Category Archives: Extremophiles

September 28, 2018

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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 26, 2018

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Today’s mid-week short digest includes articles on integrating human genetics and the gut microbiome to find potent risk factors in cardiovascular disease; comparison of bariatric surgery techniques on the gut microbiota; transmission of antibiotic resistance genes from mothers to infants and importance of breastfeeding. News updates on growth prediction of human microbiome based diagnostics and first rapid test to determine Bifidobacteria in infant gut!

Human gut microbiome

Individual variations in cardiovascular-disease-related protein levels are driven by genetics and gut microbiome – Daria V. Zhernakova – Nature Genetics

Maternal gut and breast milk microbiota affect infant gut antibiotic resistome and mobile genetic elements – Katariina Pärnänen – Nature Communications

Multidrug-resistant Gram-negative bacteria from patients, hospital environment and healthcare workers: a six-month cross-sectional study – Aline Fernanda Rodrigues Sereia – bioRxiv

Microbiota stability in healthy individuals after single-dose lactulose challenge – a randomized controlled study – Sandra Y Wotzkas – bioRxiv

Laparoscopic Roux-en-Y gastric bypass profoundly changes gut microbiota compared to laparoscopic sleeve gastrectomy: a metagenomic comparative analysis – William Farin – bioRxiv

Subgingival microbiome of rheumatoid arthritis patients in relation to their disease status and periodontal health – Kathrin Beyer – PlosOne

Profiling of microorganism-binding serum antibody specificities in professional athletes – Rajna Minić – PlosOne

Animal experiments

Human Breast-Milk Feeding Enhances the Humoral and Cell-Mediated Immune Response in Neonatal Piglets – John J Miklavcic – The Journal of Nutrition

Glyphosate perturbs the gut microbiota of honey bees – Erick V. S. Motta – PNAS

Water and extremophile microbiome 

Microbiome profiling in extremely acidic soils affected by hydrothermal fluids: the case of Solfatara Crater (Campi Flegrei, southern Italy) – Crognale Simona – Fems Microbiology Ecology

Techniques

The Smallest Intestine (TSI) – a low volume in vitro model of the small intestine with increased throughput – T Cieplak – FEMS microbiology Letters

Microbes in the news

First-Ever Rapid Response Test for Levels of Bifidobacterium in Baby’s Gut Microbiome – Microbiome Times

Human Microbiome Market will Likely to expanding at a CAGR of 9.8% during the forecast period from 2018 to 2026 – Business Analyst

Puppies spread antibiotic-resistant infections to 118 people, CDC reports – CBS News

Non-microbiology picks

The best of intentions: Prenatal breastfeeding intentions and infant health – Kerri M. Raissian – SSM Population Health

 

September 25, 2018

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Events and jobs

4th Annual European Microbiome Congress – London UK – November 14-15 2018

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General microbiome

Review: “Under the Skin” and into the Gut: Social Epidemiology of the Microbiome – Jennifer Beam Dowd – Current Epidemiology Reports

Review: Concurrent cross‐reactivity of microbiota‐derived epitopes to both self and pathogens may underlie the “Hygiene hypothesis” – David Usharauli – Scandinavian Journal of Immunology

Pregnancy and early life

Influence of non-polio enteroviruses and the bacterial gut microbiota on oral poliovirus vaccine response: a study from south India – Ira Praharaj – The Journal of Infectious Diseases

A reverse metabolic approach to weaning: in silico identification of immune-beneficial infant gut bacteria, mining their metabolism for prebiotic feeds and sourcing these feeds in the natural product space – Samanta Michelini – Microbiome

Human respiratory microbiome

Review: Paradigms of Lung Microbiota Functions in Health and Disease, Particularly, in Asthma – Elliot Mathieu – Frontiers in Physiology

Different Upper Airway Microbiome and Their Functional Genes Associated with Asthma in Young Adults and Elderly Individuals – Jin‐Jae Lee – Allergy

