Strain – Thibault Allain – Frontiers In Microbiology

** A reservoir of ‘historical’ antibiotic resistance genes in remote pristine Antarctic soils. – Marc W Van Goethem – Microbiome

PAHs accelerate the propagation of antibiotic resistance genes in coastal water microbial community. – Jing Wang – Environmental Pollution (Barking, Essex : 1987)

Short-term Oral Antibiotics Treatment Promotes Inflammatory Activation of Colonic Invariant Natural Killer T and Conventional CD4 – Claudia Burrello – Frontiers In Medicine

Comparative genomic analysis of the multispecies probiotic-marketed product VSL#3 – François P. Douillard – Plos One

A probiotic complex, rosavin, zinc, and prebiotics ameliorate intestinal inflammation in an acute colitis mouse model. – Jin-Sil Park – Journal Of Translational Medicine

Phages and viruses
** Viral insulin-like peptides activate human insulin and IGF-1 receptor signaling: A paradigm shift for host-microbe interactions. – Emrah Altindis – Proceedings Of The National Academy Of Sciences Of The United States Of America

Quantitative Viral Community DNA Analysis Reveals the Dominance of Single-Stranded DNA Viruses in Offshore Upper Bathyal Sediment from Tohoku, Japan. – Mitsuhiro Yoshida – Frontiers In Microbiology

A virus or more in (nearly) every cell: ubiquitous networks of virus-host interactions in extreme environments. – Jacob H Munson-McGee – The Isme Journal

Bioinformatics
MUGAN: Multi-GPU accelerated AmpliconNoise server for rapid microbial diversity assessment. – Byunghan Lee – Bioinformatics (Oxford, England)

Techniques
Time Radically Alters Ex Situ Evidentiary Soil 16S Bacterial Profiles Produced Via Next-Generation Sequencing – Alyssa J. Badgley – Forensic Sciences

Non-biological synthetic spike-in controls and the AMPtk software pipeline improve mycobiome data – Jonathan M Palmer – bioRxiv

Genomes
Complete Genome Sequence and Genomic Characterization of – Won-Hyong Chung – Frontiers In Pharmacology

Luteimonas rhizosphaerae sp. nov., isolated from the rhizosphere of Triticum aestivum L. –  Guo-Yan Zhao – International Journal of Systematic and Evolutionary Microbiology

Science, publishing, and career
Testing Hypotheses on Risk Factors for Scientific Misconduct via Matched-Control Analysis of Papers Containing Problematic Image Duplications – Daniele Fanelli – Scientific and Engineering Ethics

Bioscience-scale automated detection of figure element reuse – Daniel E Acuna – bioRxiv

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February 23, 2018

This Friday: A nice set of papers focused in pathogens such as Salmonella and C. difficile, several papers about soil/root microbiome and more…

Human Microbiome

Review: Skin microbiota and human 3D skin models – Franziska Rademacher – Experimental Dermatology

News and Views: Gut microbiota: Beyond metagenomics, metatranscriptomics illuminates microbiome functionality in IBD – Aonghus Lavelle – Nature Reviews Gastroenterology & Hepatology

Letter: Concomitant resolution through fecal microbiota transplantation of Clostridium difficile and OXA-48-producing Klebsiella pneumoniae –  Giovanni Bruno – Infectious Diseases

Oral cholera vaccination promotes homing of IgA+ memory B cells to the large intestine and the respiratory tract – M van Splunter – Mucosal Immunology

Review: Signalling from the periphery to the brain that regulates energy homeostasis – Ki-Suk Kim – Nature Reviews Neuroscience

Research Highlight: Colorectal cancer: Bacterial biofilms and toxins prompt a perfect storm for colon cancer – Iain Dickson – Nature Reviews Gastroenterology & Hepatology

Research Highlight: Metabolism: The small intestine — a new player in fructose metabolism – Ivone Leong – Nature Reviews Endocrinology

Akkermansia muciniphila-derived extracellular vesicles influence gut permeability through the regulation of tight junctions – Chaithanya Chelakkot – Experimental & Molecular Medicine

 

Animal Microbiome / Animal Experiments

Effects of a galacto-oligosaccharide-rich diet on fecal microbiota and metabolite profiles in mice – W. Cheng – Food and Function

Impact of oral fidaxomicin administration on the intestinal microbiota and susceptibility to Clostridium difficile colonization in mice – N. J. Ajami – Antimicrobial Agents and Chemotherapy

Interplay between gut microbiota and p66Shc affects obesity-associated insulin resistance – Stefano Ciciliot – The FASEB Journal

CD Obesity-Prone Rats, but not Obesity-Resistant Rats, Robustly Ferment Resistant Starch Without Increased Weight or Fat Accretion – Diana Obanda – Obesity

Dietary live yeast and increased water temperature influence the gut microbiota of rainbow trout – David Huyben – Journal of Applied Microbiology

Remodeling of the Candida glabrata cell wall in the gastrointestinal tract affects the gut microbiota and the immune response – Rogatien Charlet – Scientific Reports

Absence of receptor guanylyl cyclase C enhances ileal damage and reduces cytokine and antimicrobial peptide production during oral Salmonella Typhimurium infection – Shamik Majumdar – Infection and Immunity

