December 16, 2018

A Happy Weekend to one and all. 

Today’s Microbiome Digest features the recent articles covering the techniques and treatments, microbiome of infants, gut, oral, eye and vaginal microbiome, host-microbe interactions, diet and probiotic supplementations, co-culture models and its impact on biofilm reduction, soil microbiome and microbial ecology, comparative study of microbiome in various diseases, role of microbiome on various cancers, metabolomics, animal and insect microbiome, myco and yeast biome, genes and genomics of good and bad bacteria.  ENJOY READING.

TECHNIQUES:

Rapid Determination of Antibiotic Susceptibility by Stimulated Raman Scattering Imaging of D2O Metabolism – Weili Hong – bioRxiv

CaptureSeq: Capture-based enrichment of cpn60 gene fragments empowers pan-Domain profiling of microbial communities without universal PCR – Matthew G Links – bioRxiv

Characterization of Hydrocarbon-Degrading Bacteria in Constructed Wetland Microcosms Used to Treat Crude Oil Polluted Water– Amer Jamal Hashmat- Bulletin of Environmental Contamination and Toxicology

A Probe-Enabled Approach for the Selective Isolation and Characterization of Functionally Active Subpopulations in the Gut Microbiome – Whidbey C – J Am Chem Soc.

Combined extraction method for metabolomic and PLFA analysis of soil – Jeffrey S.Buyer – Applied Soil Ecology

CLAME: a new alignment-based binning algorithm allows the genomic description of a novel Xanthomonadaceae from the Colombian Andes – Andres Benavides – BMC Genomics

Harnessing CRISPR-Cas systems for precision engineering of designer probiotic lactobacilli – Yong JunGoh – Current Opinion in Biotechnology

Evaluating the Efficiency of Primer Extension Capture as a Method to Enrich DNA Extractions – Winters M – J Forensic Sci

TREATMENTS:

Intestinal Anti-Inflammatory Activity of the Aqueous Extract from Ipomoea asarifolia in DNBS-Induced Colitis in Rats – da Silva VC – Int J Mol Sci.

Effect of Marine Microalga Chlorella pyrenoidosa Ethanol Extract on Lipid Metabolism and Gut Microbiota Composition in High-Fat Diet-Fed Rats – Wan X – Mar Drugs

Flavonoids and Colorectal Cancer Prevention – Li Y – Antioxidants (Basel)

Effects of Rich-Polyphenols Extract of Dendrobium loddigesii on Anti-Diabetic, Anti-Inflammatory, Anti-Oxidant, and Gut Microbiota Modulation in db/db Mice – Li XW – Molecules

Evidence-based mixture containing Lactobacillus strains and lactoferrin to prevent recurrent bacterial vaginosis: a double blind, placebo controlled, randomised clinical trial – R. Russo – Beneficial Microbes

ORAL MICROBIOME:

Bacterial profile of the supragingival dental biofilm in children with deciduous and early mixed dentition using next generation sequencing (HOMINGS) technique – Harris-Ricardo J – Enferm Infecc Microbiol Clin.

Oral Dysbiosis in Pancreatic Cancer and Liver Cirrhosis: A Review of the Literature – Mohammed H – Biomedicines

Subgingival lipid A profile and endotoxin activity in periodontal health and disease – Strachan A – Clin Oral Investig

GENOME AND GENOMICS:
Iron-associated protein interaction networks reveal the key functional modules related to survival and virulence of Pasteurella multocida – Theeraphol Jatuponwiphat – Microbial Pathogenesis

Identification of putative non-host essential genes and novel drug targets against Acinetobacter baumannii by in silico comparative genome analysis – Reaz Uddin – Microbial pathogenesis

Epilithic Biofilms in Lake Baikal: Screening and Diversity of PKS and NRPS Genes in the Genomes of Heterotrophic Bacteria – Sukhanova E – Pol J Microbiol.

Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa – Fitzgerald CB – BMC Genomics

INSECT MICROBIOME:

Metagenomic 16S rRNA gene sequencing survey of Borrelia species in Irish samples of Ixodes ricinus ticks – John S Lambert – bioRxiv

MARINE MICROBIOME:

Uncultured marine cyanophages encode for active NblA, phycobilisome proteolysis adaptor protein – Omer Nadal – bioRxiv

A fundamental difference between macrobiota and microbial eukaryotes: Protistan plankton has a species maximum in the freshwater-marine transition zone of the Baltic Sea – Filker S – Environ Microbiol

ANTIBIOTIC RESISTANCE:

Antibiotic usage promotes the evolution of resistance against gepotidacin, a novel multi-targeting drug – Petra Szili – bioRxiv

Role of Bentonite on the Mobility of Antibiotic Resistance Genes, and Microbial Community in Oxytetracycline and Cadmium Contaminated Soil – Guo H – Front Microbiol

HflXr, a homolog of a ribosome-splitting factor, mediates antibiotic resistance – Duval M – Proc Natl Acad Sci U S A.

