January 20, 2018

Our Saturday digest has microbes associated with oesophageal region; sore throat; aphids, stingless bees; common carps, Italian cheeses and many more!

General microbiome

Bipartite network analysis of gene sharings in the microbial world – Eduardo Corel –

FEMS Microbiology Ecology

Is the impact of starvation on the gut microbiota specific or unspecific to anorexia nervosa? A narrative review based on a systematic literature search – Isabelle Mack – Current Neuropharmacology

Pregnancy and early life

Association between sn-2 fatty acid profiles of breast milk and development of the infant intestinal microbiome – Teimin Jiang – Food and Function

Multi-site human microbiome

The microbiology and treatment of human mastitis. – A Angelopoulou – Medical Microbiology and Immunology

Human respiratory microbiome

Initial acquisition and succession of the cystic fibrosis lung microbiome is associated with disease progression in infants and preschool children – Marianne S. Muhlebach – PLoS Pathogens

Analysis of the tonsillar microbiome in young adults with sore throat reveals a high relative abundance of Fusobacterium necrophorum with low diversity – T. Preskott Atkinson – PLoS One

Human gut microbiome

Diet Affects Gut Microbiota and Modulates Hospitalization Risk Differentially In an International Cirrhosis Cohort – JS Bajaj – Hepatology

Emerging Insights into the Esophageal Microbiome – M May – Current Treatment Options in Gastroenterology

Analysis of gut microbiota diversity and auxiliary diagnosis as a biomarker in patients with schizophrenia: A cross-sectional study –  Y Shen – Schizophrenia Research

Animal experiments 

Colonization of the cervicovaginal space with Gardnerella vaginalis leads to local inflammation and cervical remodeling in pregnant mice – Luz-Jeannette Sierra – PLoS One

Kudingcha and Fuzhuan Brick Tea Prevent Obesity and Modulate Gut Microbiota in High-Fat Diet Fed Mice – Guijie Chen – Molecular Nutrition & Food Research

Sequential BMP7/TGF-β1 signaling and microbiota instruct mucosal Langerhans cell differentiation. – Tal Capucha – Journal of Experimental Medicine

A host-pathogen interaction screen identifies ada2 as a mediator of Candida glabrata defences against reactive oxygen species – I Kounatidis – bioRxiv

Animal microbiome 

A large-scale field study of bacterial communities in cereal aphid populations across Morocco – Samir Fakhour – FEMS Microbiology Ecology

Common cuckoos (Cuculus canorus) affect the bacterial diversity of the eggshells of their great reed warbler (Acrocephalus arundinaceus) hosts  – Nikoletta Geltsch – PLoS One

Stingless Bee Larvae Require Fungal Steroid to Pupate. – Camila R. Paludo – Scientific Reports

Plant, root and soil microbiome

Succession of microbial communities and changes of incremental oil in a post-polymer flooded reservoir with nutrient stimulation – Peike Gao – Applied Microbiology and Biotechnology

Draft Genome Sequence of Bacillus subtilis 2C-9B, a Strain with Biocontrol Potential against Chili Pepper Root Pathogens and Tolerance to Pb and Zn – Claudia Y. Muñoz-Moreno – Genome Announcements

Biotic elicitation of ginsenoside metabolism of mutant adventitious root culture in Panax ginseng – Kim-Cuong Le – Applied Microbiology and Biotechnology

Streptomyces AcH 505 triggers production of a salicylic acid analogue in the fungal pathogen Heterobasidion abietinum that enhances infection of Norway spruce seedlings – Nadine Keilhofer – Antonie van Leeuwenhoek

Seed Endophyte Microbiome of Crotalaria pumila Unpeeled: Identification of Plant-Beneficial Methylobacteria – AS Sánchez-López – International Journal of Molecular Sciences

Extreme rainfall affects assembly of the root-associated fungal community – CJ Barnes – The New Phytologist

Abrupt burial imparts persistent changes to the bacterial diversity of turbidite-associated sediment profiles. – BK Harrison – Geobiology

Review: Fungal-Mediated Solid Waste Management: A Review –  A Jain – Mycoremediation and Environmental Sustainability

The PEG-responding desiccome of the alder microsymbiont Frankia alni – K Ghedira – Scientific Reports

Composition of pelagic microbial communities in Mediterranean coastal aquatic ecosystems under extreme drought conditions – N Àvila –  Estuarine, Coastal and Shelf Science

Water microbiome and extremophile 

What color should glacier algae be? – Roman J dial – FEMS Microbiology Ecology

Microbial Community Structure of Sea Spray Aerosols at Three California Beaches – Katherine Graham – FEMS Microbiology Ecology

The early conversion of deep-sea wood falls into chemosynthetic hotspots revealed by in situ monitoring – Dimitri Kalenitchenko – Scientific Reports

Microbial communities and their predicted metabolic functions in a desiccating acid salt lake – Elena Zaikova – Extremophiles

Protein adaptations in extremophiles: An insight into extremophilic connection of mycobacterial proteome – A Kumar – Seminars in Cell & Developmental Biology

Built environment 

Composition and role of the attached and planktonic microbial communities in mesophilic and thermophilic xylose-fed microbial fuel cells – Paolo Dessi – RSC Advances

Food microbiology

Development and implementation of multilocus sequence typing to study the diversity of the yeast Kluyveromyces marxianus in Italian cheeses – Fabrizia Tittarelli – Microbial Genomics

Application of molecular tools to elucidate the microbiota of seafood – Paloma Almeida Rodrigues – Journal of Applied Microbiology

Review: Recent Past, Present, and Future of the Food Microbiome – Francesca De Filippis – Annual Review of Food Science and Technology

Extracellular Enzyme Composition and Functional Characteristics of Aspergillus niger An-76 Induced by Food Processing Byproducts and Based on Integrated Functional-omics – L Liu – Journal of Agricultural and Food Chemistry

Changes in microbial communities and quality attributes of white muscle and dark muscle from common carp (Cyprinus carpio) during chilled and freeze-chilled storage – Q Li – Food Microbiology

Phages and viruses

Comparative transcriptomics reveals a conserved Bacterial Adaptive Phage Response (BAPR) to viral predation – BG Blasdel – bioRxiv

Single-cell transcriptional dynamics of flavivirus infection – F Zanini – bioRxiv

Techniques

A distance-based approach for testing the mediation effect of the human microbiome – J Zhang – Bioinformatics

ReprDB and panDB: minimalist databases with maximal microbial representation – W Zhou – Microbiome

Diverse spatial organization of photosynthetic membranes among purple nonsulfur bacteria – B LaSarre – bioRxiv

Microbes in the news 

WEBINAR REVIEW: IMMUNO-ONCOLOGY AND THE MICROBIOME – Taconic

Scientists Peek Inside The ‘Black Box’ Of Soil Microbes To Learn Their Secrets – npr

Broadways Nursing Home: Legionella bacteria found in plumbing – BBC

Agros refuses Troodos water after coliform bacteria found – Cyprus Mail Online

Strange Weather Triggered Bacteria That Killed 200,000 Endangered Antelope – npr

Bacterial biofilm cellulose found to differ from plant cellulose – Phys.org

This is what happens to your gut when you go on a juice cleanse – Well and Good

New Course in Virus Hunting – SDSU NewsCenter

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January 13, 2018

100+ alerts, meaning great papers in every category. Enjoy!