Human oral microbiome

In-vivo shift of the microbiota in oral biofilm in response to frequent sucrose consumption – Annette Carola Anderson – Scientific Reports

Human gut microbiome

Alterations in the Abundance and Co-occurrence of Akkermansia muciniphila and Faecalibacterium prausnitzii in the Colonic Mucosa of Inflammatory Bowel Disease Subjects – Mireia Lopez-Siles – Frontiers in Cellular and Infection Microbiology

Influence of gender and menopausal status on gut microbiota – Jose A.Santos-Marcos – Maturitas

Review: High-protein diets for weight management: Interactions with the intestinal microbiota and consequences for gut health. A position paper by the my new gut study group – François Blachier – Clinical Nutrition

Review: Review of the effects of sliver nanoparticle exposure on gut bacteria – Jiangyan Li – Journal of Applied Toxicology

Review: Interactions between Bitter Taste, Diet and Dysbiosis: Consequences for Appetite and Obesity – Alexandria Turner – Nutrients

Review: Progress in characterizing the linkage between Fusobacterium nucleatum and gastrointestinal cancer – Yang Liu – Journal of Gastroenterology

The Amount of Bifidobacterium Genus in Colorectal Carcinoma Tissue in Relation to Tumor Characteristics and Clinical Outcome – Keisuke Kosumi – The American Journal of Pathology

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Animal experiments

Commensal microbiota induces colonic barrier structure and functions that contribute to homeostasis – Christina L. Hayes – Scientific Reports

Palmatine ameliorated murine colitis by suppressing tryptophan metabolism and regulating gut microbiota – Xiao-Jun Zhang – Pharmacological Research

Behavioral response to fiber feedingis cohort-dependent and associated with gut microbiota composition in mice – Lucy J.Mailing – Behavioural Brain Research

Human Breast-Milk Feeding Enhances the Humoral and Cell-Mediated Immune Response in Neonatal Piglets – John J Miklavcic – The Journal of Nutrition

Goji Berry Modulates Gut Microbiota and Alleviates Colitis in IL‐10‐Deficient Mice – Yifei Kang – Molecular Nutrition and Food Research

Konjaku flour reduces obesity in mice by modulating the composition of the gut microbiota – Yongbo Kang – International Journal of Obesity

Polysaccharide from fermented Momordica charantia L. with Lactobacillus plantarum NCU116 ameliorates type 2 diabetes in rats – He Gao – Carbohydrate Polymers

Allergen Immunization Induces Major Changes in Microbiota Composition and Short-Chain Fatty Acid Production in Different Gut Segments in a Mouse Model of Lupine Food Allergy – Andreassen M – Allergy and Immunology

In vitro experiments

Dietary fatty acids sustain growth of human gut microbiota – Richard Agans – Applied and Environmental Microbiology

Animal microbiome

Microbial communities in different regions of the gastrointestinal tract in East Asian finless porpoises (Neophocaena asiaeorientalis sunameri) – Xiao-Ling Wan – Scientific Reports

Differences in the Gut Microbiota Establishment and Metabolome Characteristics Between Low- and Normal-Birth-Weight Piglets During Early-Life – Na Li – Frontiers in Microbiology

Direct-fed microbial supplementation influences the bacteria community composition of the gastrointestinal tract of pre- and post-weaned calves – Bridget E. Fomenky – Scientific Reports

Evaluation of microbial communities associated with the liquid and solid phases of the rumen of cattle offered a diet of perennial ryegrass or white clover – Jenna M. Bowen – Frontiers in Microbiology

Possibilities of early life programming in broiler chickens via intestinal microbiota modulation – Luis A Rubio – Poultry Science

A Comparative Analysis of Microbial DNA Preparation Methods for Use With Massive and Branching Coral Growth Forms – Alejandra Hernandez-Agreda – Frontiers in Microbiology

Plant, root, and soil microbiome

Interactions of mycorrhiza and protists in the rhizosphere systemically alter microbial community composition, plant shoot-to-root ratio and within-root system nitrogen allocation – Gunnar J. Henkes – Frontiers in Environmental Science