Antibiotics may increase triazine herbicide exposure risk via disturbing gut microbiota – Zhan J – Microbiome

SOIL MICROBIOME:

REVIEW: The rhizosphere microbiome: A key component of sustainable cork oak forests in trouble – Fatima Zahra Maghnia – Forest Ecology and Management

VIROME:

The intestinal virome of malabsorption syndrome-affected and unaffected broilers through shotgun metagenomics – Diane A.Lima – Virus Research

MYCO and YEAST-BIOME:

Snf2 controls pulcherriminic acid biosynthesis and connects pigmentation and antifungal activity of the yeast Metschnikowia pulcherrima – Deborah Gore-Lloyd – bioRxiv

Nitrogen deprivation in Fusarium oxysporum promotes mycotoxin production via intermediates in the Krebs cycle and unreported methylmalonyl-CoA mutase activity – A. V. Karpe – Metabolomics

METABOLOMICS:

Gut microbiome structure and metabolic activity in inflammatory bowel disease – Eric A. Franzosa – Nature Microbiology

Active Acupoints Differ from Inactive Acupoints in Modulating Key Plasmatic Metabolites of Hypertension: A Targeted Metabolomics Study – Yang M – Sci Rep

Isobaric Labeling Quantitative Metaproteomics for the Study of Gut Microbiome Response to Arsenic – Liu CW – J Proteome Res.

GENERAL MICROBIOME:

The Human Microbiome in Health and Disease – Wyatt M. Arnold – Genomic Applications in Pathology

Microbes: possible link between modern lifestyle transition and the rise of metabolic syndrome – Moossavi S – Obes Rev.

CANCER and MICROBIOTA:

Microbiota in cancer development and treatment – Muhammad Hassan Raza – Journal of Cancer Research and Clinical Oncology

Alcohol and gastrointestinal cancers – Vanella G – Curr Opin Gastroenterol.

Gut microbiota in patients after surgical treatment for colorectal cancer – Jin Y – Environ Microbiol

The Microbiome in Bipolar Depression: A Longitudinal Study of One Pair of Monozygotic Twins – Jiang HY – Bipolar Disord.

Gut Microbiota, Fusobacteria, and Colorectal Cancer – Kelly D – Diseases

PRENATAL AND INFANT MICROBIOME:

The Prenatal Microbiome: A New Player for Human Health – D’Argenio V – High Throughput

Enteric dysbiosis and fecal calprotectin expression in premature infants – Thao T. B. Ho – Pediatric Research

Long-term colonization exceeding six years from early infancy of Bifidobacterium longum subsp. longum in human gut. – Oki K – BMC Microbiol.

EYE MICROBIOME:

Alterations in gut bacterial and fungal microbiomes are associated with bacterial Keratitis, an inflammatory disease of the human eye – Jayasudha R – J Biosci.

GUT MICROBIOME:

Gut microbiota dysbiosis in male patients with chronic traumatic complete spinal cord injury – Zhang C – J Transl Med.

Traumatic Brain Injury in Mice Induces Acute Bacterial Dysbiosis Within the Fecal Microbiome – Treangen TJ – Front Immunol.

A comparative study of the gut microbiota in immune-mediated inflammatory diseases-does a common dysbiosis exist – Forbes JD – Microbiome.

Microbiome-The Missing Link in the Gut-Brain Axis: Focus on Its Role in Gastrointestinal and Mental Health – Skonieczna-Żydecka K – J Clin Med.

ANIMAL MICROBIOME:

The valproic acid rat model of autism presents with gut bacterial dysbiosis similar to that in human autism – Fang Liu – Molecular Aurtism

Effects of smoking on the lower respiratory tract microbiome in mice – Zhang R – Respir Res

Evaluating the profound effect of gut microbiome on host appetite in pigs – Yang H – BMC Microbiol.

Comparative analysis of the intestinal bacterial community and expression of gut immunity genes in the Chinese Mitten Crab (Eriocheir sinensis) – Dong J – AMB Express.

Rumen methanogen and protozoal communities of Tibetan sheep and Gansu Alpine Finewool sheep grazing on the Qinghai-Tibetan Plateau, China – Huang J – BMC Microbiol.

PSXIV-15 The Effect Of Intravaginal Progesterone Implant In The Vaginal Microbiota Of Holstein Cows – E Zanella – Journal of Animal Science

The role of the bovine respiratory microbiota in health and disease – T Alexander – Journal of Animal Science

MICROBIAL ECOLOGY:

Polychaete mucopolysaccharide alters sediment microbial diversity and stimulates ammonia-oxidising functional groups – Dale H – FEMS Microbiol Ecol.

Profiling grapevine trunk pathogens in planta: a case for community-targeted DNA metabarcoding – Morales-Cruz A – BMC Microbiol.

The bacterial community significantly promotes cast iron corrosion in reclaimed wastewater distribution systems – Zhang G – Microbiome

Long-term soil metal exposure impaired temporal variation in microbial metatranscriptomes and enriched active phages – Jacquiod S – Microbiome

Shotgun Metagenomics Reveals Taxonomic and Functional Shifts in Hot Water Microbiome Due to Temperature Setting and Stagnation – Dai D – Front Microbiol

HOST-MICROBE CROSSTALK:

Neutrophils Restrict Tumor-Associated Microbiota to Reduce Growth and Invasion of Colon Tumors in Mice – Triner D – Gastroenterology

Impact of CFTR modulation with Ivacaftor on Gut Microbiota and Intestinal Inflammation– Ooi CY – Sci Rep

Using Enteric Pathogens to Probe the Gut Microbiota – Spiga L – Trends Microbiol.