General microbiome
ReviewSphingolipids in host-microbial interactions – Stacey L Heaver – Current Opinion In Microbiology

EditorialThe Human Microbiome – Emily P Balskus – ACS Infectious Diseases

ReviewEmergent Heterogeneous Micro-environments in Biofilms:Substratum Surface Heterogeneity and Bacterial Adhesion Force-sensing – Yijin Ren – Fems Microbiology Reviews

Pregnancy and early life
Maturation of the gut microbiome and risk of asthma in childhood – Jakob Stokholm – Nature Communications

Haemophilus is overrepresented in the nasopharynx of infants hospitalized with RSV infection and associated with increased viral load and enhanced mucosal CXCL8 responses – Thomas H A Ederveen – Microbiome

Fetal and early life antibiotics exposure and very early onset inflammatory bowel disease: a population-based study – Anne K Örtqvist – Gut

Review: Early Microbes Modify Immune System Development and Metabolic Homeostasis-The “Restaurant” Hypothesis Revisited – Michael J Nash – Frontiers In Endocrinology

Human respiratory microbiome
Genomics of Corynebacterium striatum, an emerging multi-drug resistant pathogen of immunocompromised patients – Kathleen Nudel – Clinical Microbiology And Infection

Human skin microbiome
Transcriptomic profiling of interacting nasal staphylococci species reveals global changes in gene and non-coding RNA expression – Grith M M Hermansen – Fems Microbiology Letters

Human oral microbiome
Association of Oral Microbiome With Risk for Incident Head and Neck Squamous Cell Cancer – Richard B Hayes – JAMA Oncology

Composition of salivary microbiota in elderly subjects – Taiji Ogawa – Scientific Reports

Human gut microbiome
CX3CR1+ mononuclear phagocytes control immunity to intestinal fungi – Irina Leonardi – Science (New York, N.Y.)

Antagonism toward the intestinal microbiota and its effect on Vibrio cholerae virulence. – Wenjing Zhao – Science (New York, N.Y.)

Evaluation of bloodstream infections, Clostridium difficile infections, and gut microbiota in pediatric oncology patients – Bryan T. Nycz – PLoS One

Antibiotic Treatments for Clostridium difficile Infection Are Associated with Distinct Bacterial and Fungal Community Structures – Regina Lamendella – mSphere

Alterations of the gut microbiota in Hashimoto’s thyroiditis patients – Fuya Zhao – Thyroid : Official Journal Of The American Thyroid Association

Structural insights into a family 39 glycoside hydrolase from the gut symbiont Bacteroides cellulosilyticus WH2 – Ahmad Ali-Ahmad – Journal Of Structural Biology

Review: Gut Microbiota Dysbiosis Drives and Implies Novel Therapeutic Strategies for Diabetes Mellitus and Related Metabolic Diseases – Xuan Li – Frontiers In Immunology

ReviewPathogens, microbiome and the host: emergence of the ecological Koch’s postulates – Pascale Vonaesch – FEMS Microbiology Reviews

ReviewBiochemistry of Complex Glycan Depolymerisation by the Human Gut Microbiota – Didier Ndeh – FEMS Microbiology Reviews

Review: Segmented filamentous bacteria, Th17 inducers and helpers in a hostile world – Pamela Schnupf – Current Opinion In Microbiology

Microbial Ecology
Simulation of Escherichia coli Dynamics in Biofilms and Submerged Colonies with an Individual-Based Model Including Metabolic Network Information – Ignace L M M Tack – Frontiers In Microbiology

Initial evenness determines diversity and cell density dynamics in synthetic microbial ecosystems – Elham Ehsani – Scientific Reports

Pan-genome analysis of the genus Finegoldia identifies two distinct clades, strain-specific heterogeneity, and putative virulence factors – Holger Brüggemann – Scientific Reports

Specifying the Harsh Conditions of Life: Resource Competition and Predation in the 1970s – Alita R. Burmeister – The American Naturalist

Animal experiments
Maternal metabolic, immune, and microbial systems in late pregnancy vary with malnutrition in mice – Kristin L Connor – Biology of Reproduction

Fecal Microbiota Transplantation, Commensal Escherichia coli and Lactobacillus johnsonii Strains Differentially Restore Intestinal and Systemic Adaptive Immune Cell Populations Following Broad-spectrum Antibiotic Treatment – Ira Ekmekciu – Frontiers In Microbiology

Impacts of feeding preweaned calves milk containing drug residues on the functional profile of the fecal microbiota – Richard Van Vleck Pereira – Scientific Reports

Gama-aminobutyric Acid Enriched Rice Bran Diet Attenuates Insulin Resistance and Balances Energy Expenditure via Modification of Gut Microbiota and SCFAs – Xu Si – Journal Of Agricultural And Food Chemistry

Proton Pump Inhibitors Increase the Susceptibility of Mice to Oral Infection with Enteropathogenic Bacteria – Eiichiro Yasutomi – Digestive Diseases And Sciences

Rhubarb supplementation promotes intestinal mucosal innate immune homeostasis through modulating intestinal epithelial microbiota in goat kids – Jinzhen Jiao – Journal Of Agricultural And Food Chemistry

Impact of dietary induced precocious gut maturation on cecal microbiota and its relation to the blood-brain barrier during the postnatal period in rats – N Marungruang – Neurogastroenterology And Motility : The Official Journal Of The European Gastrointestinal Motility Society

Exercise Prevents Enhanced Postoperative Neuroinflammation and Cognitive Decline and Rectifies the Gut Microbiome in a Rat Model of Metabolic Syndrome – Xiaomei Feng – Frontiers In Immunology

Rifampicin treatment of Blattella germanica evidences a fecal transmission route of their gut microbiota – Tania Rosas – Fems Microbiology Ecology

Gut Flora-Dependent Metabolite Trimethylamine-N-oxide Accelerates Endothelial Cell Senescence and Vascular Aging through Oxidative Stress – Yilang Ke – Free Radical Biology & Medicine

Nanocomposite of Half-Fin Anchovy Hydrolysates/Zinc Oxide Nanoparticles Exhibits Actual Non-Toxicity and Regulates Intestinal Microbiota, Short-Chain Fatty Acids Production and Oxidative Status in Mice – Ru Song – Marine Drugs

Animal microbiome
Is there a link between aging and microbiome diversity in exceptional mammalian longevity? – Graham M. Hughes – PeerJ (Specifically, bats or Myotis myotis)

Gut Microbes Egested during Bites of Infected Sand Flies Augment Severity of Leishmaniasis via Inflammasome-Derived IL-1β – Ranadhir Dey – Cell Host & Microbe

The Sarda Sheep Host Fecal Proteome – Antonio Palomba – Proteomics

Host Specificity for Bacterial, Archaeal and Fungal Communities Determined for High- and Low-Microbial Abundance Sponge Species in Two Genera – Maryam Chaib De Mares – Frontiers In Microbiology (from December 2017)

Comparative Metagenomics of Cellulose- and Poplar Hydrolysate-Degrading Microcosms from Gut Microflora of the Canadian Beaver (Castor canadensis) and North American Moose (Alces americanus) after Long-Term Enrichment. – Mabel T Wong – Frontiers In Microbiology (from December 2017)

Regular Wounding in a Natural System: Bacteria Associated With Reproductive Organs of Bedbugs and Their Quorum Sensing Abilities – Oliver Otti – Frontiers In Immunology

Plant, root, and soil microbiome
Forest conversion induces seasonal variation in microbial β-diversity – Shengen Liu – Environmental Microbiology

Specificity in Arabidopsis thaliana recruitment of root fungal communities from soil and rhizosphere – Hector Urbina – Fungal Biology

Different impacts of manure and chemical fertilizers on bacterial community structure and antibiotic resistance genes in arable soils – Peng Liu – Chemosphere

Intra-species variation in a widely distributed tree species regulates the responses of soil microbiome to different temperature regimes – Cui-Jing Zhang – Environmental Microbiology Reports