Thermal regime and host clade, rather than geography, drive Symbiodinium and bacterial assemblages in the scleractinian coral Pocillopora damicornis sensu lato – Kelly Brener-Raffalli – Microbiome

Chitin Oligosaccharide Modulates Gut Microbiota and Attenuates High-Fat-Diet-Induced Metabolic Syndrome in Mice – Junping Zheng – Marine Drugs

Targeting the PXR–TLR4 signaling pathway to reduce intestinal inflammation in an experimental model of necrotizing enterocolitis – Kezhen Huang – Pediatric Research

Hypoglycemic and hypolipidemic effect of S-allyl-cysteine sulfoxide (alliin) in DIO mice – Baiqiang Zhai –  Scientific Reports

 

Human Pathogens

Clostridioides (Clostridium) difficile infection: current and alternative therapeutic strategies – Fernando Gil – Future Medicine

Emergence of an Extensively Drug-Resistant Salmonella enterica Serovar Typhi Clone Harboring a Promiscuous Plasmid Encoding Resistance to Fluoroquinolones and Third-Generation Cephalosporins – Elizabeth J. Klemm – mBio

Metronidazole-Loaded Polyethyleneimine and Chitosan-Based Liquid Crystalline System for Treatment of Staphylococcal Skin Infections – Francesca Damiani Victorelli –  Journal of Biomedical Nanotechnology

Cost-Effectiveness of Competing Treatment Strategies for Clostridium difficile Infection: A Systematic Review – Phuc Le – Infection Control & Hospital Epidemiology

 

Food Microbiome

Antibiotic Resistance Genetic Markers and Integrons in White Soft Cheese: Aspects of Clinical Resistome and Potentiality of Horizontal Gene Transfer –  Ana Caroline L. de Paula – Genes

Effect of the environment microbiota on the flavour of light-flavour Baijiu during spontaneous fermentation – Xiao-Na Pang – Scientific Reports

 

Plant and Environmental Microbiomes

Pseudomonas rhizophila S211, a New Plant Growth-Promoting Rhizobacterium with Potential in Pesticide-Bioremediation – Wafa Hassen – Frontiers in Microbiology

Indigenous Pseudomonas spp. Strains from the Olive (Olea europaea L.) Rhizosphere as Effective Biocontrol Agents against Verticillium dahliae: From the Host Roots to the Bacterial Genomes – Carmen Gómez-Lama Cabanás – Frontiers in Microbiology

Preprint: Network hubs in root-associated fungal metacommunities – Hirokazu Toju – BioRxiv

Preprint: Microbial Treatment of Soil Contaminated with Spent engine Oil / Biotreatment of Soil Contaminated with Spent Engine by Microorganisms – Abiodun A. Ayandele – BioRxiv

Bacterial Preferences for Specific Soil Particle Size Fractions Revealed by Community Analyses – Michael Hemkemeyer – Frontiers in Microbiology

Peatland Acidobacteria with a dissimilatory sulfur metabolism – Bela Hausmann – The ISME Journal

Systemic Homeostasis in Metabolome, Ionome, and Microbiome of Wild Yellowfin Goby in Estuarine Ecosystem – Feifei Wei – Scientific Reports

 

Microbes in General

Review: Ethanolamine Utilization in Bacteria – Karan Gautam Kavala – mBio

Review: The Genome-Scale Integrated Networks in Microorganisms – Tong Hao – Frontiers in Microbiology

 

February 22, 2018

 

Events and jobs

Microbiology Adjunct Instructor – Diablo Valley College

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Pregnancy and early life

Review: Maternal Microbiota, Prepregnancy Weight, and Mode of Delivery
Intergenerational Transmission of Risk for Childhood Overweight and Obesity – Giulia Paolella – JAMA Pediatrics

 

Human ear, nose and throat microbiome

*A microbiome case-control study of recurrent acute otitis media identified potentially protective bacterial genera – Rachael Lappan – BMC Microbiology

The Tracheal Microbiota in Patients with a Tracheostomy Before, During, and After an Acute Respiratory Infection – Pérez-Losada, Marcos – The Pediatric Infectious Disease Journal

Human oral microbiome

Shift of microbial composition of peri-implantitis-associated oral biofilm as revealed by 16S rRNA gene cloning – Ali Al-Ahmad – Journal of Medical Microbiology

Human vaginal microbiome

Short- and long-term influence of the levonorgestrel-releasing intrauterine system (Mirena®) on vaginal microbiota and Candida – Gilbert Gerard Ghislain Donders – Journal of Medical Microbiology

Human gut microbiome

Transitional and temporal changes in the mucosal and submucosal intestinal microbiota in advanced Crohn’s disease of the terminal ileum – Rodrick J. Chiodini – Journal of Medical Microbiology

Gut microbiota trajectory in early life may predict development of celiac disease – Marta Olivares – BMC Microbiome

A comparison of the microbial community structure between inflamed and non-inflamed sites in patients with ulcerative colitis – Atsushi Hirano – Journal of Gastroenterology and Hepatology