DIET, NUTRITION AND PROBIOTICS:

Treatment of Active Crohn’s Disease With an Ordinary Food-based Diet That Replicates Exclusive Enteral Nutrition – Svolos V – Gastroenterology

The Dietary Intervention of Transgenic Low-Gliadin Wheat Bread in Patients with Non-Celiac Gluten Sensitivity (NCGS) Showed No Differences with Gluten Free Diet (GFD) but Provides Better Gut Microbiota Profile – Haro C – Nutrients.

SIRT3 Deficiency Promotes High-Fat Diet-Induced Non-Alcoholic Fatty Liver Disease In Correlation With Impaired Intestinal Permeability Through Gut Microbial Dysbiosis – Chen M – Mol Nutr Food Res

Maternal probiotic supplementation for prevention of morbidity and mortality in preterm infants – Grev J – Cochrane Database Syst Rev

Role of prebiotics and probiotics in the functionality of the microbiota in the patients receiving enteral nutrition – Ballesteros Pomar – Nutr Hosp.

Probiotics Streptococcus salivarius 24SMB and Streptococcus oralis 89a interfere with biofilm formation of pathogens of the upper respiratory tract – Bidossi A – BMC Infect Dis

VAGINAL MICROBIOME:

Vaginal dysbiosis, and the risk of human papillomavirus and cervical cancer: systematic review and meta-analysis – Brusselaers N – Am J Obstet Gynecol.

Microbiota dysbiosis is associated with HPV-induced cervical carcinogenesis – Kwasniewski W – Oncol Lett.

CO-CULTURE MODEL and EFFECTS:

Dynamics of Biofilm Formation by Salmonella Typhimurium and Beef Processing Plant Bacteria in Mono- and Dual-Species Cultures – Visvalingam J – Microb Ecol

Anaerobic Degradation of the Plant Sugar Sulfoquinovose Concomitant With H2S Production: Escherichia coli K-12 and Desulfovibrio sp. Strain DF1 as Co-culture Model – Burrichter A – Front Microbiol.

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December 15, 2018

Colonizing FMT patients with donor bacteriophages, the microbial communities of tigers, fruit bats, hemlocks, and rainbow trout, a review on the advances in urinary microbiome research.

Multi-site human microbiome

Review: The role of the microbiota in infectious diseases – Josie Libertucci – Nature Microbiology

Human skin microbiome

Ultraviolet radiation, both UVA and UVB, influences the composition of the skin microbiome – Erin M Burns – Experimental Dermatology

Human urinary microbiome

Review: Urobiome updates: advances in urinary microbiome research – Alan J Wolfe – nature Reviews Urology

Human gut microbiome

Pre-print: Gut microbiome response to a modern Paleolithic diet in a Western lifestyle context – Monica Barone – bioRxiv

Difference in Pathomechanism Between Crohn’s Disease and Ulcerative Colitis Revealed by Colon Transcriptome – Lili Yang – Inflammatory Bowel Diseases

GABA-modulating bacteria of the human gut microbiota – Philip Strandwitz – Nature Microbiology

Impact of Individual Traits, Saturated Fat, and Protein Source on the Gut Microbiome – Jennifer M Lang – mBio

Animal experiments

Microbiome interactions shape host fitness – Alison L Gould – PNAS

Gut microbiota dysbiosis worsens the severity of acute pancreatitis in patients and mice – Yin Zhu – Journal of Gastroenterology

Microbiota-Derived Lactate Accelerates Intestinal Stem-Cell-Mediated Epithelial Development – Yong-Soo Lee – Cell Host & Microbe

A Microbiota-Derived Bacteriocin Targets the Host to Confer Diarrhea Resistance in Early-Weaned Piglets – Jun Hu – Cell Host & Microbe

Animal microbiome

Exploring variation in phyllosphere microbial communities across four hemlock species – Timothy J Rogers – Ecosphere

Analysis of the gut and gill microbiome of resistant and susceptible lines of rainbow trout (Oncorhynchus mykiss) – Ryan M Brown – Fish & Shellfish Immunology

Metagenomic analysis of captive Amur tiger faecal microbiome – Fengping He – BMC Veterinary Research

Coordinated change at the colony level in fruit bat fur microbiomes through time – Oren Kolodny – Nature Ecology & Evolution

Plant, root, and soil microbiome

Remediation of deterioration in microbial structure in continuous Pinellia ternata cropping soil by crop rotation – Zhigui He – Candadian Journal of Microbiology

Plant compartment and genetic variation drive microbiome composition in switchgrass roots – Esther Singer – Environmental Microbiology Reports

Desert plant bacteria reveal host influence and beneficial plant growth properties – Abdul Aziz Eida – PLOS ONE