Combined effects of biochar addition and nitrogen fertilizer reduction on the rhizosphere metabolomics of maize (Zea mays L.) seedlings – Nan Cheng – Plant and Soil

Does sulfur fertilizer influence Cu migration and transformation in colloids of soil pore water from the rice (Oryza sativa L.) rhizosphere? – Lijuan Sun – Environmental Pollution

The Alleopathic Compound Luteolin from Peanut Litter Affects Peanut Nodule Formation and the Rhizosphere Microbial Community – Hong-Wei Wang – Agronomy Journal

Seasonal comparison of bacterial communities in rhizosphere of alpine cushion plants in the Himalayan Hengduan Mountains – Shuai Chang – Plant Diversity

The effect of a medic-wheat rotational system and contrasting degrees of soil disturbance on nematode functional groups and soil microbial communities – Johan Habig – Agriculture, Ecosystems & Environment

Soil-microbial communities indexing from mangroves rhizophere and barren sandy habitats – Kandasamy Saravanakumar – Physiological and Molecular Plant Pathology

Soil productivity and structure of bacterial and fungal communities in unfertilized arable soil – Boxi Wang – PLOS One

Microbiome profiling in extremely acidic soils affected by hydrothermal fluids: the case of Solfatara Crater (Campi Flegrei, southern Italy) – Crognale Simona – FEMS Microbiology Ecology

Responses of arbuscular mycorrhizal fungi to long-term inorganic and organic nutrient addition in a lowland tropical forest – Merlin Sheldrake – The ISME Journal

Genetic correlation network prediction of forest soil microbial functional organization
Bin Ma – The ISME Journal

Analysis of microbial communities in heavy metals-contaminated soils using the metagenomic approach – M. H. Hemmat-Jou – Ecotoxicology

Water and extremophile microbiome

Investigating the Composition and Metabolic Potential of Microbial Communities in Chocolate Pots Hot Springs – Nathaniel W. Fortney – Frontiers in Microbiology

Methanogens and iron-reducing bacteria: the overlooked members of mercury methylating microbial communities in boreal lakes – Andrea G. Bravo – Applied and Environmental Microbiology

Metagenomics reveals microbial diversity and metabolic potentials of seawater and surface sediment from a hadal biosphere at the Yap Trench – Xinxu Zhang – Frontiers in Microbiology

Dynamics and determinants of amoeba community, occurrence and abundance in subtropical reservoirs and rivers – Kexin Ren – Water Research

Microbial Ecology

Review: A coexistence theory in microbial communities – Marina Dohi – Royal Society Open Science

Inhibition of anaerobic digestion by phenol and ammonia: Effect on degradation performances and microbial dynamics – Simon Poirier – Data in Brief

Resistome

Selection for increased quorum-sensing cooperation in Pseudomonas aeruginosa through the shut-down of a drug resistance pump – Ron D. Oshri – The ISME Journal

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Fecal Transplants

A Systematic Review of the Efficacy and Safety of Fecal Microbiota Transplant for Clostridium difficile Infection in Immunocompromised Patients – Oluwaseun Shogbesan – Canadian Journal of Gastroenterology and Hepatology

Faecal microbiota transplantation as a treatment for inflammatory bowel disease: a national survey of adult and paediatric gastroenterologists in the UK – James Roger Mcilroy – Frontline Gastroenterology

Introduction to the joint British Society of Gastroenterology (BSG) and Healthcare Infection Society (HIS) faecal microbiota transplant guidelines – Benjamin H. Mullish – The Journal of Hospital Infection

Phages and viruses

Detection of Viruses in Clinical Samples Using Metagenomic Sequencing and Targeted Sequence Capture – Kristine M. Wylie – Journal of Clinical Microbiology

Waste and Pollution

Pathogens, faecal indicators and human‐specific microbial source‐tracking markers in sewage – Cristina García‐Aljaro – Journal of Applied Microbiology

September 17, 2018

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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 24, 2018

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Intra-individual microbiome biogeography, a review on IgA responses to the microbiota, seasonal fluctuations in the gut microbiota of white-faced capuchin monkeys, and the microbial composition of fog.