Positive diversity-functioning relationships in model communities of methanotrophic bacteria – Elvira Schnyder – Ecology

Plant Phylogeny and Life History Shape Rhizosphere Bacterial Microbiome of Summer Annuals in an Agricultural Field – Bryan D. Emmett – Frontiers in Microbiology (from December 2017)

Soil microbial communities and enzyme activities in sea-buckthorn (Hippophae rhamnoides) plantation at different ages – Miao Yang – Plos One

The genome and microbiome of a dikaryotic fungus (Inocybe terrigena, Inocybaceae) revealed by metagenomics – Mohammad Bahram – Environmental Microbiology Reports

Ecological mechanisms underlying soil bacterial responses to rainfall along a steep natural precipitation gradient – Bonnie Waring – FEMS Microbiology Ecology

ReviewCurrent Insights into the Role of Rhizosphere Bacteria in Disease Suppressive Soils – Ruth Gómez Expósito – Frontiers in Microbiology (from December 2017)

Water and extremophile microbiome
Microbially mediated aluminosilicate formation in acidic anaerobic environments: A cell-scale chemical perspective – J. Sánchez-España – GeoBiology

Responses of Periphyton to Fe2O3 Nanoparticles: A Physiological and Ecological Basis for Defending Nanotoxicity – Jun Tang – Environmental Science & Technology

Variations in bacterial and archaeal communities along depth profiles of Alaskan soil cores – Binu Mani Tripathi – Scientific Reports

Microbiological and Geochemical Survey of CO2-Dominated Mofette and Mineral Waters of the Cheb Basin, Czech Republic – Patryk Krauze – Frontiers In Microbiology

In Situ Field Sequencing and Life Detection in Remote (79°26’N) Canadian High Arctic Permafrost Ice Wedge Microbial Communities – J Goordial – Frontiers In Microbiology (from December 2017)

Built environment
Diversity of Microbial Communities and Quantitative Chemodiversity in Layers of Marine Sediment Cores from a Causeway (Kaichu-Doro) in Okinawa Island, Japan – Taha Soliman – Frontiers In Microbiology

Microbial Contamination on Touch Surfaces in Sick- and Well-Child Waiting Rooms in Pediatric Outpatient Facilities – Irina Gudakova – The Pediatric Infectious Disease Journal

Biostimulation and bioaugmentation of native microbial community accelerated bioremediation of oil refinery sludge – Ajoy Roy – Bioresource Technology

Temporal variation in bacterial and methanogenic communities of three full-scale anaerobic digesters treating swine wastewater – Gyuseong Han – Environmental Science And Pollution Research International

Microbial community of a gasworks aquifer and identification of nitrate-reducing Azoarcus and Georgfuchsia as key players in BTEX degradation – Martin Sperfeld – Water Research

Review: Microbiome analysis and -omics studies of microbial denitrification processes in wastewater treatment: recent advances – Lili Miao – Science China. Life Sciences

Food microbiology
Absorption and Metabolism of Phenolics from Digests of Polyphenol-Rich Potato Extracts Using the Caco-2/HepG2 Co-Culture System – Shima Sadeghi Ekbatan – Foods (Basel, Switzerland)

Effects of polysaccharides from purple sweet potatoes on immune response and gut microbiota composition in normal and cyclophosphamide treated mice – Chao Tang – Food & Function

A Combined LC-MS Metabolomics- and 16S rRNA Sequencing Platform to Assess Interactions between Herbal Medicinal Products and Human Gut Bacteria in Vitro: a Pilot Study on Willow Bark Extract – Eva-Maria Pferschy-Wenzig – Frontiers In Pharmacology

Review: Inflammatory Bowel Diseases and Fermentable Oligosaccharides, Disaccharides, Monosaccharides, and Polyols: An Overview – Sandra Maria Barbalho – Journal Of Medicinal Food

Probiotics / prebiotics / antibiotics
The antimicrobial peptide SAAP-148 combats drug-resistant bacteria and biofilms – Anna de Breij – Science Translational Medicine

Low amounts of dietary fibre increase in vitro production of short-chain fatty acids without changing human colonic microbiota structure – Daisuke Sasaki – Scientific Reports

Single Cell Observations Show Persister Cells Wake Based on Ribosome Content – Jun-Seob Kim – bioRxiv

Evidence for PMAT- and OCT-like biogenic amine transporters in a probiotic strain of Lactobacillus: Implications for interkingdom communication within the microbiota-gut-brain axis. – Mark Lyte – Plos One

Phages and viruses
Metagenomic Virome Analysis of Culex Mosquitoes from Kenya and China. – Evans Atoni – Viruses

Virus Dynamics Are Influenced by Season, Tides and Advective Transport in Intertidal, Permeable Sediments – Verona Vandieken – Frontiers In Microbiology

Influenza A virus infection impacts systemic microbiota dynamics and causes quantitative enteric dysbiosis – Soner Yildiz – Microbiome

Genome Announcements
Draft Genome Sequence of Megamonas funiformis Strain Marseille-P3344, Isolated from a Human Fecal Microbiota. – Mossaab Maaloum – Genome Announcements

Draft Genome Sequences of Bifidobacterium Strains N4G05 and N5G01, Isolated from the Human Vaginal Microbiome. – Aline C Freitas – Genome Announcements

Lactomassilus timonensis,’ a new anaerobic bacterial species isolated from the milk of a healthy African mother – A H Togo – New Microbes And New Infections

Microbes in the news
AGA enrolls 1st patient into largest planned fecal microbiota transplantation study – Eric Oliver – GI & Endoscopy

Will This Swallowable Sensor Replace Colonoscopies? – Bob Curley – HealthLine

**A Patient’s Journey: Taming the Glucose Monster – Howard Wolinsky – MedPage Today**

Microbes on the market
CoreBiome Bolsters Its Board of Directors with the Addition of Daniel Pomp, Ph.D. – BusinessWire

Curetis and MGI Advance Strategic Partnership in NGS-Based Molecular Microbiology – BioSpace

Science, publishing, and career
“Available upon request”: not good enough for microbiome data! – Morgan G I Langille – Microbiome

Tiffany’s non-microbiology picks
Chemists go green to make better blue jeans – Nature
I did not know demin was so dirty until I heard about Everlane’ new jeans – and now there are new method to make them!

January 11, 2018

Today’s Microbiome Digest is quite long, since it contains alerts from two days. There are many interesting articles in Gut, Plant and Water Microbiome Sections. Interesting review to highlight is from L. Tipton about lung mycobiome  and the one from D. Rose Ewald about human microbiota. Today we also have quite few articles about viruses, among which P.C. Hsu revails gene targets of Ebola virus microRNAs involved in the human skin microbiome,  S. S. Jagdale reports on  mutualistic interactions of viruses with lower eukaryotes and C. Winter explains how mixing alters the lytic activity of viruses in the dark ocean.