Water and extremophile microbiome

Marine probiotics: increasing coral resistance to bleaching through microbiome manipulation – Phillipe M Rosado – The ISME Journal

Microbes in space

International Space Station conditions alter genomics, proteomics, and metabolomics in Aspergillus nidulans – Jillian Romsdahl – Applied Microbiology and Biotechnology

Phages and viruses

Long-term colonisation with donor bacteriophages following successful faecal microbial transplantation – L A Draper – Microbiome

Metatranscriptomic Analysis and In Silico Approach Identified Mycoviruses in the Arbuscular Mycorrhizal Fungus Rhizophagus spp. – Achal Neupane – Viruses

The intestinal virome of malabsorption syndrome-affected and unaffected broilers through shotgun metagenomics – Diane A Lima – Virus Research

Techniques

Detection of Bacteriophages: Sequence-Based Systems – Siân V Owen – Bacteriophages

More microbes

Pseudomonas aeruginosa quorum-sensing metabolite induces host immune cell death through cell surface lipid domain dissolution – Dingka Song – Nature Microbiology

December 2, 2018

Highlights: Colonocyte metabolism shapes the gut microbiota, skin and gut microbiome of wild mammals, bacterial diversity in waterholes of Kruger National Park, Yeast diversity of glaciers, Laser MICROSAMPLING of soil community, origin & evolution of global RNA virome, Lymphoma virome dynamics, PUMA-for processing 16S rRNA taxonomy data  for analysis and visualization and many more.

General microbiome

Contamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations – Raphael Eisenhofer – Trends in Microbiology

Review: Gut microbiota – our new important organ  – Rositsa Sandeva – Albanian Journal of Agricultural Sciences

Human gut microbiome

Altered gut microbiota after traumatic splenectomy is associated with endotoxemia – Hua Zhu – Emerging Microbes & Infections

Review: Colonocyte metabolism shapes the gut microbiota – Yael Litvak – Science

Gut Microbiota Modulates Interactions Between Polychlorinated Biphenyls and Bile Acid Homeostasis – Sunny Lihua Cheng – Toxilogical Sciences

Animal experiments 

An intensive milk replacer feeding program benefits immune response and intestinal microbiota of lambs during weaning – Qian Zhang – BMC Veterinary Research

Animal microbiome 

Bacterial diversity in the waterholes of the Kruger National Park: an eDNA metabarcoding approach – Maxwell J Farrell – Genome

Skin and gut microbiomes of a wild mammal respond to different environmental cues – Anton Lavrinienko – BMC Microbiome

Meta-Omics Tools in the World of Insect-Microorganism Interactions – Antonino Malacrinò – MDPI

Land Use Influences Antibiotic Resistance in the Microbiome of Soil Collembolans Orchesellides sinensis – Dong Zhu – Environmental Science and Technology

The equine gastrointestinal microbiome: Impacts of age and obesity – Philippa K. Morrison – Systems Microbiology

Changes in gut bacterial communities in canaries infected by Macrorhabdus ornithogaster – Patrizia Robino – Journal of Avian Pathology

Plant, root, and soil microbiome

Laser MICROSAMPLING of soil microbial community – M. V. Gorlenko – Journal of Biological Engineering

Poplar phyllosphere harbors disparate isoprene-degrading bacteria – Andrew T. Crombie – PNAS

Changes in litter quality induced by N deposition alter soil microbial communitiesYingbin Li – Soil Biology and Biochemistry

Analysis of Bacterial Communities in White Clover Seeds via High-Throughput Sequencing of 16S rRNA Gene – Wenna Gao – Current Microbiology

Impact of Bactrocera oleae on the fungal microbiota of ripe olive drupes – Ahmed Abdelfattah – PLoS One

Water and extremophile microbiome 

Preprint: Extent of the annual Gulf of Mexico hypoxic zone influences microbial community structure Lauren Gillies Campbell – bioRxiv

Review: Microbiologically influenced corrosion and current mitigation strategies: A state of the art review – Bhavya Kachiprath – Data in Brief

Habitat-specificity and diversity of culturable cold-adapted yeasts of a cold-based glacier in the Tianshan Mountains, northwestern China – Baolong Luo – Applied Microbiology and Biotechnology

Bacterial Communities in Areas of Oil and Methane Seeps in Pelagic of Lake Baikal  – Aleksandra S. Zakharenko – Microbial Ecology

Phages and viruses

Origins and Evolution of the Global RNA Virome – Yuri I. Wolf – mBio

Lymphoma Virome Dynamics Revealed By Cell-Free DNA Sequencing – Joseph G Schroers-Martin – Blood

Techniques

Inner Workings: Mapping the microbiome location helps elucidate its role – Marcus Woo – PNAS

Preprint: FDA-ARGOS: A Public Quality-Controlled Genome Database Resource for Infectious Disease Sequencing Diagnostics and Regulatory Science Research – Heike Sichtig – bioRxiv

Preprint: PUMA: A tool for processing 16S rRNA taxonomy data for analysis and visualization – Keith Mitchell – bioRxiv

EMA-amplicon-based taxonomic characterisation of the viable bacterial community present in untreated and SODIS treated roof-harvested rainwater – André Strauss  -Environmental Science: Water Research & Technology

 

November 29, 2018

Today’s digest covers updates on human milk oligosaccharides, microbial life in cemetry, intestinal resistome, and benefits of intermittent fasting in human cohort and the gut microbiota in mice.