The Impact of NOD2 Variants on Fecal Microbiota in Crohn’s Disease and Controls Without Gastrointestinal Disease – Nicholas A Kennedy – Inflammatory Bowel Diseases

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Animal experiments

Regulation of vitamin D metabolism following disruption of the microbiota using broad spectrum antibiotics – Stephanie A. Bora – The Journal of Nutritional Biochemistry

Soluble dietary fiber improves energy homeostasis in obese mice by remodeling the gut microbiota – Haiyuan Wang – Biochemical and Biophysical Research Communications

Lactobacillus and Bifidobacterium Ameliorate Memory and Learning Deficits and oxidative stress in Aβ (1-42) Injected Rats – Somayeh Athari Nik Azm – Applied Physiology, Nutrition, and Metabolism

*Chronic helminth infection perturbs the gut-brain axis, promotes neuropathology and alters behaviour – Paul R Giacomin – The Journal of Infectious Diseases

*Endometriosis induces gut microbiota alterations in mice – Ming Yuan – Human Reproduction

*Strain differences in the susceptibility to the gut–brain axis and neurobehavioural alterations induced by maternal immune activation in mice – Morais, Livia H – Behavioural Pharmacology

Specific synbiotics in early life protect against diet-induced obesity in adult mice
Mona Mischke – Diabetes, Obesity, and Metabolism

Transcriptomic and Proteomic Profiling Revealed High Proportions of Odorant Binding and Antimicrobial Defense Proteins in Olfactory Tissues of the House Mouse – Barbora Kuntová – Frontiers in Genetics

Lactobacillus accelerates ISCs regeneration to protect the integrity of intestinal mucosa through activation of STAT3 signaling pathway induced by LPLs secretion of IL-22 – Qihang Hou – Cell Death and Differentiation

Animal microbiome

Review: Gut barrier function: Effects of (antibiotic) growth promoters on key barrier components and associations with growth performance – Leon J Broom – Poultry Science

Fecal microbiota transplantation in puppies with canine parvovirus infection – Giorgio Q. Pereira – Journal of Veterinary Internal Medicine

Water and extremophile microbiome

Phylogeny and bioactivity of epiphytic Gram-positive bacteria isolated from three co-occurring antarctic macroalgae – Pamela Alvarado – Antonie van Leeuwenhoek

 

Resistome

The antibiotic resistome and microbiota landscape of refugees from Syria, Iraq and Afghanistan in Germany – Robert Häsler – BMC Microbiome

Transferable vancomycin resistance in clade B commensal-type Enterococcus faecium – François Lebreton – Journal of Antimicrobial Chemotherapy

 

Bioinformatics

Deciphering the trophic interaction between Akkermansia muciniphila and the butyrogenic gut commensal Anaerostipes caccae using a metatranscriptomic approach – Loo Wee Chia – Antonie van Leeuwenhoek

Biotechnology

*A 3D intestinal tissue model supports Clostridioides difficile germination, colonization, toxin production and epithelial damage – Lamyaa Shaban – Anaerobe

Design of synthetic bacterial communities for predictable plant phenotypes – Sur Herrera Paredes – PLOS Biology

Harnessing a Methane-Fueled, Sediment-Free Mixed Microbial Community for Utilization of Distributed Sources of Natural Gas – Jeffrey J. Marlow – Biotechnology and Bioengineering

Dissertation: Microbial Communities Involved in Carbon Monoxide and Syngas Conversion to Biofuels and Chemicals – Sofia Victoria Esquivel Elizondo – Arizona State University

 

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Microbes in the news

This Vibrant Bacteria Could Be Used to “Grow” Paint – Meilan Solly – Smithsonian

Bacteria-eaters to prevent food poisoning? Phages eliminate Yersinia from food – Science Daily

A ‘Grueling and Grotesque’ Biohacking Experiment – Kate McLean – The Atlantic

 

February 21, 2018

Events and jobs

BioData World West 2018 – March 13-14 – Hotel Kabuki, San Francisco, CA

General microbiome

[editorial] Systems biology of the human microbiome – BP Bernabé, L Cralle, JA Gilbert – Current Opinion in Biotechnology, 2018

[pre-print] Growth tradeoffs produce complex microbial communities without direct interactions – Michael Manhart – bioRxiv

Exploring the Multifaceted Role of Microbes in Pharmacology – Mitali Mishra – Microbial Biotechnology

Human reproductive or urinary microbiome

Seminal bacterial composition in patients with obstructive and non-obstructive azoospermia – Houyang Chen – Experimental and Therapeutic Medicine

Human respiratory microbiome

Virome and bacteriome characterization of children with pneumonia and asthma in Mexico City during winter seasons 2014 and 2015 – Jose A. Romero-Espinoza – PLOS One

Human gut microbiome

[pdf[ Phytochemicals that influence gut microbiota as prophylactics and for the treatment of obesity and inflammatory diseases – Lucrecia Carrera-Quintanar – Hindawi

Dietary Fiber Treatment Corrects the Composition of Gut Microbiota, Promotes SCFA Production, and Suppresses Colon Carcinogenesis – F Bishehsari – Genes