Pregnancy and early life

Sex-specific associations of infants’ gut microbiome with arsenic exposure in a US population – Anne G Hoen – Scientific Reports

Multi-site human microbiome

Assessing and Interpreting the Within-Body Biogeography of Human Microbiome Diversity – Zhanshan Ma – Frontiers in Microbiology

Human vaginal microbiome

Review: Investigating the effect of an abnormal cervico‐vaginal and endometrial microbiome on assisted reproductive technologies: A systematic review – Timothy Bracewell-Milnes – American Journal of Reproductive Immunology

Human gut microbiome

Review: IgA Responses to Microbiota – Jeffrey J Bunker – Immunity

Review: Comparing fecal microbiota transplantation to standard-of-care treatment for recurrent Clostridium difficile infection: a systematic review and meta-analysis – Muhammad Y Khan – European Journal of Gastroenterology & Hepatology

Animal experiments

Dietary L-Tryptophan Modulates the Structural and Functional Composition of the Intestinal Microbiome in Weaned Piglets – Haiwei Liang – Frontiers in Microbiology

Animal microbiome

Seasonality of the gut microbiota of free-ranging white-faced capuchins in a tropical dry forest – Joseph D Orkin – The ISME Journal

The microbiota in the intestinal and respiratory tracts of naked mole-rats revealed by high-throughput sequencing – Wei Cong – BMC Microbiology

Differential effects of selective and non-selective cyclooxygenase inhibitors on fecal microbiota in adult horses – Canaan M Whitfield-Cargile – PLOS ONE

Plant, root, and soil microbiome

Soil microbiomes with distinct assemblies through vertical soil profiles drive the cycling of multiple nutrients in reforested ecosystems – Shuo Jiao – Microbiome

Fungal Communities Along a Small-Scale Elevational Gradient in an Alpine Tundra Are Determined by Soil Carbon Nitrogen Ratios – Yingying Ni – Frontiers in Microbiology

Water and extremophile microbiome

The biology of fog: results from coastal Maine and Namib Desert reveal common drivers of fog microbial composition – Sarah E Evans – Science of the Total Environment

Growth promotion and inhibition induced by interactions of groundwater bacteria – Patricia Geesink – FEMS Microbiology Ecology

Microbial diversity along a gradient in peatlands treating mining-affected waters – Katharina Kujala – FEMS Microbiology Ecology

Food microbiology

Volatile Flavor Components, Microbiota and Their Correlations in Different Sufu, a Chinese Fermented Soybean Food – Chunzhi Xiv – Journal of Applied Microbiology

Biogenic amines analysis and microbial contribution in traditional fermented food of Douchi – Lu Li – Scientific Reports

Changes in the microbial communities in vacuum-packaged smoked bacon during storage – Xinfu Li – Food Microbiology

Phages and viruses

MARVEL, a Tool for Prediction of Bacteriophage Sequences in Metagenomic Bins – Deyvid Amgarten – Frontiers in Genetics

Techniques

Comparative evaluation of a new magnetic bead-based DNA extraction method from fecal samples for downstream next-generation 16S rRNA gene sequencing – Kara D McGaughey – PLOS ONE

August 22, 2018

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Today’s digest is a mix of exciting reviews and research articles. The research articles are about – association between (site-specific) microbiota changes and stunded chilhood growth, bronchopulmonary dysplasia and Ankylosing Spondylitis; new tools to analyze mother-infant phage transmission; and low cost platform to analyze gut microbiota and host biomarkers. Also includes statement from FDA on regulation of live microbiome-based products, and comparison of single versus multiple strain probiotics in intestinal dysbiosis.