General microbiome
Next steps in studying the human microbiome and health in prospective studies, Bethesda, MD, May 16–17, 2017 – Rashmi Sinha – Microbiome

Human gut microbiome

Human milk oligosaccharides, milk microbiome and infant gut microbiome modulate neonatal rotavirus infection – Sasirekha Ramani – Nature Communications

Interpersonal Variations in Gut Microbiota Profiles Supersedes the Effects of Differing Fecal Storage Conditions – Caspar Bundgaard-Nielsen – Scientific Reports

In-and-Out Molecular Changes Linked to the Type 2 Diabetes Remission after Bariatric Surgery: An Influence of Gut Microbes on Mitochondria Metabolism – Paulina Samczuk – International Journal of Molecular Sciences

Characterization of fungal dysbiosis in Japanese patients with inflammatory bowel disease – Takayuki Imai – Journal of Gastroenterology

Gut microbiota features of the geographically diverse Indian population – Sudarshan A. Shetty – BioRxiv

Animal experiments

Intermittent administration of a fasting-mimicking diet intervenes in diabetes progression, restores β cells and reconstructs gut microbiota in mice Siying Wei – Nutrition and Metabolism

Skin and gut microbiomes of a wild mammal respond to different environmental cues – Anton Lavrinienko – Microbiome

Mouse intestinal microbiota reduction favors local intestinal immunity triggered by antigens displayed in Bacillus subtilis biofilm – Cédric M. Vogt – Microbial Cell Factories

The murine vaginal microbiota and its perturbation by the human pathogen group B Streptococcus – Alison Vrbanac – BMC Microbiology

Use of next generation sequencing to investigate the microbiota of experimentally induced wounds and the effect of bandaging in horses – Louis J. Kamus – PlosOne

Soil microbiome

Expansive microbial metabolic versatility and biodiversity in dynamic Guaymas Basin hydrothermal sediments – Nina Dombrowski – Nature Communications

Built Environment

Microbial life beyond the grave: 16S rRNA gene-based metagenomic analysis of bacteria diversity and their functional profiles in cemetery environments – Akebe Luther King Abia – Science of the Total Environment

Techniques

Prediction of the intestinal resistome by a three-dimensional structure-based method – Etienne Ruppé – Nature Microbiology

Quantitative PCR provides a simple and accessible method for quantitative microbiome profiling – Ching Jian – BioRxiv

Microbes in the news

Poo found on every McDonald’s touchscreen tested – Metro

Non-microbiology picks

Effects of intermittent and continuous calorie restriction on body weight and metabolism over 50 wk: a randomized controlled trial – Ruth Schübel – The American Journal of Clinical Nutrition

 

November 13, 2018

Today’s Digest features several soil and environmental microbiome papers, including the effect of fire on soil ecosystems, insights into the freshwater microbiome associated with the world’s largest mining disaster, applications of soils in forensics, and chemical leaching from LCD screens due to synergistic bacteria. Plus, check out some animal work in marine invertebrates (Sea stars and Ascidians) as well as minks, flying squirrels, and bees!

Pregnancy and early life
The profile of human milk metabolome, cytokines and antibodies in inflammatory bowel diseases versus healthy mothers and potential impact on the newborn – Xuanyi Meng -Journal of Crohn’s and Colitis

Human multi-site microbiome
Shared gut, but distinct oral microbiota composition in primary Sjögren’s syndrome and systemic lupus erythematosus – Taco A. van der Meulen – Journal of Autoimmunity

Urine Bacteria-Derived Extracellular Vesicles and Allergic Airway Diseases in Children – Mona Samra – International Archives of Allergy and Immunology

Review: Repertoire of bacterial species cultured from the human oral cavity and respiratory tract – Maxime DM Fonkou – Future Microbiology

Gut-brain axis
Schizophrenia and gut-flora related epigenetic factors – Chuanjun Zhuo – Progress in Neuro-Psychopharmacology and Biological Psychiatry

The structure of resilience in irritable bowel syndrome and its improvement through hypnotherapy: Cross-sectional and prospective longitudinal data – Johannes Peter – PLOS One

Fermented foods, the gut and mental health: a mechanistic overview with implications for depression and anxiety – Hajara Aslam – Nutritional Neuroscience

Chronic alcohol exposure induced gut microbiota dysbiosis and its correlations with neuropsychic behaviors and brain BDNF/Gabra1 changes in mice – Zheng Xu – Biofactors

Microbial treatment: the potential application for Parkinson’s disease – Xin Fang – Neurological Sciences

Multiple Sclerosis-Associated Changes in the Composition and Immune Functions of Spore-Forming Bacteria. – Egle Cekanaviciute – mSystems

