March 18, 2019

Good morning everyone! In today’s microbiome digest, we have a limited number of articles including reviews, studies and meeting report about the role of microbiome in various health and disease including Atopic Dermatitis, microbiome as a therapeutic target. And many more. Enjoy reading.

General microbiome

Exploring the impacts of raw materials and environments on the microbiota in Chinese Daqu starter – Hai Du – International Journal of Food Microbiology

Review: Microbiome diurnal rhythmicity and its impact on host physiology and disease risk – Samuel Philip Nobs – EMBO reports

Gut microbiome

Unconjugated and secondary bile acid profiles in response to higher-fat, lower-carbohydrate diet and associated with related gut microbiota: A 6-month randomized controlled-feeding trial – Yi Wan – Clinical Nutrition

Meeting report: Exploring human host–microbiome interactions in health and disease—how to not get lost in translation – Sarah Lebeer – Genome Biology

Interactions between a pathogenic Blastocystissubtype and gut microbiota: in vitro and in vivo studies – John Anthony Yason – Microbiome

Review: Intestinal microbiome as a novel therapeutic target for local and systemic inflammation – KazuhikoUchiyama – Pharmacology & Therapeutics

The Role of Probiotics and Prebiotics in the Prevention and Treatment of ObesityTomás Cerdo – Nutrients

Skin microbiome

Host-microbial Dialogues in Atopic Dermatitis – Tetsuro Kobayashi – International immunology

Animal microbiome / Animal experiments

Effect of different challenge models to induce necrotic enteritis on the growth performance and intestinal microbiota of broiler chickens – C Bortoluzzi – Poultry Science

The Effect of Inulin on Lifespan, Related Gene Expression and Gut Microbiota in InRp5545/TM3 Mutant Drosophila melanogaster: A Preliminary Study – Yuling Dong – Nutrients

Bioinformatics

Streaming histogram sketching for rapid microbiome analytics – Will PM Rowe – Microbiome

Modelling microbiome recovery after antibiotics using a stability landscape framework – Shaw LP – ISME Journal

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March 17, 2019

Have a good sunday! Today, we have a quite long digest, containing a variety of articles and studies: reviews about the microbiome and breastfeeding and Parkinson’s disease; microbiota alterations in pulmonary fibrosis, association with stress in pregnant women, and relationships between oral microbiome and pancreatic cancer. And so much more!

 

Human/General Microbiome

Review: Microbiome programming of brain development: implications for neurodevelopmental disorders – Hans Forssberg – Developmental Medicine and Child Neurology

Review: Microbiome, Parkinson’s Disease and Molecular Mimicry – Fabiana Miraglia – Cells

Review: The Use of Defined Microbial Communities To Model Host-Microbe Interactions in the Human Gut – Janneke Elzinga – Microbiology and Molecular Biology Reviews

Review: Indoles: metabolites produced by intestinal bacteria capable of controlling liver disease manifestation – T. Hendrikx – Journal of Internal Medicine

Review: Shaping the Gut Microbiota by Breastfeeding: The Gateway to Allergy Prevention? – Lieke W. J. van den Elsen – Frontiers in Pediatrics

Minireview: Nonalcoholic fatty liver disease and the gut microbiome: Are bacteria responsible for fatty liver? – Tien S Dong – Experimental Biology and Medicine

Perspectives: Is the fountain of youth in the gut microbiome?John F. Cryan – The Journal of Physiology

Bugs to debug? The exploration of gut microbiome in human health and diseases – Yen-Hsuan Ni – Journal of the Formosan Medical Association

Impact of a bathing tradition on shared gut microbe among Japanese families – Toshitaka Odamaki – Scientific Reports

Metagenomic analysis of microbe-mediated vitamin metabolism in the human gut microbiome – Promi Das – BMC Genomics

Fecal and blood microbiota profiles and presence of nonalcoholic fatty liver disease in obese versus lean subjects – Yeojun Yun – PLoS One

H. pylori eradication with antibiotic treatment causes changes in glucose homeostasis related to modifications in the gut microbiota – Gracia Mª Martín-Núñez – PLoS One

Oral microbial dysbiosis in patients with Kostmann syndrome – Nursen Topcuoglu – Journal of Medical Microbiology

Alterations in the gut microbiota of patients with silica-induced pulmonary fibrosis – Yao Zhou – Journal of Occupational Medicine and Toxicology

Association between Psychosocial Stress and Fecal Microbiota in Pregnant Women – C. Hechler – Scientific Reports

Differential composition of gut microbiota among healthy volunteers, morbidly obese patients and post-bariatric surgery patients – Fu‑Gang Wang – Experimental and Therapeutic Medicine

Role of Fecal Microbiota Transplantation for Maintenance of Remission in Patients with Ulcerative Colitis: A Pilot Study – Ajit Sood – Journal of Crohn’s and Colitis

Differential effects of depot medroxyprogesterone acetate administration on vaginal microbiome in Hispanic White and Black women – Liying Yang – Emerging Microbes & Infections

Spatial and Temporal Analysis of the Stomach and Small-Intestinal Microbiota in Fasted Healthy Humans – Anna M. Seekatz – mSphere

Persistence of Candida albicans in the Oral Mucosa Induces a Curbed Inflammatory Host Response That Is Independent of Immunosuppression – Florian R. Kirchner – Frontiers in Immunology

Enrichment of oral microbiota in early cystic precursors to invasive pancreatic cancer – Rogier Aäron Gaiser – Gut

Disordered intestinal microbes are associated with the activity of Systemic Lupus Erythematosus – Yao Li – Clinical Science

