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

Advertisements

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

October 15, 2018

In today’s Digest, you’ll find a method for museum collections to identify helminth communities in small mammals, new results in the urinary and vaginal microbiome, the effects of HIV PrEP and broccoli on the gut microbiome, and fungal communities associated with plant roots. Happy reading!

General microbiome
Review: Probiotics importance and their immunomodulatory properties. – Bahman Yousefi – Journal of Cellular Physiology

Review: An insight into gut microbiota and its functionalities. – Atanu Adak – Cellular and Molecular Life Sciences

Gut-brain axis
Review: A primer on investigating the role of the microbiome in brain and cognitive development. – Caroline Kelsey – Developmental Psychobiology

Human vaginal microbiome
Preprint: Comparative genomics of human Lactobacillus crispatus isolates reveals genes for glycosylation and glycogen degradation: Implications for in vivo dominance of the vaginal microbiota – Charlotte van der Veer – bioRxiv

Human urinary microbiome
Community profiling of the urinary microbiota: considerations for low-biomass samples. – Lisa Karstens – Nature Reviews Urology

Human gut microbiome
Daily HIV pre-exposure prophylaxis (PrEP) with tenofovir disoproxil fumarate-emtricitabine reduced Streptococcus and increased Erysipelotrichaceae in rectal microbiota. – Michael P. Dubé – Scientific Reports

Broccoli consumption affects the human gastrointestinal microbiota – Jennifer L. Kaczmarek – The Journal of Nutritional Biochemistry

Intestinal dysbiosis in Inflammatory Bowel Disease associated with primary immunodeficiency. – Harry Sokol – Journal of Allergy and Clinical Immunology

Chronic kidney disease after 5/6 nephrectomy disturbs the intestinal microbiota and alters intestinal motility. – Kazuhiro Nishiyama – Journal of Cellular Physiology

Animal microbiome
Museum metabarcoding: a novel method revealing gut helminth communities of small mammals across space and time. – Stephen E. Greiman – International Journal for Parasitology

Showcasing the role of seawater in bacteria recruitment and microbiome stability in sponges. – Marta Turon – Scientific Reports

Animal experiments
Microcapsule of sweet orange essential oil changes gut microbiota in diet-induced obese rats. – Dahu Li – Biochemical and Biophysical Research Communications

Changes in ruminal and reticular pH and bacterial communities in Holstein cattle fed a high-grain diet. – Yo-Han Kim – BMC Veterinary Research

Plant, root, and soil microbiome
Dibutyl phthalate contamination remolded the fungal community in agro-environmental system – Xiao Kong – Chemosphere

Plant‐mediated effects of soil phosphorus on the root‐associated fungal microbiota in Arabidopsis thaliana – Izabela Fabiańska – New Phytologist

Water and extremophile microbiome
Prokaryotic Diversity and Distribution in Different Habitats of an Alpine Rock Glacier-Pond System. – I. Mania – Microbial Ecology

Preprint: Response of extremophile microbiome to a rare rainfall reveals a two-step adaptation mechanism – Gherman Uritskiy – bioRxiv

Bioinformatics
Preprint: Nomenclature Errors in Public 16S rRNA Gene Reference Databases – Kyle James Lesack – bioRxiv

October 1, 2018

To kick off October, we have a Microbiome Digest filled with ecological approaches to microbial communities and techniques for analysis. Plus: what the Nobels are doing to encourage diversity, and what ecstasy does to octopuses. Happy reading!

General Microbiome
Neutral and selective dynamics in a synthetic microbial community. – Nate J. Cira – PNAS

Microbiomes as Metacommunities: Understanding Host-Associated Microbes through Metacommunity Ecology. – Elizabeth Theresa Miller – Trends in Ecology and Evolution

Clinician Guide to Microbiome Testing – Christopher Staley – Digestive Diseases and Sciences

Human Urinary Microbiome
NMR-based metabonomic approach reveals changes in the urinary and fecal metabolome caused by resveratrol. – Gabriela Torres Santiago – Journal of Pharmaceutical and Biomedical Analysis

Urinary microbes and postoperative urinary tract infection risk in urogynecologic surgical patients – Krystal J. Thomas-White – International Urogynecology Journal

Human Gut Microbiome
Metagenomic insights into resistant starch degradation by human gut microbiota. – Marius Vital – Applied and Environmental Microbiology

Pathogenic functions of host microbiota. – Silke Rath – Microbiome

Prebiotics and Probiotics in Digestive Health – Eamonn M.M. Quigley – Clinical Gastroenterology and Hepatology

Animal Experiments
Isolation and characterization of the Bacillus cereus BC7 strain, which is capable of zearalenone removal and intestinal flora modulation in mice. – Yue Wang – Toxicon