Human gut microbiome
The effect of drinking water pH on the human gut microbiota and glucose regulation: results of a randomized controlled cross-over intervention – Tue H. Hansen – Scientific Reports

Composition of gut microbiota and its association with body mass index and lifestyle factors in a cohort of 7–18 years old children from the American Gut Project – Jinbing Bai – Pediatric Obesity

Long-term impact of oral vancomycin, ciprofloxacin and metronidazole on the gut microbiota in healthy humans. – Bastiaan W Haak – Journal of Antimicrobial Chemotherapy

Helicobacter pylori Infection: New Facts in Clinical Management. – Peter Malfertheiner – Current Treatment Options in Gastroenterology

Animal experiments
The protective effects of fecal microbiota transplantation in an experimental model of necrotizing enterocolitis – Christian Prado – Journal of Pediatric Surgery

Intestinal Snakeskin Limits Microbial Dysbiosis during Aging and Promotes Longevity – Anna M. Salazar – iScience

Animal microbiome
Microbiome shifts with onset and progression of Sea Star Wasting Disease revealed through time course sampling – Melanie M. Lloyd – Scientific Reports

Core and Dynamic Microbial Communities of Two Invasive Ascidians: Can Host–Symbiont Dynamics Plasticity Affect Invasion Capacity?– Hila Dror – Microbial Ecology

Fecal bacterial microbiota of Canadian commercial mink (Neovison vison): Yearly, life stage, and seasonal comparisons – Nicole R. Compo – PLOS One

Variations in Gut Microbiota of Siberian Flying Squirrels Correspond to Seasonal Phenological Changes in Their Hokkaido Subarctic Forest Ecosystem – Po-Yu Liu – Microbial Ecology

Influence of Feeding Type and Nosema ceranae Infection on the Gut Microbiota of Apis cerana Workers – Shao K. Huang – mSystems

Host selectively contributes to shaping intestinal microbiota of carnivorous and omnivorous fish – Kristian Daly – The Journal of General and Applied Microbiology

Plant, root, and soil microbiome
Fire modulates ecosystem functioning through the phylogenetic structure of soil bacterial communities – Eduardo Pérez-Valera – Soil Biology and Biochemistry

Assessment of soil microbial communities involved in cellulose utilization at two contrasting Alpine forest sites – José A. Siles – Soil Biology and Biochemistry

Experimental Testing of Dispersal Limitation in Soil Bacterial Communities with a Propagule Addition Approach – Fen-Guo Zhang – Microbial Ecology

Influence of different biological control agents and compost on total and nitrification driven microbial communities at rhizosphere and soil level in a lettuce – Fusarium oxysporum f. sp. lactucae pathosystem – Maria Alexandra Cucu – Journal of Applied Microbiology

Assessment of 16S rRNA gene primers for studying bacterial community structure and function of aging flue-cured tobaccos. – Fan Wang – AMB Express

Changes in bacterial diversity and catabolic gene abundance during the removal of dimethylphenol isomers in laboratory-scale constructed wetlands. – Mónica A. Vásquez Piñeros – Applied Microbiology and Biotechnology

Abiotic factors determine functional outcomes of microbial inoculation of soils from a metal contaminated brownfield – Jay Prakash Singh – Ecotoxicology and Environmental Safety

Applying microbial biogeography in soil forensics – Habteab Habtom – Forensic Science International: Genetics

eDNA metabarcoding supporting community assessment of environmental stressor in a field-based sediment microcosm study – Jianghua Yang – Environmental Science and Technology

Water and extremophile microbiome
Analysis of the diversity of aerobic, thermophilic endospore-forming bacteria in two Algerian hot springs using cultural and non-cultural methods – Mohamed Amine Gomri – Annals of Microbiology

Anaerobic biological treatment of industrial saline wastewater: Fixed bed Reactor performance and analysis of the microbial community structure and abundance – Mariem Jeddi – Environmental Technology

Microbiome triggered transformations of trace organic chemicals in the presence of effluent organic matter in managed aquifer recharge (MAR) systems – Karin Hellauer – Environmental Science and Technology

Insights on the freshwater microbiomes metabolic changes associated with the world’s largest mining disaster – Marcelle C. Cordeiro – Science of the Total Environment

Microbial Functional Responses to Cholesterol Catabolism in Denitrifying Sludge – Sean Ting-Shyang Wei – mSystems

Built environment
Leaching of indium from end-of-life LCD panels via catalysis by synergistic microbial communities – Yaling Xie – Science of the Total Environment

Probiotics/Prebiotics
Probiotic and synbiotic therapy in the critically ill: State of the art – James M. Davison – Nutrition

Butyrate Producers as Potential Next-Generation Probiotics: Safety Assessment of the Administration of Butyricicoccus pullicaecorum to Healthy Volunteers. – Leen Boesmans – mSystems

Divergent short-chain fatty acid production and succession of colonic microbiota arise in fermentation of variously-sized wheat bran fractions – Yunus E. Tuncil – Scientific Reports

Bioinformatics
Machine Learning Reveals Missing Edges and Putative Interaction Mechanisms in Microbial Ecosystem Networks – Demetrius DiMucci – mSystems