General microbiome

Review: Microbiology of the built environment – Jack A Gilbert – Nature Reviews Microbiology

Considerations for Best Practices in Studies of Fiber or Other Dietary Components and the Intestinal Microbiome – David M Klurfeld – American Journal of Physiology Endocrinology and Metabolism

Review: Impact of the commensal microbiota in atherosclerosis and arterial thrombosis – Klytaimnistra Kiouptsi – British Journal of Pharmacology

Pregnancy and early life

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

Human respiratory microbiome

Early Airway Microbial Metagenomic and Metabolomic Signatures are Associated with Development of Severe Bronchopulmonary Dysplasia – Charitharth V Lal – American Journal of Physiology

Human gut microbiome

Stunted childhood growth is associated with decompartmentalization of the gastrointestinal tract and overgrowth of oropharyngeal taxa – Pascale Vonaesch – PNAS

Tracing mother-infant transmission of bacteriophages by means of a novel analytical tool for shotgun metagenomic datasets: METAnnotatorX – Christian Milani – Microbiome

Altered Bacteria-Fungi Inter-Kingdom Network in Gut of Ankylosing Spondylitis Patients – Ming Li – bioRxiv

Animal experiments

Hyperactivated PI3Kd promotes self and commensal reactivity at the expense of optimal humoral immunity – Silvia Preite – Nature Immunology

The Potential Role of the Dipeptidyl Peptidase-4-Like Activity From the Gut Microbiota on the Host Health – Marta Olivares – Frontiers in Microbiology

Plant, root, and soil microbiome

Effects of compost containing oxytetracycline on enzyme activities and microbial communities in maize rhizosphere soil – Lisha Zhen – Environmental Science and Pollution Research

Impact of soil salinity on the microbial structure of halophyte rhizosphere microbiome – Salma Mukhtar – World Journal of Microbiology and Biotechnology

Water and extremophile microbiome

Inter-Kingdom beach warfare: Microbial chemical communication activates natural chemical defences – Zeinab G Khalil – The ISME Journal

Biogeography and taxonomic overview of terrestrial hot spring thermophilic phages – Olivier Zablocki – Extremophiles

Food microbiology

How Fine Structural Differences of Xylooligosaccharides and Arabinoxylooligosaccharides Regulate Differential Growth of Bacteroides Species – Mihiri Mendis – Journal of Agricultural and Food Chemistry

Probiotics / prebiotics

Influence of monostrain and multistrain probiotics on immunity, intestinal ultrastructure and microbiota in experimental dysbiosis – E Ermolenko – Beneficial Microbes

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

Techniques

A low-cost paper-based synthetic biology platform for analyzing gut microbiota and host biomarkers – Melissa K Takahashi – Nature Communications

Microbes in the news

Statement from FDA Commissioner Scott Gottlieb, M.D., on advancing the science and regulation of live microbiome-based products used to prevent, treat, or cure diseases in humans – Food and Drug Administration

Non-microbiology picks

Mechanisms regulating intestinal barrier integrity and its pathological implications – Chaithanya Chelakkot – Experimental and Molecular Medicine

 

August 20, 2018

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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

August 19, 2018

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Featured today: culturing novel bacteria, microbiota of cystic fibrosis, marker in urine for determining gut microbial diversity, stress determinant of soil microbial communities, fescue enhances the PAH degradation by rhizospheric microbes, phages from healthy skin metavirome.

General microbiome

Dietary specialization in mutualistic acacia‐ants affects relative abundance but not identity of host‐associated bacteria – BER Rubin – Journal Molecular Ecology

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

Multi-site human microbiome

The urinary microbiome associated with bladder cancer – V Bučević Popović – Scientific Reports

Human respiratory microbiome

Review: Cystic fibrosis respiratory microbiota: unraveling complexity to inform clinical practice – LJ Caverly – Expert Review of Respiratory Medicine

Human vaginal microbiome

Vulvovestibular Syndrome and Vaginal Microbiome: A Simple Evaluation – M Vadala – Journal of Clinical Medicine Research

Human gut microbiome

Gut microbiota composition explains more variance in the host cardiometabolic risk than genetic ancestry – SJ Guzman-Castaneda – bioRxiv