Sulfated Polysaccharide from Sea Cucumber and its Depolymerized Derivative Prevent Obesity in Association with Modification of Gut Microbiota in High‐Fat Diet‐Fed Mice – Zhenjun Zhu – Molecular Nutrition and Food Research

Animal Microbiome
Cultivable microbiome and its resistance to antimicrobials isolated from Zaprionus indianus – Graziele Aparecida Fernandes da Cruz – Environmental Monitoring and Assessment

Plant, root, and soil microbiome
Impact of weather conditions, leaf age and irrigation water disinfection on the major epiphytic bacterial genera of baby spinach grown in an open field – Pilar Truchado – Food Microbiology

Influence of light on plant – phyllosphere interaction – Sofia D. Carvalho – Frontiers in Plant Science

Techniques
PCR-based quantification of taxa-specific abundances in microbial communities: Quantifying and avoiding common pitfalls. – Fabian Bonk – Journal of Microbiological Methods

Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes. – Johannes Alneberg – Microbiome

Progress of analytical tools and techniques for human gut microbiome research – Eun-Ji Song – Journal of Microbiology

Preprint: Dynamic interaction network inference from longitudinal microbiome data – Jose Lugo-Martinez – bioRxiv

Science, Publishing, and Career
What the Nobels are — and aren’t — doing to encourage diversity – Elizabeth Gibney -Nature

Alyson’s Non-Microbiology Pick
What Ecstasy Does to Octopuses – Ed Yong – The Atlantic

September 28, 2018

Happy Friday! Today we have a long Digest with several interesting reviews and preprints. Learn about the fallopian tube microbiome, the bacterial communities in Icelandic volcanic deposits, the effect of ammonia on anaerobic digesters, skin defense peptides that modulate a frog’s resistance to a pathogen, and a new tool for constructing pan-genomes from shotgun metagenomic data. Enjoy!

General Microbiome
The mammalian mycobiome: A complex system in a dynamic relationship with the host
– Ghee Chuan Lai – WIREs Systems Biology and Medicine

Niche and fitness differences determine invasion success and impact in laboratory bacterial communities. – Shao-peng Li – ISMEJ

Pregnancy and Early Life
Fallopian tube microbiota: evidence beyond DNA. -Elise S Pelter – Future Microbiology

Human Oral Microbiome
Titanium as a modifier of the peri‐implant microbiome structure – Diane Daubert – Clinical Implant Dentistry and Related Research

Human Gut Microbiome
Linking gut microbiota, metabolic syndrome and economic status based on a population-level analysis. – Yan He – Microbiome

Metagenomic analysis of intestinal mucosa revealed a specific eukaryotic gut virome signature in early-diagnosed inflammatory bowel disease – Federica Ungaro – Gut Microbes

Obesity-Linked Gut Microbiome Dysbiosis Associated with Derangements in Gut Permeability and Intestinal Cellular Homeostasis Independent of Diet. – Ravinder Nagpal – Journal of Diabetes Research

Preprint: Social relationships, social isolation, and the human gut microbiota – Kimberly Dill-McFarland – bioRxiv

Review: Gut Microbiota: IgA Protects the Pioneers – Whitman B. Schofield – Current Biology

Review: The Gut Microbiota and Dysbiosis in Autism Spectrum Disorders. – Heather K. Hughes – Current Neurology and Neuroscience Reports

Animal Experiments
Modulation of Pulmonary Microbiota by Antibiotic or Probiotic Aerosol Therapy: A Strategy to Promote Immunosurveillance against Lung Metastases. – Valentino Le Noci – Cell Reports

Nod2 Deficiency in mice is Associated with Microbiota Variation Favouring the Expansion of mucosal CD4+ LAP+ Regulatory Cells – A. Butera – Scientific Reports

Fermented Astragalus in diet altered the composition of fecal microbiota in broiler chickens – Hongxing Qiao – AMB Express

Chronic nonbacterial prostate inflammation in a rat model is associated with changes of gut microbiota that can be modified with a galactoglucomannan‐rich hemicellulose extract in diet – Yvonne Konkol – BJU International

Animal Microbiome
Microbiota and skin defense peptides may facilitate coexistence of two sympatric Andean frog species with a lethal pathogen. – Sandra V. Flechas – ISMEJ

Green forage and fattening duration differentially modulate cecal microbiome of Wanxi white geese. – Xingyong Chen – PLoS One

Plant, root, and soil microbiome
Succession and diversity of microbial communities in landfills with depths and ages and its association with dissolved organic matter and heavy metals. – Si-jia Liu – Science of The Total Environment

Characterization of the bacterial communities on recent Icelandic volcanic deposits of different ages.– Bo Byloos – BMC Microbiology