Techniques
A tridecaptin-based fluorescent probe for differential staining of Gram-negative bacteria. – Wei Wang – Analytical and Bioanalytical Chemistry

High-Throughput Miniaturized 16S rRNA Amplicon Library Preparation Reduces Costs while Preserving Microbiome Integrity – Jeremiah J. Minich – mSystems

Book Chapter: Activity-Based Protein Profiling—Enabling Multimodal Functional Studies of Microbial Communities – Christopher Whidbey – Current Topics in Microbiology and Immunology

November 7, 2018

There’s lots of new work to catch up on! Some highlights include the skin virome in patients with immune deficiency, a mechanism for host-microbe mutualism in zebrafish, ecological pressures in soil that lead to smaller genomes, and a book chapter about the future of microbial forensics.

General Microbiome
Genotype to phenotype: Diet-by-mitochondrial DNA haplotype interactions drive metabolic flexibility and organismal fitness – Wen C. Aw – PLOS Genetics

Antifungal immune responses: emerging host–pathogen interactions and translational implications – Vinod Kumar – Genome Medicine

Pregnancy and early life
Childhood Adversity Impact on Gut Microbiota and Inflammatory Response to Stress During Pregnancy. – Liisa Hantsoo – Brain, Behavior, and Immunity

Enabling precision medicine in neonatology, an integrated repository for preterm birth research – Marina Sirota – Scientific Data

Associations of birth mode with cord blood cytokines, white blood cells, and newborn intestinal bifidobacteria – Isabel Cristina Ribas Werlang – PLOS One

HPV infection and bacterial microbiota in breast milk and infant oral mucosa – Heidi Tuominen – PLOS One

Human skin microbiome
Expanded skin virome in DOCK8-deficient patients – Osnat Tirosh – Nature Medicine

Microbiological Profile of Sarecycline: A Novel Targeted Spectrum Tetracycline for the Treatment of Acne Vulgaris – George Zhanel – Antimicrobial Agents and Chemotherapy

Human vaginal microbiome
Preprint: Glycan cross-feeding drives mutualism between Fusobacterium and the vaginal microbiota – Kavita Agarwal – bioRxiv

Human multi-site microbiome
The altered human serum metabolome induced by a marathon – Zinandré Stander – Metabolomics

The unsolved problem of otitis media in indigenous populations: a systematic review of upper respiratory and middle ear microbiology in indigenous children with otitis media
Andrea Coleman
Microbiome

Human gut microbiome
An exploration of Prevotella-rich microbiomes in HIV and men who have sex with men – Abigail J. S. Armstrong – Microbiome

Safety and preliminary efficacy of orally administered lyophilized fecal microbiota product compared with frozen product given by enema for recurrent Clostridium difficile infection: A randomized clinical trial – Zhi-Dong Jiang – PLOS One

The long term effect of metabolic profile and microbiota status in early gastric cancer patients after subtotal gastrectomy – Xi-Hsuan Lin – PLOS One

Animal experiments
A bacterial immunomodulatory protein with lipocalin-like domains facilitates host–bacteria mutualism in larval zebrafish – Annah S Rolig – eLife

Gut microbiota and intestinal FXR mediate the clinical benefits of metformin – Lulu Sun – Nature Medicine

Interactions between Roseburia intestinalis and diet modulate atherogenesis in a murine model – Kazuyuki Kasahara – Nature Microbiology

Enteric infection coupled with chronic Notch pathway inhibition alters colonic mucus composition leading to dysbiosis, barrier disruption and colitis – Ishfaq Ahmed – PLOS One

Toxoplasma gondii infection triggers chronic cachexia and sustained commensal dysbiosis in mice – Jessica A. Hatter – PLOS One

Plant, root, and soil microbiome
Ecological selection for small microbial genomes along a temperate-to-thermal soil gradient – Jackson W. Sorensen – Nature Microbiology

Decomposition responses to climate depend on microbial community composition -Sydney I. Glassman – PNAS

The nanotechnology among US: are metal and metal oxides nanoparticles a nano or mega risk for soil microbial communities? – J. Parada – Critical Reviews in Biotechnology

Water and extremophile microbiome
Diversity and Coding Potential of the Microbiota in the Photic and Aphotic Zones of Tropical Man-Made Lake with Intensive Aquaculture Activities: a Case Study on Temengor Lake, Malaysia. – Nyok-Sean Lau – Microbial Ecology

Quantifying the changes in genetic diversity within sequence-discrete bacterial populations across a spatial and temporal riverine gradient – Alexandra Meziti – The ISME Journal

Probiotics
Anti-diabetic effects of Lactobacillus casei fermented-yogurt through re-shaping gut microbiota structure in type 2 diabetic rats – Ling Qu – Journal of Agricultural and Food Chemistry

Probiotics-fermented Massa Medicata Fermentata ameliorates weaning stress in piglets related to improving intestinal homeostasis – Yanbo Wang – Applied Microbiology and Biotechnology

Techniques
Impact of DNA extraction method and targeted 16S-rRNA hypervariable region on oral microbiota profiling – Fei Teng – Scientific Reports