Assessment of urinary 3-indoxyl sulfate as a marker for gut microbiota diversity and abundance of Clostridiales – F Farowski – Gut Microbes

Periodontal Therapy Favorably Modulates the Oral-Gut-Hepatic Axis in Cirrhosis – JS Bajaj – American Journal of Physiology-Gastrointestinal and Liver Physiology

Animal experiments

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

Effects of Astragalus membranaceus fiber on growth performance, nutrient digestibility, microbial composition, VFA production, gut pH, and immunity of weaned pigs – D Che – Microbiology Open

Plant, root, and soil microbiome

Soil microbial communities alter conspecific and congeneric competition consistent with patterns of field coexistence in three Trifolium congeners – A Siefert – Journal of Ecology

Initial state of soil microbial communities determines their stress response – W Riah-Anglet – Journal of Environmental Chemical Engineering

Natural grassland as the optimal pattern of vegetation restoration in arid and semi-arid regions: Evidence from nutrient limitation of soil microbes – Y Cui – Science of The Total Environment

Characteristics of microbial community indicate anthropogenic impact on the sediments along the Yangtze Estuary and its coastal area, China – X-p Guo – Science of The Total Environment

Soil bacterial communities exhibit systematic spatial variation with landform across a commercial potato field – S Neupane – Geoderma

Plant host habitat and root exudates shape fungal diversity – M Hugoni – Mycorrhiza

Enhanced polycyclic aromatic hydrocarbons degradation in rhizosphere soil planted with tall fescue: Bacterial community and functional gene expression mechanisms – M Guo – Chemosphere

Microbial community of nitrogen cycle‐related genes in aquatic plant rhizospheres of Lake Liangzi in winter – X Yin – Journal of Basic Microbiology

Water and extremophile microbiome 

Surviving in hot and cold: psychrophiles and thermophiles from Deception Island volcano, Antarctica – AG. Bendia – Extremophiles

Probiotics / prebiotics

Probiotics and Evidence-based Medicine: To All Involved – M Koch – Journal of Clinical Gastroenterology

Co‐Administration of Probiotics with Prescribed Antibiotics for Preventing Clostridium difficile Diarrhea – SI Ahmed – Academic Emergency Medicine

Phages and viruses

Novel phages of healthy skin metaviromes from South Africa – LJ van Zyl – Scientific Reports

 

August 18, 2018

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The virome of California mosquitoes, effects of climate warming on grassland microbial communities, and a few “bacteria and art” entries including a 92-foot inflatable E. coli sculpture.

General microbiome

Communities of Niche-Optimized Strains: Small-Genome Organism Consortia in Bioproduction – Stephan Noack – Trends in Biotechnology

Growth tradeoffs produce complex microbial communities on a single limiting resource – Michael Manhart – Nature Communications

Human oral microbiome

Oral microbiome development during childhood: an ecological succession influenced by postnatal factors and associated with tooth decay – Majda Dzidic – The ISME Journal

Animal experiments

Loss of HDAC6 alters gut microbiota and worsens obesity – Arnon D Lieber – The FASEB Journal

Animal microbiome

Pre-print: CRISPR/Cas9-mediated gene deletion of the ompA gene in an Enterobacter gut symbiont impairs biofilm formation and reduces gut colonization of Aedes aegypti mosquitoes – Shivanand Hegde – bioRxiv

Plant, root, and soil microbiome

Climate warming leads to divergent succession of grassland microbial communities – Xue Guo – Nature Climate Change

Water and extremophile microbiome

Bacterial Diversity in Replicated Hydrogen Sulfide-Rich Streams – Scott Hotaling – Microbial Ecology

Long-term in situ permafrost thaw effects on bacterial communities and potential aerobic respiration – Sylvain Monteux – The ISME Journal

Phages and viruses

Virome of > 12 thousand Culex mosquitoes from throughout California – Mohammadreza Sadeghi – Virology

Comprehensive comparative analysis of methods and software for identifying viral integrations – Xun Chen – Briefings in Bioinformatics