General microbiome

Complete genomic characterisation of two Escherichia coli lineages responsible for a cluster of carbapenem resistant infections in a Chinese hospital – Zhiyong Zong – bioRxiv

Geometrical Distribution of Cryptococcus neoformans Mediates Flower-Like Biofilm Development – William Lopes – Frontiers in Microbiology

Pregnancy and early life

Editorial: The Neonatal Immune System: A Unique Host-Microbial Interface – Joseph M. Bliss – Frontiers in Pediatrics

Modeling Metabolic Interactions in a Consortium of the Infant Gut Microbiome – Francisco Pinto – Frontiers in Microbiology

Gene-trait matching across the Bifidobacterium longum pan-genome reveals considerable diversity in carbohydrate catabolism among human infant strains – Silvia Arboleya – Genomics

Early-life gut microbiome and egg allergy – Mina Fazlollahi – Allergy

Human respiratory microbiome

Perspective: Fungal Microbiota in Chronic Airway Inflammatory Disease and Emerging Relationships with the Host Immune Response – Irene Zhang – Frontiers in Microbiology

Microbiome and asthma – Milena Sokolowska – Asthma Research and Practice

Review: The lung mycobiome in the next-generation sequencing era – Laura Tipton – Virulence

The lung tissue microbiota of mild and moderate chronic obstructive pulmonary disease – Alexa A. Pragman – Microbiome

 Oral microbiome

Profiling of subgingival plaque biofilm microbiota in female adult patients with clear aligners: a three-month prospective study – Runzhi Guo – PeerJ

Ecological Approaches to Dental Caries Prevention: Paradigm Shift or Shibboleth? – Nebu Philip  – Caries Research

Human skin microbiome

On revealing the gene targets of Ebola virus microRNAs involved in the human skin microbiome – Pei-Chun Hsu – PeerJ

Temporal Variation of the Skin Bacterial Community and Batrachochytrium dendrobatidis Infection in the Terrestrial Cryptic Frog Philoria loveridgei – Mariel Familiar López – Frontiers in Microbiology

Human vaginal microbiome

Microbiota-based analysis reveals specific bacterial traits and a novel strategy for the diagnosis of infectious infertility – Simon Graspeuntner – PLOS One

Human nearly-sterile sites 

Culture-independent analysis of liver abscess using nanopore sequencing – Liang Gong – PLOS One

Human gut microbiome

The Gut Microbiome and Control of Weight Gain – Anita L. Kozyrskyj – Pediatric Obesity

Immunosuppressive effect of the gut microbiome altered by high-dose tacrolimus in mice – Z. Zhang – American Journal of Transplatation

Review: Human microbiota, blood group antigens, and disease – D. Rose Ewald – WIREs

Microbiome, Immunomodulation, and the Neuronal System – Eric Marietta – Neurotherapeutics

Editorial: Improve gut microbiome: a new horizon of cancer therapy – Hiroshi Fukui – Hepatobiliary Surgery and Nutrition

The Gut Microbiome and Multiple Sclerosis – Javier Ochoa-Repáraz – Cold Spring Harbor Perspectives in Medicine

Genomic diversity and distribution of Bifidobacterium longum subsp. longum across the human lifespan – Toshitaka Odamaki – Scientific Reports

Dynamics of metatranscription in the inflammatory bowel disease gut microbiome – Melanie Schirmer – Nature Microbiology

Links between Dietary Protein Sources, the Gut Microbiota, and Obesity – Lise Madsen – Frontiers in Physiology

Ceftriaxone promotes the emergence of AmpC-overproducing Enterobacteriaceae in gut microbiota from hospitalized patients – Victoire de Lastours – European Journal of Clinical Microbiology & Infectious Diseases

Functional analysis of arginine decarboxylase gene speA of Bacteroides dorei by markerless gene deletion – Mikiyasu Sakanaka – FEMS Microbiology Letters

SadA-Expressing Staphylococci in the Human Gut Show Increased Cell Adherence and Internalization – Arif Luqman – Cell Reports

Gut microbiome populations are associated with structure-specific changes in white matter architecture – Irene M. Ong – Translational Psychiatry

Spatiotemporally Heterogeneous Population Dynamics of Gut Bacteria Inferred from Fecal Time Series Data – Hidetoshi Inaminea – mBio

Animal experiments 

Identification of a protective B-cell epitope of the Staphylococcus aureus GapC protein by screening a phage-displayed random peptide library – Mengyao Wang – PLOS One

Lactobacillus plantarum CCFM10 alleviating oxidative stress and restoring the gut microbiota in D-galactose-induced aging mice – Jichun Zhao – Food and Function

Effect of dark sweet cherry powder consumption on the gut microbiota, short-chain fatty acids, and biomarkers of gut health in obese db/db mice – Jose F. Garcia-Mazcorro – PeerJ

Dietary Corn Bran Fermented by Bacillus subtilis MA139 Decreased Gut Cellulolytic Bacteria and Microbiota Diversity in Finishing Pigs – Ping Liu – Frontiers in Cellular and Infection Microbiology

Intestinal and Systemic Immune Responses upon Multi-drug Resistant Pseudomonas aeruginosa Colonization of Mice Harboring a Human Gut Microbiota – Eliane von Klitzing – Frontiers in Microbiology

Modulation of Intestinal Microbiome Prevents Intestinal Ischemic Injury – Alessandra Bertacco – Frontiers in Physiology

Animal microbiome 

Influence of fruit and invertebrate consumption on the gut microbiota of wild white-faced capuchins (Cebus capucinus) – Elizabeth K. Mallott – American Journal of Physical Anthropology

Differential Ecological Specificity of Protist and Bacterial Microbiomes across a Set of Termite Species – Lena Waidele – Frontiers in Microbiology

Molecular identification and phylogenetic analysis of Bothrops insularis bacterial and fungal microbiota – Lidiane Nunes Barbosa – Journal of Toxicology and Environmental Health

Plant, root, and soil microbiome

Diazotroph abundance and community composition in an acidic soil in response to aluminum-tolerant and aluminum-sensitive maize (Zea mays L.) cultivars under two nitrogen fertilizer forms – Chao Wang – Plant and Soil

The influence of microbial communities for triadimefon enantiomerization in soils with different pH values – Khaled Mohamed Ahmed Talab – Chirality

Antimony Redox Biotransformation in the Subsurface: Effect of Indigenous Sb(V) Respiring Microbiota – Liying Wang – Encironmental Science and Technology

Biostimulant Action of Protein Hydrolysates: Unraveling Their Effects on Plant Physiology and Microbiome – Giuseppe Colla – Frontiers in Plant Science

Inner Plant Values: Diversity, Colonization and Benefits from Endophytic Bacteria – Hongwei Liu – Frontiers in Microbiology

Bacillus amyloliquefaciens L-S60 Reforms the Rhizosphere Bacterial Community and Improves Growth Conditions in Cucumber Plug Seedling – Yuxuan Qin – Frontiers in Microbiology

Exploring the Microbiota of Faba Bean: Functional Characterization of Lactic Acid Bacteria – Michela Verni –  Frontiers in Microbiology

Contribution of Zinc Solubilizing Bacteria in Growth Promotion and Zinc Content of Wheat – Sana Kamran – Frontiers in Microbiology

Application of Endophytic Pseudomonas fluorescens and a Bacterial Consortium to Brassica napus Can Increase Plant Height and Biomass under Greenhouse and Field Conditions –  Richard D. Lally – Frontiers in Microbiology

Exploiting rhizosphere microbial cooperation for developing sustainable agriculture strategies – Yoann Besset-Manzoni – Environmental Science and Pollution Research

Dynamics of oxygen and carbon dioxide in rhizospheres of Lobelia dortmanna – a planar optode study of belowground gas exchange between plants and sediment – Nikola Lenzewski – New Phytologist

Characterization of Microbial Communities in Acidified, Sulfur Containing Soils – Grzegorz Czerwonka – Polish Journal of Microbiology

Comparison of Microbial Communities Associated with Halophyte (Salsola stocksii) and Non-Halophyte (Triticum aestivum) Using Culture-Independent Approaches – Salma Mukhtar – Polish Journal of Microbiology

Water and extremophile microbiome 

Data-mining of Antibiotic Resistance Genes Provides Insight into the Community Structure of Ocean Microbiome – Shiguang Hao – bioRxiv

Mixing alters the lytic activity of viruses in the dark ocean – Christian Winter – Ecology

Biological Characterization of Microenvironments in a Hypersaline Cold Spring Mars Analog – Haley M. Sapers – Frontiers in Microbiology