Science career/training and publishing
Preprint: The CURE for Culturing Fastidious Microbes – Arundhati Bakshi – bioRxiv

Meeting Report: Current progress and future opportunities in applications of bioinformatics for biodefense and pathogen detection: report from the Winter Mid-Atlantic Microbiome Meet-up, College Park, MD, January 10, 2018. – Jacquelyn S. Meisel -Microbiome

In win for open access, two major funders won’t cover publishing in hybrid journals

Microbial Forensics
Book Chapter: Unique Individualistic Microflora: The Future of DNA Fingerprinting Technique – Pankaj Shrivastava – DNA Fingerprinting: Advancements and Future Endeavors

Alyson’s non-microbiology picks
Science candidates prevail in US midterm elections

November 3, 2018

Human Microbiome

Defining Dysbiosis in Disorders of Movement and Motivation – Christopher T. Fields – The Journal of Neuroscience

The Microbiotic Highway to Health-New Perspective on Food Structure, Gut Microbiota, and Host Inflammation – Nina Wærling Hansen – Nutrients

Compounding to Prevent and Treat Dysbiosis of the Human Vaginal Microbiome – Riepl Mike – International Journal Of Pharmaceutical Compounding

Multiple sessions of antimicrobial photodynamic therapy associated with surgical periodontal treatment in patients with chronic periodontitis – Uislen B. Cadore – Journal of Periodontology

Gastrointestinal microbiota disruption and risk of colonization with carbapenem-resistant Pseudomonas aeruginosa in ICU patients – Melinda M Pettigrew – Clinical Infectious Diseases

Efficacy of Probiotics Supplementation On Chronic Kidney Disease: a Systematic Review and Meta-Analysis – L. Jia – Kidney and Blood Pressure Research

Antibiotic resistance genes distribution in microbiomes from the soil-plant-fruit continuum in commercial Lycopersicon esculentum fields under different agricultural practices – Francisco Cerqueira – Science of The Total Environment

Repeated rectal application of a hyperosmolar lubricant is associated with microbiota shifts but does not affect PrEP drug concentrations: results from a randomized trial in men who have sex with men – Richard E Haaland – Journal of The International AIDS Society

Modulation of gut microbiome in nonalcoholic fatty liver disease: pro-, pre-, syn-, and antibiotics – Min Seok Cho – Journal of Microbiology

Does Modification of the Large Intestinal Microbiome Contribute to the Anti-Inflammatory Activity of Fermentable Fiber? – Shiu-Ming Kuo – Current Developments in Nutrition

 

Animal Microbiome

Pubertal exposure to the endocrine disruptor mono-2-ethylhexyl ester at body burden level caused cholesterol imbalance in mice – Cui Wang – Environmental Pollution

Effects of hexavalent chromium on intestinal histology and microbiota in Bufo gargarizans tadpoles – Qiong Yao – Chemosphere

Dietary shifts influenced by livestock grazing shape the gut microbiota composition and co-occurrence networks in a local rodent species – Guoliang Li – Journal of Animal Ecology

The Impact of Fructo-Oligosaccharides on Gut Permeability and Inflammatory Responses in the Cecal Mucosa Quite Differs between Rats Fed Semi-Purified and Non-Purified Diets – Tomomi Genda – Journal of Nutritional Science and Vitaminology

Temperature-mediated inhibition of a bumblebee parasite by an intestinal symbiont – Evan C. Palmer-Young – Proceedings of The Royal Society B

Combined Consumption of Beef-Based Cooked Mince and Sucrose Stimulates Oxidative Stress, Cardiac Hypertrophy, and Colonic Outgrowth of Desulfovibrionaceae in Rats – Thomas Van Hecke – Molecular Nutrition and Food Research

Host diet mediates a negative relationship between abundance and diversity of Drosophila gut microbiota – Berra Erkosar – Ecology and Evolution

 

Food Microbiome

Monitoring of assertive Lactobacillus sakei and Lactobacillus curvatus strains using an industrial ring trial experiment – Dorothee Janßen – Journal of Applied Microbiology

 

Plant Microbiome

The bacterial volatile dimethyl-hexa-decylamine reveals an antagonistic interaction between jasmonic acid and cytokinin in controlling primary root growth of Arabidopsis seedlings – Ernesto Vázquez-Chimalhua – Protoplasma

Smells from the desert: microbial volatiles that affect plant growth and development of native and non-native plant species – David A. Camarena‐Pozos – Plant, Cell and Environment

 

Bioinformatics, Methodologies and Analysis

Identification and removal of contaminating microbial DNA from PCR reagents: impact on low biomass microbiome analyses – Lisa F Stinson – Letters in Applied Microbiology

A computational framework to integrate high-throughput ‘-omics’ datasets for the identification of potential mechanistic links – Helle Krogh Pedersen – Nature Protocols

 

Other

Studying the microbiome and its complexities: an interview with Alan WalkerBMC Biology

When a physicist wanders into biology…: an interview with KC HuangBMC Biology

From bacterial genomics to clinical epidemiology: an interview with Bill HanageBMC Biology