Phage-inducible chromosomal islands are ubiquitous within the bacterial universe – Alfred Fillol-Salom – The ISME Journal

Metabolomics

Metabotypes Related to Meat and Vegetable Intake Reflect Microbial, Lipid and Amino Acid Metabolism in Healthy People – Runmin Wei – Molecular Nutrition & Food Research

More microbes

Comparative Genomics of Nitrogen Cycling Pathways in Bacteria and Archaea – Michaeline B N Albright – Microbial Ecology

Bacteria art

Linen and Bacteria: The Hidden History of Microbiology – Clara Rodríguez Fernández – Labiotech.eu

Pomona Arts: Sara Parent Ramos: Jumble, Bunch, Grow – Inland Empire

Oxford Natural History exhibition explores benefits of bacteria – BBC News

August 3, 2018

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Happy Friday! Today’s digest includes the axolotl microbiome, carbon processing in thawing permafrost, and esterases discovered in hot spring microbial mats. In addition, there’s a Nature career column discussing why it’s not a ‘failure’ to leave academia. Enjoy!

Multi-site human microbiome

Optimizing body fluid recognition from microbial taxonomic profiles – Eirik Nataas Hanssen – Forensic Science International

Human oral microbiome

Dysbiosis of the buccal mucosa microbiome in primary Sjögren’s syndrome patients – Taco A van der Meulen – Rheumatology

Human respiratory microbiome

Comparison of the upper and lower airway microbiota in children with chronic lung diseases – Bushra Ahmed – PLoS One

Human vaginal microbiome

Review: Case for a role of the microbiome in gynecologic cancers: Clinician’s perspective – Ismail Mert – Journal of Obstetrics and Gynecology Research

Human gut microbiome

Enhanced preservation of the human intestinal microbiota by ridinilazole, a novel Clostridium difficile-targeting antibacterial, compared to vancomycin – Cheleste M. Thorpe – PLoS One

Animal experiments

Euphorbia kansui fry-baked with vinegar modulates gut microbiota and reduces intestinal toxicity in rats – DongjingJiang – Journal of Ethnopharmacology

Animal microbiome

Experimentally induced metamorphosis in highly regenerative axolotl (ambystoma mexicanum) under constant diet restructures microbiota – Turan Demircan – Scientific Reports

Response of host–bacterial colonization in shrimp to developmental stage, environment and disease – Jinbo Xiong – Molecular Ecology

Wild Bee Pollen Usage and Microbial Communities Co-vary Across Landscapes – Quinn S. McFrederick – Microbial Ecology

Microbiomes of gall-inducing copepod crustaceans from the corals Stylophora pistillata (Scleractinia) and Gorgonia ventalina (Alcyonacea) – Pavel V. Shelyakin – Scientific Reports

Effect of dietary fat to starch content on fecal microbiota composition and activity in dogs – Sofia Schauf – Journal of Animal Science

Primer: The importance of being persistent: The first true resident gut symbiont in Drosophila – Dali Ma – PLoS Biology

Plant, root, and soil microbiome

Genome-centric view of carbon processing in thawing permafrost – Ben J. Woodcroft – Nature

Review: Uptake of bacteria into living plant cells, the unifying and distinct feature of the nitrogen-fixing root nodule symbiosis – Martin Parniske – Current Opinion in Plant Biology

Pre-print: Unlocking a high bacterial diversity in the coralloid root microbiome from the cycad genus Dioon – Pablo de Jesus Suarez-Moo – bioRxiv

Water and extremophile microbiome

Discovery of a diverse set of esterases from hot spring microbial mat and sea sediment metagenomes – RaviRanjan – International Journal of Biological Macromolecules

Built environment

Microbial communities and functional genes of nitrogen cycling in an electrolysis augmented constructed wetland treating wastewater treatment plant effluent – Pengfei Zhang – Chemosphere

Science, publishing, and career

Why it is not a ‘failure’ to leave academia – Philipp Kruger – Nature