A Cross-Talk Between Microbiota-Derived Short-Chain Fatty Acids and the Host Mucosal Immune System Regulates Intestinal Homeostasis and Inflammatory Bowel Disease – Pedro Gonçalves – Inflammatory Bowel Diseases

Animal microbiome

Differential microbial communities of omnivorous and herbivorous cattle in Southern China – Susanna K.P. Lau – Computational and Structural Biotechnology Journal

The gills of reef fish support a distinct microbiome influenced by host-specific factors – Zoe A. Pratte – Applied and Environmental Microbiology

Metagenomic analysis of orange colored protrusions from the muscle of Queen Conch Lobatus gigas (Linnaeus, 1758) – Jaison H. Cuartas – PeerJ

Plant, root, and soil microbiome

Bulk soil and maize rhizosphere resistance genes, mobile genetic elements and microbial communities are differently impacted by organic and inorganic fertilization – Birgit Wolters – FEMS Microbiology Ecology

Structural and metabolic diversity of rhizosphere microbial communities of Phragmites karka in a tropical coastal lagoon – Pratiksha Behera – Applied Soil Ecology

Responses of soil microbial communities to a short-term application of seaweed fertilizer revealed by deep amplicon sequencing – Mingpeng Wang – Applied Soil Ecology

[pdf] The Green Roof Microbiome: Improving Plant Survival for Ecosystem Service Delivery – Roberta Fulthorpe – Frontiers in Ecology and Evolution

Microbes and Their Role in Drought Tolerance of Agricultural Food Crops – Rout George Kerry – Microbial Biotechnology

Microscopic and Metagenomic Analyses of Peltigera ponojensis (Peltigerales, Ascomycota) – Linda E. Graham – International Journal of Plant Sciences

Frankia Diversity in Host Plant Root Nodules Is Independent of Abundance or Relative Diversity of Frankia Populations in Corresponding Rhizosphere Soils – Seifeddine Ben Tekaya – Applied and Environmental Microbiology

High frequency cropping of pulses modifies soil nitrogen level and the rhizosphere bacterial microbiome in 4-year rotation systems of the semiarid prairie – Chantal Hamel – Applied Soil Ecology

Bulk soil and maize rhizosphere resistance genes, mobile genetic elements and microbial communities are differently impacted by organic and inorganic fertilization – Birgit Wolters – FEMS Microbiology Ecology

Water and extremophile microbiome

Variability in metagenomic samples from the Puget Sound: Relationship to temporal and anthropogenic impacts – James C. Wallace – PLOS One

Linking the effect of antibiotics on partial-nitritation biofilters: performance, microbial communities and microbial activities – Alejandro Gonzalez-Martinez – Frontiers in Microbiology

The effect of epiphytic macroinvertebrates on microbial communities in different types of macrophyte-dominated shallow lakes – Tomasz Mieczan –  Knowl. Manag. Aquat. Ecosyst

Watershed-induced limnological and microbial status in two oligotrophic Andean lakes exposed to the same climatic scenario – Alex Echeverría-Vega – Frontiers in Microbiology

** A novel β-glucosidase isolated from the microbial metagenome of Lake Poraquê (Amazon, Brazil) – Danyelle Toyama – Biochimica et Biophysica Acta (BBA) – Proteins and Proteomics

Variations in culturable bacterial communities and biochemical properties in the foreland of the retreating Tianshan No. 1 glacier – Xiukun Wu – Brazilian Journal of Microbiology

Food microbiology

Microbial diversity and component variation in Xiaguan Tuo Tea during pile fermentation – Haizhou Li – PLOS One

Metagenomic Insights into Environmental Microbiome and Their Application in Food/Pharmaceutical Industry – Ramya Sree Boddu – Microbial Biotechnology

Phages and viruses

[pre-print] THEA: A novel approach to gene identification in phage genomes – Katelyn McNair – bioRxiv

Bioinformatics

* [pdf] Microbiome Data Accurately Predicts the Postmortem Interval Using Random Forest Regression Models – Aeriel Belk – Genes

COREMIC: a web-tool to search for a niche associated CORE MICrobiome – Richard R. Rodrigues – PeerJ

Techniques

Isotope fractionation in biogas allows direct microbial community stability monitoring in anaerobic digestion – Jo De Vrieze – Environmental Science & Technology

Statistical assessment of DNA extraction methodology for culture-independent analysis of microbial community associated with diverse environmental samples – Rishi Mahajan – Molecular Biology Reports

Microbes in the news

These Bacteria Eat Toxic Metal, ‘Poop’ Gold Nuggets – Live Science

Ed’s non-microbiology picks (can use your own name of course!) (cool non-microbiology science)

Earthquakes follow wastewater disposal patterns in southern Kansas

Ultra-processed foods ‘linked to cancer’

Promising cancer vaccine would use patient’s own cells to train the immune system

Does GMO corn increase crop yields? 21 years of data confirm it does—and provides substantial health benefits

Poor fitness linked to weaker brain fiber, higher dementia risk

Low cigarette consumption and risk of coronary heart disease and stroke: meta-analysis of 141 cohort studies in 55 study reports

Fewer Infants Died In States That Allowed Affordable Care Act

February 20, 2018

In today’s digest you can read: about advantages of Atomic Force Microscopy in studying of oral microbiota in the paper by S. S. Salavadhi; about gut microbiome association with Type 1 diabetes in the paper by J.A. Mullaney; about influence of steroids on the gut microbiota in the review by M.J Tetel and about the ability of Synechococcus cyanobacteria to dynamically change their pigment content to match the ambient light color, in the paper by T. Grébert. These are of course just a few of many interesting articles today. Enjoy!