Linking microbial co-occurrences to soil ecological processes across a woodland-grassland ecotone. – Samiran Banerjee – Ecology and Evolution

Water and Extremophile Microbiome
Independent and interactive effects of reduced seawater pH and oil contamination on subsurface sediment bacterial communities – António Louvado – Environmental Science and Pollution Research

Effects of nutrient enrichment on surface microbial community gene expression in the oligotrophic North Pacific Subtropical Gyre – J. C. Robidart – ISMEJ

Food and Industrial Microbiology
Lacto-fermented sauerkraut improves symptoms in IBS patients independent of product pasteurisation – a pilot study – Elsa Sandberg Nielsen – Food & Function

Relationship between microbial community, operational factors and ammonia inhibition resilience in anaerobic digesters at low and moderate ammonia background concentrations. – Y. Lu – New Biotechnology

Microbial Community Enhances Biodegradation of Bisphenol A Through Selection of Sphingomonadaceae. – Seungdae Oh – Microbial Ecology

Bioinformatics
MSPminer: abundance-based reconstitution of microbial pan-genomes from shotgun metagenomic data. – Florian Plaza Oñate – Bioinformatics

Preprint: A unified framework for unconstrained and constrained ordination of microbiome read count data – Stijn Hawinkel – bioRxiv

September 17, 2018

In today’s Microbiome Digest, look for rhizobacteria that affect plant size, methanogenesis in salt marsh sediments, a murine model for periodontitis, and an exciting preprint that identifies a microbiome in dinosaur bones! Plus, as bonus non-microbiology topics, we consider authorship norms across different disciplines and how forensics might work on Mars.

General Microbiome
(preprint) Life Inside A Dinosaur Bone: A Thriving Microbiome – Evan Thomas Saitta – bioRxiv

Metabolic Interactions of a Chain Elongation Microbiome – Wenhao Han – Applied and Environmental Microbiology

Human Gut Microbiome
Passing the “Acid Test”: Do Proton Pump Inhibitors Affect the Composition of the Microbiome? – Tien Dong – Digestive Diseases and Sciences

The gastric mucosal-associated microbiome in patients with gastric polyposis – Rongrong Ren – Scientific Reports

Animal Experiments
An experimental murine model to study periodontitis – Julie Marchesan – Nature Protocols

The gut microbiota promotes hepatic fatty acid desaturation and elongation in mice – Alida Kindt – Nature Communications

Animal Microbiome
Global Networks of Symbiodinium-Bacteria Within the Coral Holobiont – Rachele Bernasconi – Microbial Ecology

(preprint) Gut microbial compositions mirror caste-specific diets in a major lineage of eusocial insects – Saria Otani -bioRxiv

Plant, Root, and Soil Microbiome
Plant growth-promoting rhizobacteria promote plant size inequality – Alan C. Gange – Scientific Reports

Diversity of active viral infections within the Sphagnum microbiome – Joshua MA Stough – Applied and Environmental Microbiology

The impact of high throughput sequencing on plant health diagnosticsThe impact of high throughput sequencing on plant health diagnostics – Ian Adams -European Journal of Plant Pathology

Deltaproteobacteria (Pelobacter) and Methanococcoides are responsible for choline-dependent methanogenesis in a coastal saltmarsh sediment – Eleanor Jameson – ISME Journal

Water and Extremophile Microbiome
Living at the frontiers of life: extremophiles in Chile and their potential for bioremediation – Roberto Orellana – Frontiers in Microbiology

Spatial structuring of bacterial communities in epilithic biofilms in the Acquarossa river (Italy) – Carolina Chiellini – FEMS Microbial Ecology

Bioinformatics
A small‐sample kernel association test for correlated data with application to microbiome association studies – Xiang Zhan – Genetic Epidemiology

Science, Publishing, and Career
Thousands of scientists publish a paper every five days – John P. A. Ioannidis – Nature

Alyson’s Non-Microbiology Picks
Sensing with tools extends somatosensory processing beyond the body – Luke E. Miller- Nature

How Will Police Solve Murders on Mars? – Geoff Manaugh – The Atlantic

August 20, 2018

Happy Monday! Today’s Microbiome Digest is chock-full. You’ll find: a review of approaches towards predictive microbial ecology, insights into function gleaned from rumen metatranscriptomics, diet studies in hunter-gatherers and mice, characterization of the mosquito and termite microbiota, the wild side of plant microbiomes, fermentation for traditional liquors, and much more!