Patterns and Drivers of Vertical Distribution of the Ciliate Community from the Surface to the Abyssopelagic Zone in the Western Pacific Ocean – Feng Zhao – Frontiers in Microbiology

Aerobic and Anaerobic Methanotrophic Communities Associated with Methane Hydrates Exposed on the Seafloor: A High-Pressure Sampling and Stable Isotope-Incubation Experiment – David H. Case – Frontiers in Microbiology

A Multi-season Investigation of Microbial Extracellular Enzyme Activities in Two Temperate Coastal North Carolina Rivers: Evidence of Spatial but Not Seasonal Patterns – Avery Bullock – Frontiers in Microbiology

Functional Stability and Community Dynamics during Spring and Autumn Seasons Over 3 Years in Camargue Microbial Mats – Mercedes Berlanga – Frontiers in Microbiology

Oxygenation of Hypoxic Coastal Baltic Sea Sediments Impacts on Chemistry, Microbial Community Composition, and Metabolism – Elias Broman – Frontiers in Microbiology

Exploring the Cultivable Ectocarpus Microbiome – Hetty KleinJan – Frontiers in Microbiology

Phylogenetic Structure and Metabolic Properties of Microbial Communities in Arsenic-Rich Waters of Geothermal Origin – Simona Crognale – Frontiers in Microbiology

Prokaryotic Community Composition in Arctic Kongsfjorden and Sub-Arctic Northern Bering Sea Sediments As Revealed by 454 Pyrosequencing – Yin-Xin Zeng – Frontiers in Microbiology

Comparative Metagenomics Reveals the Distinctive Adaptive Features of the Spongia officinalis Endosymbiotic Consortium – Elham Karimi – Frontiers in Microbiology

Comparative genomics highlights symbiotic capacities and high metabolic flexibility of the marine genus Pseudovibrio  – Dennis Versluis – GBE Genome BIology and Evolution

Geobacteraceae are important members of mercury-methylating microbial communities of sediments impacted by waste water releases – Andrea G. Bravo – ISME

Dynamics of phytoplankton and heterotrophic bacterioplankton in the western tropical South Pacific Ocean along a gradient of diversity and activity of diazotrophs – France Van Wambeke – Biogeosciences

Microbial methanogenesis in the sulfate-reducing zone of sediments in the Eckernförde Bay, SW Baltic Sea – Johanna Maltby – Biogeosciences

Built environment

Control of corrosive bacterial community by bronopol in industrial water system – Jayaraman Narenkumar – 3 Biotech

A metaproteomics method to determine carbon sources and assimilation pathways of species in microbial communities –  Manuel Kleiner – bioRxiv

Uncovering the Potential of Termite Gut Microbiome for Lignocellulose Bioconversion in Anaerobic Batch Bioreactors – Lucas Auer – Frontiers in Microbiology

Microbial Communities Shaped by Treatment Processes in a Drinking Water Treatment Plant and Their Contribution and Threat to Drinking Water Safety – Qi Li – Frontiers in Microbiology

Food microbiology

Development of novel quinoa-based yoghurt fermented with dextran producer Weissella cibaria MG1 – Emanuele Zannini – International Journal of Food Microbiology

Bacterial Community and Spoilage Profiles Shift in Response to Packaging in Yellow-Feather Broiler, a Highly Popular Meat in Asia – Huhu Wang – Frontiers in Microbiology

Metagenomic Profiling of the Bacterial Community Changes from Koji to Mash Stage in the Brewing of Soy Sauce – Hongbin Wang – Polish Journal of Microbiology

Probiotics / prebiotics

Probiotics or Pro-healers the Role of Beneficial Bacteria in Tissue Repair – Jovanka Lukic – Wound Reparation and Regeneration

Probiotic Lactobacillus sp. inhibit growth, biofilm formation and gene expression of caries-inducing Streptococcus mutans – Reham Wasfi – Journal of Cellular and Molecular Medicine

A mixture of Lactobacillus species isolated from traditional fermented foods promote recovery from antibiotic-induced intestinal disruption in mice – Ying Shi – Journal of Applied Microbiology

Beneficial changes in rumen bacterial community profile in sheep and dairy calves as a result of feeding the probiotic Bacillus amyloliquefaciens H57 – Benjamin J Schofield – Journal of Applied Microbiology

Phages and viruses

Enemies with benefits: mutualistic interactions of viruses with lower eukaryotes – Shounak S. Jagdale – Archives of Virology

Biogeography & environmental conditions shape bacteriophage-bacteria networks across the human microbiome – Geoffrey D. Hannigan – bioRxiv

Investigation of prevalence of free Shiga toxin-producing Escherichia coli (STEC)-specific bacteriophages and its correlation with STEC bacterial hosts in a produce-growing area in Salinas, California – Yen-Te Liao – PLOS One

Component tree analysis of cystovirus φ6 nucleocapsid Cryo-EM single particle reconstructions – Lucas M. Oliveira – PLOS One

Bioinformatics

HTSSIP: An R package for analysis of high throughput sequencing data from nucleic acid stable isotope probing (SIP) experiments – Nicholas D. Youngblut – PLOS One

Biotechnology

Cyanobacterial diversity held in microbial biological resource centers as a biotechnological asset: the case study of the newly established LEGE culture collection – Vitor Ramos – Journal of Applied Phycology

Rapidly moving new bacteria to model-organism status – Hualan Liu – Current Opinion in Biotechnology

Techniques

Development of a biosensor protein bullet as a fluorescent method for fast detection of Escherichia coli in drinking water – Ignacio Gutiérrez-del-Río – PLOS One

Research Note: Methods for detecting Gemmata spp. bacteremia in the microbiology laboratory – Jacques-Robert Christen – BMS Genomics

A metaproteomics method to determine carbon sources and assimilation pathways of species in microbial communities – Manuel Kleiner – bioRxiv

Microbes in the news 

Gene/cell connection provides new insight into how our gut microbiome stays healthy

A powerful new weapon against drug-resistant bacteria was inspired by the human body

ASU developing biodegradable plastics made from bacteria

Pharmaceutical Pollution Drives Microbial Resistance in Urban Streams

Microbes and Art

This scientist creates ephemeral works of art with bioluminescent bacteria

January 8, 2018

 

Today’s Microbiome Digest has many interesting articles. Read how microscope-based artificial intelligence could alleviate shortage of clinical microbiologists, the article by K. P. Smith. N. A. Kamennaya reports on “Pomacytosis”, a semi-extracellular phagocytosis of cyanobacteria, while M. F. Dias investigated the effect of different drinking waters on mouse gut microbiota.