Events and jobs

MS graduate position: Amoeba microbiome, Conway, Arkansas, US

Research Fellow in Cell Biology – Microscopy, Warwick, UK

PhD Student, ROYAL NIOZ-TEXEL, Texel, the Netherlands

General microbiome

Review: A new piece in the microbiome puzzle – Lindsay J. Pike – Nature Reviews Microbiology

The importance of resolving biogeographic patterns of microbial microdiversity – Alexander B Chase – Microbiology Australia

Consistent changes in the taxonomic structure and functional attributes of bacterial communities during primary succession – Rüdiger Ortiz-Álvarez – the ISME Journal

Pregnancy and early life

Infant formulae supplemented with prebiotics: Are they better than unsupplemented formulae? An updated systematic review – Agata Skórka – British Journal of Nutrition

Early Dietary Patterns and Microbiota Development: Still a Way to Go from Descriptive Interactions to Health-Relevant Solutions – Patricia Iozzo – Frontiers in Nutrition

Roles of Birth Mode and Infant Gut Microbiota in Intergenerational Transmission of Overweight and Obesity From Mother to Offspring – Hein M. Tun – JAMA Pediatrics

Multi-site human microbiome

A blinded observational cohort study of the microbiological ecology associated with pyuria and overactive bladder symptoms – Kiren Gill – International Urogynecology Journal

Oral microbiome

Atomic force microscopy: A three-dimensional reconstructive tool of oral microbiota in gingivitis and periodontitis – Shyam Sunder Salavadhi – Journal of Indian Society of Periodontology

Human gut microbiome

Review: Steroids, stress and the gut microbiome-brain axis – M. J. Tetel – Journal of Neuroendocrinology

Alterations of the Gut Microbiota in Hashimoto’s Thyroiditis Patients – Zhao Fuya – Thyroid

Endospores and other lysis-resistant bacteria comprise a widely shared core community within the human microbiota – Sean Michael Kearney – bioRxiv

Alterations in Intestinal Microbiota Lead to Production of Interleukin 17 by Intrahepatic γδ T-cell Receptor-positive Cells and Pathogenesis of Cholestatic Liver Disease – Dana Tedesco – Gastroenterology

Type 1 diabetes susceptibility alleles are associated with distinct alterations in the gut microbiota – Jane A. Mullaney – BMC Microbiome

Animal experiments

Effect of Dietary Chestnut or Quebracho Tannin Supplementation on Microbial Community and Fatty Acid Profile in the Rumen of Dairy Ewes – Arianna Buccioni – BioMed Research International

Long-Term Treatment with Green Tea Polyphenols Modifies the Gut Microbiome of Female Sprague-Dawley Rats – Jincheng Wang – The Journal of Nutritional Biochemistry

Microbiota-Derived Indole Metabolites Promote Human and Murine Intestinal Homeostasis through Regulation of Interleukin-10 Receptor – Erica E. Alexeev – The Americn Journal of Pathology

Interrelations between the rumen microbiota and production, behavioral, rumen-fermentation, metabolic, and immunological attributes of dairy cows – M. Schären – Journal of Diary Science

Animal microbiome

Disentangling metabolic functions of bacteria in the honey bee gut – Lucie Kešnerová – PLOS One

Plant, root, and soil microbiome

Soil mixture composition alters Arabidopsis susceptibility to Pseudomonas syringae infection – Jana A. Hassan – Plant Direct

Taxonomic structure and function of seed-inhabiting bacterial microbiota from common reed (Phragmites australis) and narrowleaf cattail (Typha angustifolia L.) – Ting Gao – Archives of Microbiology

The soil microbiome — from metagenomics to metaphenomics – Janet K Jansson – Current Opinion in Microbiology

Exometabolomic profiling of bacterial strains cultivated using Arabidopsis root extract as the sole carbon source – Richard Paul Jacoby – Molecular Plant-Microbiome Interactions

A strain of Streptomyces sp. isolated from rhizospheric soil of Crataegus oxycantha producing Nalidixic acid, a synthetic antibiotic – Nidhi Arora – Journal of Applied Microbiology

High microbial diversity promotes soil ecosystem functioning – Pierre-Alain Maron – Applied and Environmental Microbiology

Water and extremophile microbiome 

Apportioning bacterial carbon source utilization in soil using 14C isotope analysis of FISH-targeted bacterial populations sorted by Fluorescence Activated Cell Sorting (FACS): 14C-FISH-FACS – Christos Gougoulias – Environmental Microbiology Reports

Insights into the fundamental physiology of the uncultured Fe-oxidizing bacterium Leptothrix ochracea – E. J. Fleming – Applied and Environmental Microbiology