General microbiome
Systems biology approaches towards predictive microbial ecology – Anne E. Otwell – Environmental Microbiology

One Health Relationships Between Human, Animal, and Environmental Microbiomes: A Mini-Review – Pauline Trinh – Frontiers in Public Health

Tuning of human MAIT cell activation by commensal bacteria species and MR1-dependent T-cell presentation – Cihan Tastan – Mucosal Immunology

Holistic Assessment of Rumen Microbiome Dynamics through Quantitative Metatranscriptomics Reveals Multifunctional Redundancy during Key Steps of Anaerobic Feed Degradation – Andrea Söllinger – mSystems

Multi-site human microbiome
A prospective study to examine the association of the urinary and fecal microbiota with prostate cancer diagnosis after transrectal biopsy of the prostate using 16sRNA gene analysis – Shaheen Alanee – Prostate

Streptococcus and Prevotella are associated with the prognosis of oesophageal squamous cell carcinoma – Yanfang Liu – Journal of Medical Microbiology

Urinary symptoms are associated with certain urinary microbes in urogynecologic surgical patients – Cynthia S. Fok – International Urogynecology Journal

Human gut microbiome
Links between environment, diet, and the hunter-gatherer microbiome – Gabriela K. Fragiadakis – Gut Microbes

Klebsiella oxytoca expands in cancer cachexia and acts as a gut pathobiont contributing to intestinal dysfunction – Sarah A. Pötgens – Scientific Reports

Co-Administration of Probiotics with Prescribed Antibiotics for Preventing Clostridium difficile Diarrhea – Ahmed S. I. Hamed – Academic Emergency Medicine

Animal experiments
Effect of industrial trans-fatty acids-enriched diet on gut microbiota of C57BL/6 mice – Yueting Ge – European Journal of Nutrition

AIEC infection triggers modification of gut microbiota composition in genetically predisposed mice, contributing to intestinal inflammation – Alexis Bretin – Scientific Reports

Effect of probiotic Bifidobacterium bifidum G9-1 on the relationship between gut microbiota profile and stress sensitivity in maternally separated rats – Hirokazu Fukui – Scientific Reports

Animal microbiome
Comparison of microbiomes of cold-water corals Primnoa pacifica and Primnoa resedaeformis, with possible link between microbiome composition and host genotype – Dawn B. Goldsmith – Scientific Reports

Neonatal gut and immune maturation is determined more by postnatal age than by post-conceptional age in moderately preterm pigs – Shuqiang Ren – American Journal of Physiology-Gastrointestinal and Liver Physiology

Functional metagenomics reveals abundant polysaccharide-degrading gene clusters and cellobiose utilization pathways within gut microbiota of a wood-feeding higher termite –  Ning Liu – ISME Journal

Mosquito microbiota cluster by host sampling location – Ephantus J. Muturi – Parasites and Vectors

Plant, root, and soil microbiome|
The wild side of plant microbiomes – Juan E. Pérez-Jaramillo – Microbiome

Unraveling the Composition of the Root-Associated Bacterial Microbiota of Phragmites australis and Typha latifolia – Laura Pietrangelo – Frontiers in Microbiology

Vermicompost addition influences symbiotic fungi communities associated with leek cultivated in metal-rich soils – Antoine Pierart – Environmental Science and Pollution Research

Plant drought resistance is mediated by soil microbial community structure and soil-plant feedbacks in a savanna tree species – Nianxun Xi – Environmental and Experimental Botany

Metabolic specialization of denitrifiers in permeable sediments controls N2 O emissions – Hannah K. Marchant – Environmental Microbiology

Bacterial Biomarkers of Marcellus Shale Activity in Pennsylvania – Jeremy R. Chen See – Frontiers in Microbiology

Eighteen-Year Farming Management Moderately Shapes the Soil Microbial Community Structure but Promotes Habitat-Specific Taxa – Huaihai Chen – Frontiers in Microbiology

Water and extremophile microbiome
Bacterial and archaeal profiling of hypersaline microbial mats and endoevaporites, under natural conditions and methanogenic microcosm experiments – José Q. García-Maldonado – Extremophiles

Subsurface landfill leachate contamination affects microbial metabolic potential and their expression in the Banisveld aquifer – Neslihan Taş – FEMS Microbiology Ecology

Food microbiology
Robust Domination of Lactobacillus sakei in Microbiota During Traditional Japanese Sake Starter Yamahai-Moto Fermentation and the Accompanying Changes in Metabolites – Atsushi Tsuji – Current Microbiology

DaQu fermentation selects for heat resistant Enterobacteriaceae and bacilli – Zhiying Wang – Applied and Environmental Microbiology

Exploitation of autochthonous Tuscan sourdough yeasts as potential starters – Michela Palla – International Journal of Food Microbiology

Techniques
Conventional culture methods with commercially available media unveil the presence of novel culturable bacteria – Tamaki Ito – Gut Microbes