Events

One-day Symposium (12 Jan 2018): Microbial symbiosis in the marine environment – live streamming

Jobs

Postdoctoral positions in evolutionary genomics, UT Austin

General microbiome

Dietary trehalose enhances virulence of epidemic Clostridium difficile – J. Collins – Nature

Transmission in the Origins of Bacterial Diversity, From Ecotypes to Phyla – Frederick M. Cohan – Microbiology Spectrum

How much do rRNA gene surveys underestimate extant bacterial diversity? – Luis M. Rodriguez-R – Applied and Environmental Microbiology

Vibrio cholerae genomic diversity within and between patients –  Inès Levade – Microbial Genomics

Automated Interpretation of Blood Culture Gram Stains using a Deep Convolutional Neural Network – Kenneth P. Smith – Applied and Environmental Microbiology

Regulated ploidy of Bacillus subtilis and three new isolates of Bacillus and Paenibacillus – Benjamin Böttinger – FEMS Microbiology Letters

Human respiratory microbiome

Heavy metal exposure and nasal Staphylococcus aureus colonization: analysis of the National Health and Nutrition Examination Survey (NHANES) – Shoshannah Eggers – Environmental Health

Oral microbiome

Microbial Analysis of Endodontic Infections in Root-filled Teeth with Apical Periodontitis before and after Irrigation Using Pyrosequencing – Homan Zandi – Journal of Endodontics

Human vaginal microbiome

Long-term Lactobacillus rhamnosus BMX 54 application to restore a balanced vaginal ecosystem: a promising solution against HPV-infection – Ettore Palma – BMC Infectious Diseases

Lactobacillus-deficient vaginal microbiota dominate post-partum women in rural Malawi – Ronan Doyle – Applied and Environmental Microbiology

Human nearly-sterile sites

Microbiota and the liver – Ting-Chin David Shen – Liver Transplatation

Human gut microbiome

Comparison of DNA extraction methods for human gut microbial community profiling – Mi Young Lim – Systematic and Applied Microbiology

Changes in Gut Microbiota–Related Metabolites and Long-term Successful Weight Loss in Response to Weight-Loss Diets: The POUNDS Lost Trial – Yoriko Heianza – Diabetes Care

Adaptation of human gut microbiota to bariatric surgeries in morbidly obese patients: A systematic review – Hanieh-Sadat Ejtahed – Microbial Pathogenesis

The germ-organ theory of non-communicable diseases – Mariana X. Byndloss – Nature Reviews Microbiology

Evolution of a dominant natural isolate of Escherichia coli in the human gut over a year suggests a neutral evolution with reduced effective population size – Mohamed Ghalayini – Applied and Environmental Microbiology

Animal experiments

Changes in mouse gut bacterial community in response to different types of drinking water – Marcela F. Dias – Water Research

Plant, root, and soil microbiome

Microbial Communities of High-Elevation Fumaroles, Penitentes, and Dry Tephra “Soils” of the Puna de Atacama Volcanic Zone – Adam J. Solon – Microbial Ecology

Shifts in soil bacterial and archaeal communities during freeze-thaw cycles in a seasonal frozen marsh, Northeast China – Jiusheng Ren – Science of The Total Environment

The ‘Neglected’ Soil Virome – Potential Role and Impact – Akbar Adjie Pratama – Trends in Microbiology

Water and extremophile microbiome 

Study of marine bacteria inactivation by photochemical processes: disinfection kinetics and growth modeling after treatment – Javier Moreno-Andrés – Environmental Science and Pollution Research

Metabolic capability and in situ activity of microorganisms in an oil reservoir – Yi-Fan Liu – Microbiome

Phylogenetic distribution of roseobacticides in the Roseobacter group and their effect on microalgae – Eva C Sonnenschein – BioRxiv

“Pomacytosis”—Semi-extracellular phagocytosis of cyanobacteria by the smallest marine algae – Nina A. Kamennaya – PLOS Biology

The Green Berry Consortia of the Sippewissett Salt Marsh: Millimeter-Sized Aggregates of Diazotrophic Unicellular Cyanobacteria – Elizabeth G. Wilbanks – Frontiers in Microbiology

Dynamic changes in carbonate chemistry in the microenvironment around single marine phytoplankton cells – Abdul Chrachri – Nature Communications

Homogenization of lake cyanobacterial communities over a century of climate change and eutrophication – Marie-Eve Monchamp – Nature Ecology & Evolution

Bacterial Recycling of Archaeal Biomass as a New Strategy for Extreme Life in the Dead Sea Deep Sediment – Camille Thomas – EarthArXiv Preprints

Food microbiology

Seasonal variances in bacterial microbiota and volatile organic compounds in raw milk – Beata Nalepa – International Journal of Food Microbiology

Phages and viruses

Is weak CD4+ gain in the course of suppressive combination antiretroviral therapy for HIV infection a current clinical challenge? A case report and brief review of the literature – Camilla Tincati – BMC Infectious Diseases

Techniques

NanoAmpli-Seq: A workflow for amplicon sequencing from mixed microbial communities on the nanopore sequencing platform – Szymon T Calus – bioRxiv

Microbes in the news

Scientists engineer sound-reflecting bacteria

Experts: ‘Raw Water’ Offers Unfiltered Risk

 

January 5, 2018

Today’s digest has an interesting commentary on the oral-gut connection and a brilliant piece on microbial diversity. Lastly, a look at how grapevines influence belowground diversity and networks

General Microbiome

A role for the endometrial microbiome in dysfunctional menstrual bleeding. Pelzer ES. Antonie Van Leeuwenhoek.

Performance and microbial community variations of anaerobic digesters under increasing tetracycline concentrations. Xiong Y. Applied Microbiology and Biotechnology

In Nature, There Is Only Diversity. McLaren MR. MBio.

Gut Microbiome

Commentary: Oral-gut connection: one step closer to an integrated view of the gastrointestinal tract? Lira-Junior R. Mucosal Immunology

Bile acids at the cross-roads of gut microbiome-host cardiometabolic interactions. Ryan PM. Diabeticology and Metabolic Syndrome

REVIEW: Diet, Microbiota, and Metabolic Health: Trade-Off Between Saccharolytic and Proteolytic Fermentation. Korpela K. Annual of Food Science and Technology

Nasal and Lung Microbiome

REVIEW: Fungi in Bronchiectasis: A Concise Review. Máiz L. Internatioanal Journal of Molecular Sciences

Alterations in the mucosa-associated fungal microbiota in patients with ulcerative colitis. Qiu X. Oncotarget

The association between anterior nares and nasopharyngeal microbiota in infants hospitalized for bronchiolitis. Luna PN. Microbiome

Fecal Microbiome

Editorial Comment: Fecal microbiota transplantation as a possible treatment of irritable bowel syndrome. Juncadella AC. Annals of Translational Medicine

Plant, Soil, and Water Microbiome

Co-variation between Distribution of Microbial Communities and Biological Metabolization of Organics in Urban Sewer Systems. Jin P. Environmental Science and Technology.

Do invasive plants structure microbial communities to accelerate decomposition in intermountain grasslands? McTee MR. Ecology and Evolution

Grapevine rootstocks shape underground bacterial microbiome and networking but not potential functionality. Marasco R. Microbiome

Biodiversity of the microbial mat of the Garga hot spring. Rozanov AS. BMC Evolutionary Biology

Animal Experiments and Microbiome

Microbiota Reconstitution Does Not Cause Bone Loss in Germ-Free Mice. Quach D. mSphere

Physiological Translocation of Lactic Acid Bacteria during Pregnancy Contributes to the Composition of the Milk Microbiota in Mice. de Andrés J. Nutrients

Extreme sensitivity to ultraviolet light in the fungal pathogen causing white-nose syndrome of bats. Palmer JM. Nature Communication

OCCURRENCE OF PASTEURELLACEAE BACTERIA IN THE ORAL CAVITY OF SELECTED MARSUPIAL SPECIES. Hansen MJ. Journal of Zoo and Wildlife Medicine

Marine Microbiome

Agelas Wasting Syndrome Alters Prokaryotic Symbiont Communities of the Caribbean Brown Tube Sponge, Agelas tubulata.Deignan LK. Microbial Ecology

Environmental drivers of heterogeneity in the trophic-functional structure of protozoan communities during an annual cycle in a coastal ecosystem. Xu G. Marine Pollution Bulletin

Antibiotic Resitance

Editorial: Empiric antibiotic use in allogeneic hematopoietic cell transplantation: should we avoid anaerobe coverage? Shono Y. Blood Advances

Characterization of genetic determinants involved in antibiotic resistance in Aeromonas spp. and fecal coliforms isolated from different aquatic environments. Carnelli A. Research in Microbiology

 

 

December 30, 2017

Enjoy your daily dose of (mostly human gut) microbiome literature!