Light color acclimation is a key process in the global ocean distribution of Synechococcus cyanobacteria – Théophile Grébert – PNAS

Microbial Functional Gene Diversity Predicts Groundwater Contamination and Ecosystem Functioning – Zhili He – mBio

Iron and phosphorus deprivation induce sociality in the marine bloom-forming cyanobacterium Trichodesmium – Yael Tzubari – the ISME Journal

Cryptophyta as major bacterivores in freshwater summer plankton – Vesna Grujcic – the ISME Journal

Phages and viruses

The impact of bacteriophages on phyllosphere bacterial abundance and composition – Norma M. Morella – Molecular Ecology

Microbes in the news 

Guts and gory: vampire bats need bacteria to digest blood

Using mutant bacteria to study how changes in membrane proteins affect cell functions

February 19, 2018

Events and jobs

Research Technician I – University at Buffalo

General microbiome

Non-antibiotic antimicrobial triclosan induces multiple antibiotic resistance through genetic mutation – Ji Lu, bioRxiv

Oncologists tap the microbiome in bid to improve immunotherapy outcomes – Asher Mullard, Nature Reviews Drug Discovery

Nasal microbiome

Establishment of the Nasal Microbiota in the first 18 Months of Life – Correlation with Early Onset Rhinitis and Wheezing – Le Duc Huy Ta, Journal of Allergy and Clinical Immunology

The nasal microbiome in chronic rhinosinusitis: analyzing the effects of atopy and bacterial functional pathways in 111 patients – Mahboobeh Mahdavinia, Journal of Allergy and Clinical Immunology

Pregnancy and early life

Metagenomic analysis with strain-level resolution reveals fine-scale variation in the human pregnancy microbiome – Daniela S. A. Goltsman, bioRxiv

Human vaginal microbiome

Microbiota changes impact on sexually transmitted infections and the development of pelvic inflammatory disease – Nathalie Loeper, Microbes and Infection

Human gut microbiome

Efficacy of Bifidobacterium breve Fermented Milk in Maintaining Remission of Ulcerative Colitis – Katsuyoshi Matsuoka, Digestive Diseases and Sciences

Comparison of Different Strategies for Providing Fecal Microbiota Transplantation to Treat Patients with Recurrent Clostridium difficile Infection in Two English Hospitals: A Review – Simon D. Goldenberg, Infectious Diseases and Therapy

Fecal Microbiota Transplant for Refractory Clostridium difficile Infection Interrupts 25-Year History of Recurrent Urinary Tract Infections – Tiffany Wang, Open Forum Infectious Diseases

Fecal microbiota transplantation for severe complicated C. difficile colitis in a patient with acquired immunodeficiency syndrome – P. Martínez-Ayala, Revista de Gastroenterología de México

Microbial Engraftment and Efficacy of Fecal Microbiota Transplant for Clostridium difficile Patients With and Without IBD – Robert P Hirten, bioRxiv

The impact of a helminth-modified microbiome on host immunity – Tara P. Brosschot &
Lisa A. Reynolds, Mucosal Immunology

Depression and obesity: evidence of shared biological mechanisms – Yuri Milaneschi, Molecular Psychiatry

Delayed gut microbiota development in high-risk for asthma infants is temporarily modifiable by Lactobacillus supplementation – Juliana Durack, Nature Communications

Roux-en-Y Gastric-Bypass and sleeve gastrectomy induces specific shifts of the gut microbiota without altering the metabolism of bile acids in the intestinal lumen – Henri Duboc, International Journal of Obesity

Effects of ewe’s milk yogurt (whole and semi-skimmed) and cow’s milk yogurt on inflammation markers and gut microbiota of subjects with borderline-high plasma cholesterol levels: a crossover study – Noemí Redondo, European Journal of Nutrition

Impact of food additives on the gut-brain axis – Mary K. Holder, Physiology & Behavior

Gut microbiota injury in allogeneic haematopoietic stem cell transplantation – Yusuke Shono, Nature Reviews Cancer

Microbiota: Pathobiont peacekeepers – Kirsty Minton, Nature Reviews Immunology

Gut Microbiomics—A Solution to Unloose the Gordian Knot of Biological Effects of Ionizing Radiation – Amy Zhang, Journal of Heredity

Oral microbiome

Host defense against oral microbiota by bone-damaging T cells – Masayuki Tsukasaki, Nature Communications

Beyond Streptococcus mutans: clinical implications of the evolving dental caries aetiological paradigms and its associated microbiome – N. Philip, BDJ

Animal experiments

The Divergence in Bacterial Components Associated with Bactrocera dorsalis across Developmental Stages – Xiaofeng Zhao, Frontiers in Microbiology

Microbiota in fermented feed and swine gut – Cheng Wang, Applied Microbiology and Biotechnology

Biogeographical Differences in the Influence of Maternal Microbial Sources on the Early Successional Development of the Bovine Neonatal Gastrointestinal tract – Carl J. Yeoman, Scientific Reports

Animal microbiome

Amphibian chytridiomycosis outbreak dynamics are linked with host skin bacterial community structure – Kieran A. Bates, Nature Communications