General microbiome

Q&A: Friends (but sometimes foes) within: the complex evolutionary ecology of symbioses between host and microbes – Nicole Gerardo, BMC Biology

The Dark Side of IFN-γ: Its Role in Promoting Cancer Immunoevasion – Marija Mojic, International Journal of Molecular Sciences

Two-stage pretreatment of excess sludge for electricity generation in microbial fuel cell – Yi Zhang, Environmental Technology

Human respiratory microbiome

Azithromycin versus placebo for the treatment of HIV-associated chronic lung disease in children and adolescents (BREATHE trial): study protocol for a randomised controlled trial – Carmen Gonzalez-Martinez, BMC Biology

Human skin microbiome

Characterization of the facial microbiome in twins discordant for rosacea – Asifa K. Zaidi, Experimental Dermatology

Human oral microbiome

Oral health in geroscience: animal models and the aging oral cavity – Jonathan Y. An, GeroScience

Extracellular matrix Influence in Streptococcus mutans gene expression in a cariogenic biofilm – Elkin Jahir Florez Salamanca, Molecular Oral Microbiology

Human gut microbiome

The Microbiome–Gut–Behavior Axis: Crosstalk Between the Gut Microbiome and Oligodendrocytes Modulates Behavioral Responses – Achilles Ntranos, Neurotherapeutics

Antibiotics Associated Disorders and Postbiotics Induced Rescue in Gut Health – Debarati Paul, Current Pharmaceutical Design

We are not alone in our body: insights into the involvement of microbiota in the etiopathogenesis and pharmacology of mental illness –  Claudia Pisanu, Current Drug Metabolism

Global transcriptional landscape and promoter mapping of the gut commensal Bifidobacterium breve UCC2003 – Francesca Bottacini, BMC Genomics

Microbiota dysbiosis in inflammatory bowel diseases: in silico investigation of the oxygen hypothesis – Michael A. Henson, BMC Systems Biology

Gut microbiota: Fibre restores healthy gut microbiota – Alan Morris, Nature Reviews Endocrinology

The human microbiome in evolution – Emily R. Davenport, BMC Biology

Clinical characteristics and long-term prognosis of elderly onset ulcerative colitis – Eun Mi Song, Gastroenterology and Hepatology

Environmental contributions to gastrointestinal and liver cancer in the Asia–Pacific region – Kwang-Pil Ko, Gastroenterology and Hepatology

Effect of oral tobacco use and smoking on outcomes of Crohn’s disease in India – Umang Arora, Gastroenterology and Hepatology

Irritable bowel syndrome in Asia: Pathogenesis, natural history, epidemiology, and management – Kok-Ann Gwee, Gastroenterology and Hepatology

Rifaximin has minor effects on bacterial composition, inflammation, and bacterial translocation in cirrhosis: A randomized trial – Nina Kimer, Gastroenterology and Hepatology

The role of the microbiome and the use of probiotics in gastrointestinal disorders in adults in the Asia-Pacific region – background and recommendations of a regional consensus meeting – Uday C Ghoshal, Gastroenterology and Hepatology

Animal experiments

Inclusion of Bacillus amyloliquefaciensstrain TOA5001 in the diet of broilers suppresses the symptoms of coccidiosis by modulating intestinal microbiota – Takamitsu Tsukahara, Animal Science Journal

Characterization of the cervical bacterial community in dairy cows with metritis and during different physiological phases – Yu Wang, Theriogenology

Replacement of alfalfa hay (Medicago sativa L.) with subabul (Leucaena leucocephala) leaf meal in diets of Najdi goats: effect on digestion activity of rumen microorganisms – Tahereh Mohammadabadi, Tropical Animal Health and Production

Animal microbiome

Individual- and Species-Specific Skin Microbiomes in Three Different Estrildid Finch Species Revealed by 16S Amplicon Sequencing – Kathrin Engel, Microbial Ecology

Plant, root, and soil microbiome

Changes of microbial population and N-cycling function genes with depth in three Chinese paddy soils – Huanhuan Wang, PLOS One

Water and extremophile microbiome

Candidatus Nitrosocaldus cavascurensis, an ammonia oxidizing, extremely thermophilic archaeon with a highly mobile genome – Sophie S Abby, bioRxiv

Microbes in the news

Artificial intelligence identifies bacteria images quickly, accurately – Greg Slabodkin, Health Data Management

Microbes on the market

Assembly Biosciences, Inc. (ASMB) Reaches $45.08 After 7.00% Up Move; GEOX SPA (GXSBF) Shorts Raised By 18.36% – Stephen Andrade, Herald KS

December 24, 2017

Events and jobs
Microbiology/bioinformatics/bioche Freshers Wanted For Medical Coding – AS Medical Coding Technologies – Chennai, Cuddalore, Vellore

General microbiome
Review: Protective Microbiota: From Localized to Long-Reaching Co-Immunity. – Lynn Chiu – Frontiers In Immunology

Pregnancy and early life
Microbiome Influences Prenatal and Adult Microglia in a Sex-Specific Manner – Morgane Sonia Thion – Cell

Human respiratory microbiome
Differentially Regulated Host Proteins Associated with Chronic Rhinosinusitis Are Correlated with the Sinonasal Microbiome. – Kristi Biswas – Frontiers In Cellular And Infection Microbiology

Sputum microbiome temporal variability and dysbiosis in chronic obstructive pulmonary disease exacerbations: an analysis of the COPDMAP study. – Zhang Wang – Thorax

Human vaginal microbiome
Evaluation of lactitol, lactulose, raffinose, and oligofructose for maintenance of a Lactobacillus-dominated vaginal microbiota establishes a promising prebiotic candidate. – Stephanie L Collins – Applied And Environmental Microbiology

Review: Human vaginal pH and microbiota: an update. – Keshav Godha – Gynecological Endocrinology

Review: Impact of microbiota on the use and effects of isoflavones in the relief of climacteric symptoms in menopausal women – A review – Naice E.S. Monteiro – Journal of Functional Foods

Human oral microbiome
Review: Tongue Coating: its characteristics and role in intra-oral halitosis and general health: A review. – Kavitha Seerangaiyan – Journal Of Breath Research

Human gut microbiome
Bifidobacteria or Fiber Protects against Diet-Induced Microbiota-Mediated Colonic Mucus Deterioration – Bjoern O. Schroeder – Cell Host and Microbe

Fiber-Mediated Nourishment of Gut Microbiota Protects against Diet-Induced Obesity by Restoring IL-22-Mediated Colonic Health – Jun Zou – Cell Host and Microbe

Dysbiosis-Associated Change in Host Metabolism Generates Lactate to Support Salmonella Growth – Caroline C. Gillis – Cell Host and Microbe

Durability and Long-Term Clinical Outcomes of Fecal Microbiota Transplant (FMT) Treatment in Patients with Recurrent Clostridium difficile Infection. – Yafet Mamo – Clinical Infectious Diseases

Evaluation of a faecal dysbiosis test for irritable bowel syndrome in subjects with and without obesity. – Martin Aasbrenn – Scandinavian Journal Of Clinical And Laboratory Investigation

Structural basis for the regulation of β-glucuronidase expression by human gut Enterobacteriaceae. – Michael S Little – PNAS

Low-to-moderate intensity aerobic exercise training modulates irritable bowel syndrome through antioxidative and inflammatory mechanisms in women: Results of a randomized controlled trial – Behzad Hajizadeh Maleki – Cytokine

Differences in fecal microbial metabolites and microbiota of children with autism spectrum disorders – Dae-Wook Kang – Anaerobe