The effect of cadmium exposure on diversity of intestinal microbial community of Rana chensinensis tadpoles – Danyang Mu, Ecotoxicology and Environmental Safety

A new cell extraction method reveals hemolymph microbiome of three aquatic invertebrates – Xinxu Zhang, Applied Microbiology and Biotechnology

The gastrointestinal tract microbiota of northern white-cheeked gibbons (Nomascus leucogenys) varies with age and captive condition – Ting Jia, Scientific Reports

Plant, root, and soil microbiome

Manipulation of the rhizosphere microbial community through application of a new bio-organic fertilizer improves watermelon quality and health – Jia Zhao, PLOS One

Water and extremophile microbiome

Seasonal dynamics of tetracycline resistance gene transport in the Sumas River agricultural watershed of British Columbia, Canada – Patricia L. Keen, Science of The Total Environment

Microbial diversity and toxin risk in tropical freshwater reservoirs of Cape Verde – Ana Paula Semedo-Aguiar, bioRxiv

Common hydraulic fracturing fluid additives alter the structure and function of anaerobic microbial communities – Adam C. Mumford, Applied and Environmental Microbiology

Bacterial Community Shift and Coexisting/Coexcluding Patterns Revealed by Network Analysis in A Bioreduced Uranium Contaminated Site after Reoxidation – Bing Li, Applied and Environmental Microbiology

Properties of bacterial communities attached to artificial substrates in a hypereutrophic urban river – Xianlei Cai, AMB Express

Food microbiology

Nitrogen removal enhancement using lactic acid fermentation products from food waste as external carbon sources: performance and microbial communities – Jialing Tang, Bioresource Technology

Probiotics/Prebiotics

Advances in Probiotic Regulation of Bone and Mineral Metabolism – Laura R. McCabe, Calcified Tissue International

Prebiotics as functional food ingredients preventing diet-related diseases – A. Florowska, Food and Function

A prebiotic mixture improved Lactobacillus acidophilus and Bifidobacterium animalisgastrointestinal in vitro resistance in petit-suisse – Marina Padilha, Food and Function

Bioinformatics

SEED 2: a user-friendly platform for amplicon high-throughput sequencing data analyses – Tomáš Větrovský, Bioinformatics

Techniques

Use of Rectal Swab Samples for Analysis of the Intestinal Microbiome in Children – Nan Zhang, Chinese Medical Journal

February 18, 2018

Quite a few articles with alerts from today and the day before. Many interesting articles on microbe/microbe and microbe-host interactions, enjoy!

Events and jobs
Senior Bioinformatician – Host Microbiota Interactions – Wellcome Trust Sanger Institute

Postdoctoral Fellow – ‘Microbiome of intestinal tract cancers’ – Centre for Molecular and Biomolecular Informatics (CMBI)

Department Chair – Department of Microbiology and Immunology – College of Veterinary Medicine Cornell University, Ithaca, New York

Associate Scientist- Microbiology – Aerotek, Los Angeles, CA

Multi-site human microbiome
Differential contributions of specimen types, culturing, and 16S – Lone Heimann Larsen – Journal Of Clinical Microbiology

Analysis of microbial sequences in plasma cell-free DNA for early-onset breast cancer patients and healthy females – Yu-Feng Huang – BMC Medical Genomics

Human oral microbiome
Bacterial microleakage at the abutment-implant interface, in vitro study. – Carlos Larrucea – Clinical Implant Dentistry And Related Research

Comparison of Oropharyngeal Microbiota from Children with Asthma and Cystic Fibrosis. – Sébastien Boutin – Mediators Of Inflammation

Human vaginal microbiome
Review: Cervicovaginal Microbiota and Reproductive Health: The Virtue of Simplicity. – Melis N Anahtar – Cell Host & Microbe

Human gut microbiome
The effect of Clostridium butyricum on symptoms and fecal microbiota in diarrhea-dominant irritable bowel syndrome: a randomized, double-blind, placebo-controlled trial. – Yi-Yuan Sun – Scientific Reports

Association of gut microbial communities with plasma lipopolysaccharide-binding protein (LBP) in premenopausal women – Jessica S Citronberg – ISME

Microbiota Accessible Carbohydrates Suppress Clostridium difficile in a Murine Model – Andrew J Hryckowian – bioRxiv

Review: Gut Microbiota-Based Therapies for Irritable Bowel Syndrome. – Emily K Stern – Clinical And Translational Gastroenterology

Review: A neuroscience perspective of the gut theory of Parkinson’s disease. – Lisa M Smith – The European Journal Of Neuroscience

Microbial-microbial/host interactions
Interactions between predation and disturbances shape prey communities. – Canan Karakoç – Scientific Reports

Elevated success of multispecies bacterial invasions impacts community composition during ecological succession. – Damian W Rivett – Ecology Letters

Competition in biofilms between cystic fibrosis isolates of Pseudomonas aeruginosa is driven by R-pyocins – Olubukola Oluyombo – bioRxiv

Linking associations of rare low-abundance species to their environments by association networks – Tatiana V. Karpinets – Frontiers in Microbiology