Review: The Microbiome in Primary Sclerosing Cholangitis: Current Evidence and Potential Concepts. – Johannes R Hov – Seminars In Liver Disease

Microbial ecology
Autoinducer 2-dependent Escherichia coli biofilm formation is enhanced in a dual-species co-culture. – Leanid Laganenka – Applied And Environmental Microbiology

Animal experiments
Prebiotic Supplementation Following Ileocecal Resection in a Murine Model is Associated With a Loss of Microbial Diversity and Increased Inflammation. – Michael Laffin – Inflammatory Bowel Diseases

An attenuated Salmonella Typhimurium strain and galacto-oligosaccharides (GOS) accelerate clearance of Salmonella infection in poultry through modifications to the gut microbiome. – M Andrea Azcarate-Peril – Applied And Environmental Microbiology

Akkermansia muciniphila induces gut microbiota remodelling and controls islet autoimmunity in NOD mice. – Arno Hänninen – Gut

Analysis of the Specificity of IgA Antibodies Produced in the Mouse Small Intestine. – N E Sharanova – Molekuliarnaia Biologiia (Molecular Biology, original in Russian)

Bacteriostatic Effect of Quercetin as an Antibiotic Alternative In Vivo and Its Antibacterial Mechanism In Vitro. – Shengan Wang – Journal Of Food Protection (in Arbor Acre (AA) broiler chickens)

Dietary protein level affects nutrient digestibility and ileal microbiota structure in growing pigs. – Kai Qiu – Animal Science Journal

Arctic berry extracts target the gut-liver axis to alleviate metabolic endotoxaemia, insulin resistance and hepatic steatosis in diet-induced obese mice. – Fernando F Anhê – Diabetologia

Microbiota transplantation reveals beneficial impact of berberine on hepatotoxicity by improving gut homeostasis. – Chenjie Qin – Science China. Life Sciences (in rats and mice)

Dysbiosis of gut microbiota by chronic coexposure to titanium dioxide nanoparticles and bisphenol A: Implications for host health in zebrafish – Lianguo Chen – Environmental Pollution

Dysbiosis of the fecal microbiota in feedlot cattle with hemorrhagic diarrhea – Mohamed Zeineldin – Microbial Pathogenesis

Characterization of Brachyspira communities from clinical cases of swine mucohaemorrhagic diarrhea through deep sequencing of the NADH oxidase (nox) gene – Lisa A. Johnson – Veterinary Microbiology

Injectable antimicrobials in commercial feedlot cattle and their effect on the nasopharyngeal microbiota and antimicrobial resistance – Devin B. Holman – Veterinary Microbiology

Grain grinding size of cereals in complete pelleted diets for growing lambs: effects on ruminal microbiota and fermentation – Sonia Andrés – Small Ruminant Research

Animal microbiome
Food Storage by the Savanna Termite Cornitermes cumulans (Syntermitinae): a Strategy to Improve Hemicellulose Digestibility? – Letícia Menezes – Microbial Ecology

The metagenome of Caracolus marginella gut microbiome using culture independent approaches and shotgun sequencing. – Robert J Rabelo-Fernandez – Data In Brief (snails)

Transcriptomic characterization of Caecomyces churrovis: a novel, non-rhizoid-forming lignocellulolytic anaerobic fungus. – John K Henske – Biotechnology For Biofuels (Found in Navajo Churro sheep fecal pellets)

** Enhancing the Resolution of Rumen Microbial Classification from Metatranscriptomic Data Using Kraken and Mothur. – Andre L A Neves – Frontiers In Microbiology **

Temporal and regional variability in the skin microbiome of humpback whales along the Western Antarctic Peninsula. – K C Bierlich – Applied And Environmental Microbiology (DOI not available yet, so linked to PubMed)

Wild eel microbiome reveals that skin mucus of fish could be a natural niche for aquatic mucosal pathogen evolution. – Miguel Carda-Diéguez – Microbiome

Seasonal, spatial, and maternal effects on gut microbiome in wild red squirrels. – Tiantian Ren – Microbiome

Water and extremophile microbiome
Biodegradation of weathered polystyrene films in seawater microcosms. – Evdokia Syranidou – Scientific Reports

Microbial stress mediated intercellular nanotubes in an anaerobic microbial consortium digesting cellulose. – Martina John – Scientific Reports

Metagenomic analysis reveals the impact of wastewater treatment plants on the dispersal of microorganisms and genes in aquatic sediments. – Binh T T Chu – Applied And Environmental Microbiology

Nutrient dynamics and stream order influence microbial community patterns along a 2914 km transect of the Mississippi River – Michael W Henson – bioRxiv

Metagenomic exploration reveals a marked change in the river resistome and mobilome after treated wastewater discharges – Itziar Lekunberri – Environmental Pollution

Built environment
Metagenomic survey of bacterial diversity in the atmosphere of Mexico City using different sampling methods – N. Serrano-Silva – Environmental Pollution

Dynamics of biofilm formation by Listeria monocytogenes on stainless steel under mono-species and mixed-culture simulated fish processing conditions and chemical disinfection challenges – Eleni Papaioannou – International Journal of Food Microbiology

Food microbiology
Modulation of gut microbiota and gut-generated metabolites by bitter melon results in improvement in the metabolic status in high fat diet-induced obese rats – Juan Bai – Journal of Functional Foods

In vitro digestion by saliva, simulated gastric and small intestinal juices and fermentation by human fecal microbiota of sulfated polysaccharides from Gracilaria rubra – Tong Di – Journal of Functional Foods

Seasonal variances in bacterial microbiota and volatile organic compounds in raw milk – Beata Nalepa – International Journal of Food Microbiology

Structure of association networks in food bacterial communities – Eugenio Parente – Food Microbiology

Review: Lactose intolerance and gastrointestinal cow’s milk allergy in infants and children – common misconceptions revisited. – Ralf G Heine – The World Allergy Organization Journal

Probiotics / prebiotics / antibiotics
Effect of the consumption of a synbiotic diet mousse containing Lactobacillus acidophilus La-5 by individuals with metabolic syndrome: A randomized controlled trial – Douglas Xavier-Santos – Journal of Functional Foods

Review: Is Metformin Poised for a Second Career as an Antimicrobial? – Faiza Malik – Diabetes/Metabolism Research And Reviews

Review: Role of probiotics in the management of lung cancer and related diseases: An update – Anshul Sharma – Journal of Functional Foods

Phages and viruses
Isolation in small populations of Wayampi Amerindians promotes endemicity and homogenization of their faecal virome, but its distribution is not entirely random. – Vicente Pérez-Brocal – Fems Microbiology Ecology

Bioinformatics
Identification of bacterial species that can utilize fructose-asparagine. – Anice Sabag-Daigle – Applied And Environmental Microbiology

Techniques
On the Identification of Culturable Microorganisms for the Assessment of Biodiversity in Bioaerosols. – Philippe Duquenne – Annals Of Work Exposures And Health

Review: Illuminating the covert mission of mononuclear phagocytes in their regional niches – Shu Zhen Chong – Current Opinion in Immunology

Genomes
Draft genomes of Enterococcus faecium strains isolated from human feces before and after eradication therapy against Helicobacter pylori. – Nikita A Prianichnikov – Data In Brief

Microbes in the news
Biota Beats: Music from the Microbiome –  Clara Rodríguez Fernández – LabBioTech
Microbes on the market (news about biotech companies)

Bacteria and Cancer Immunotherapy: What’s in Your Gut? – Medical News Bulletin

Can You Teach an Old Gene New Tricks? – Grishma Gupte – SciWorthy

Doctor warns patients to avoid unnecessary antibiotics this winter – Tammy Palmer – LocalSyr.com