Genetic Ablation of Butyrate Utilization Attenuates Gastrointestinal Salmonella Disease. – Denise N Bronner – Cell Host & Microbe

Goblet cell associated antigen passages are inhibited during Salmonella typhimur/cium infection to prevent pathogen dissemination and limit responses to dietary antigens. – Devesha H Kulkarni – Mucosal Immunology

Animal experiments
Cytosolic and secreted peptidoglycan-degrading enzymes in Drosophila respectively control local and systemic immune responses to microbiota – Bernard Charroux – Cell Host & Microbe

Differences in the intestinal microbiota between uninfected piglets and piglets infected with porcine epidemic diarrhea virus. – Mei-Zhou Huang – Plos One

Rumen-protected methionine during the peripartal period in dairy cows and its effects on abundance of major species of ruminal bacteria. – Mohamed K Abdelmegeid – Journal Of Animal Science And Biotechnology

Impact of Chestnut and Quebracho Tannins on Rumen Microbiota of Bovines. – Juan María Díaz Carrasco – Biomed Research International

Starvation influences the microbiota assembly and expression of immunity-related genes in the intestine of grass carp (Ctenopharyngodon idellus) – Ngoc Tuan Tran – Aquaculture

Animal microbiome
The Dynamic Distribution of Small-Tail Han Sheep Microbiota across Different Intestinal Segments. – Hao Zhang – Frontiers In Microbiology

Microbiome assembly of avian eggshells and their potential as transgenerational carriers of maternal microbiota. – H Pieter J van Veelen – The Isme Journal

Plant, root, and soil microbiome
Photoautotrophic organisms control microbial abundance, diversity, and physiology in different types of biological soil crusts. – Stefanie Maier – The Isme Journal

Long-term use of cover crops and no-till shift soil microbial community life strategies in agricultural soil. – Radomir Schmidt – Plos One

Genome mining of Streptomyces scabrisporus NF3 reveals symbiotic features including genes related to plant interactions. – Corina Diana Ceapă – Plos One

Select and resequence reveals relative fitness of bacteria in symbiotic and free-living environments – Liana T. Burghardt – PNAS

Microbial Flora Associated with the Halophyte- – Fehmida Bibi – Frontiers In Microbiology

Root growth improvement of mesquite seedlings and bacterial rhizosphere and soil community changes are induced by inoculation with plant growth-promoting bacteria and promote restoration of eroded desert soil – Cristina Galaviz – Land Degradation and Development

Diversity of root-associated microbial populations of Tamarix parviflora cultivated under various conditions – Marketa Polivkova – Applied Soil Ecology

Succession of the functional microbial communities and the metabolic functions in maize straw composting process – Huawei Wei – Bioresource Technology

Rhizospheric microbial communities are driven by Panax ginseng at different growth stages and biocontrol bacteria alleviates replanting mortality – Linlin Dong – Acta Pharmaceutica Sinica B

Review: Soil protists: a fertile frontier in soil biology research. – Stefan Geisen – Fems Microbiology Reviews

Water and extremophile microbiome
Composition and Activity of Microbial Communities along the Redox Gradient of an Alkaline, Hypersaline, Lake. – Christian F Edwardson – Frontiers In Microbiology

Phosphorus Solubilizing and Releasing Bacteria Screening from the Rhizosphere in a Natural Wetland – Ying Cao – Water

Effects of water flow on submerged macrophyte-biofilm systems in constructed wetlands – Bing Han – Scientific Reports

Dispersal limitation and thermodynamic constraints govern spatial structure of permafrost microbial communities – Eric M Bottos – bioRxiv

Metagenomic exploration of soils microbial communities associated to Antarctic vascular plants – Marco A. Molina-Montenegro – PeerJ Preprints

Built environment
Liquid co-substrates repower sewage microbiomes – Justus Hardegen – bioRxiv

Investigating antibiotics, antibiotic resistance genes, and microbial contaminants in groundwater in relation to the proximity of urban areas – Edina Szekeres – Environmental Pollution

Influence of secondary water supply systems on microbial community structure and opportunistic pathogen gene markers – Huan Li – Water Research

Review: A review on the applications of microbial electrolysis cells in anaerobic digestion. – Zhengsheng Yu – Bioresource Technology

Probiotics / prebiotics / antibiotics
Tacrolimus concentration to dose ratio in solid organ transplant patients treated with fecal microbiota transplantation for recurrent Clostridium difficile infection. – Michael H Woodworth – Transplant Infectious Disease : An Official Journal Of The Transplantation Society

Techniques
Functional imaging of the interaction between gut microbiota and the human host: A proof-of-concept clinical study evaluating novel use for 18F-FDG PET-CT. – Ben Boursi – Plos One

A 3D intestinal tissue model supports Clostridioides difficile germination, colonization, toxin production and epithelial damage – Lamyaa Shaban – Anaerobe

How to isolate, identify and determine antimicrobial susceptibility of anaerobic bacteria in routine laboratories? – Elisabeth Nagy – Clinical Microbiology and Infection

Microbes in the news
A trip to ‘the poopy lab’ in the interest of drug development – Eric Boodman – STAT News

Probe provides rapid lung investigation – Pallab Ghosh – BBC News