Long-Term Azithromycin Reduces Haemophilus influenzae and Increases Antibiotic Resistance in Severe Asthma – Steven L Taylor – American Journal of Respiratory and Critical Care Medicine

Dietary Nutrients Involved in One-Carbon Metabolism and Colonic Mucosa-Associated Gut Microbiome in Individuals with an Endoscopically Normal Colon – Shawn Gurwara – Nutrients

Analysis of the Effects of Dietary Pattern on the Oral Microbiome of Elite Endurance Athletes – Nida Murtaza – Nutrients

 

Animal Microbiome / Animal Experiments

TLR4 May Be Involved in the Regulation of Colonic Mucosal Microbiota by Vitamin A – Lu Xiao – Frontiers in Microbiology

Tunicate-associated bacteria show a great potential for the discovery of antimicrobial compounds – Diah Ayuningrum – PLoS One

Effects of Arsenic on Gut Microbiota and Its Biotransformation Genes in Earthworm Metaphire sieboldi – Hong-Tao Wang – Environmental Science and Technology

A metagenomics investigation of carbohydrate-active enzymes along the goat and camel intestinal tract – Saad Al-Masaudi – International Microbiology

Species identity dominates over environment in shaping the microbiota of small mammals – S. C. L. Knowles – Ecology Letters

Three types of gut bacteria collaborating to improve Kui Jie’an enema treat DSS-induced colitis in mice – Wei Yu – Biomedicine & Pharmacotherapy

The Skin Commensal Yeast Malassezia Triggers a Type 17 Response that Coordinates Anti-fungal Immunity and Exacerbates Skin Inflammation – Florian Sparber – Cell Host Microbe

Dietary inulin alleviates diverse stages of type 2 diabetes mellitus via anti-inflammation and modulating gut microbiota in db/db mice – Ke Li – Food & Function

Apple consumption is associated with a distinctive microbiota, proteomics and metabolomics profile in the gut of Dawley Sprague rats fed a high-fat diet – Jose F. Garcia-Mazcorro – PLoS One

Sema3A – mediated modulation of NR1D1 expression may be involved in the regulation of axonal guidance signaling by the microbiota – Xunzhong Qia – Life Sciences

Multi-hit early life adversity affects gut microbiota, brain and behavior in a sex-dependent manner – Marion Rincel – Brain, Behavior, and Immunity

Letrozole treatment of adult female mice results in a similar reproductive phenotype but distinct changes in metabolism and the gut microbiome compared to pubertal mice – Pedro J. Torres – BMC Microbiology

Supplementation of dietary non-digestible oligosaccharides from birth onwards improve social and reduce anxiety-like behaviour in male BALB/c mice – Kirsten Szklany – Nutritional Neuroscience

Potential Functions of the Gastrointestinal Microbiome Inhabiting the Length of the Rat Digest Tract – Dongyao Li – International Journal of Molecular Sciences

Alteration of GLP-1/GPR43 expression and gastrointestinal motility in dysbiotic mice treated with vancomycin – Xin Xu – Scientific Reports

Subchronic low-dose 2,4-D exposure changed plasma acylcarnitine levels and induced gut microbiome perturbations in mice – Pengcheng Tu – Scientific Reports

The influence of the host microbiome on 3,4-methylenedioxymethamphetamine (MDMA)-induced hyperthermia and vice versa – Emily A. Ridge – Scientific Reports

Effects of Dietary Supplementation With Enterococcus faecium and Clostridium butyricum, Either Alone or in Combination, on Growth and Fecal Microbiota Composition of Post-weaning Pigs at a Commercial Farm – Yoshiaki Sato – Frontiers in Veterinary Science

Saponin-Induced Shifts in the Rumen Microbiome and Metabolome of Young Cattle – Bing Wang – Frontiers in Microbiology

Intestinal dysbiosis augments liver disease progression via NLRP3 in a murine model of primary sclerosing cholangitis – Lijun Liao – Gut

 

Plant Microbiome

Long-Term Organic Farming Manipulated Rhizospheric Microbiome and Bacillus Antagonism Against Pepper Blight (Phytophthora capsici) – Huixiu Li – Frontiers in Microbiology

 

Other Microbes

Preview: Strain-Level Diversity in the Gut: The P. copri Case  – Amira Metwaly – Cell Host Microbe

 

Bioinformatics and ‘-Omics’

Novel insights from uncultivated genomes of the global human gut microbiome – Stephen Nayfach – Nature

Complex Microbiome in Brain Abscess Revealed by Whole-Genome Culture-Independent and Culture-Based Sequencing – Jyun-Hong Lin – Journal of Clinical Medicine

Detection of critical antibiotic resistance genes through routine microbiome surveillance – Zachary M. Burcham – PLoS One

MNEMONIC: MetageNomic Experiment Mining to create an OTU Network of Inhabitant Correlations – Aleksandra I. Perz – BMC Bioinformatics

Rarity of microbial species: In search of reliable associations – Arnaud Cougoul – PLoS One

Stoplight: De novo Assembly Vastly Expands the Known Microbial Universe – Samuel S. Minot – Trends in Microbiology

 

Beneficial Microbes and Compounds

Guarana supplementation attenuated obesity, insulin resistance, and adipokines dysregulation induced by a standardized human Western diet via brown adipose tissue activation Rafael Calixto Bortolin – Phytotherapy Research

Prebiotic supplementation in frail older people affects specific gut microbiota taxa but not global diversity – Tam T. T. Tran – Microbiome

 

Water Microbiome

Composition and Dynamics of the Activated Sludge Microbiome during Seasonal Nitrification Failure – Juliet Johnston – Scientific Reports

 

March 14, 2019

Today’s digest covers interesting reviews on microbiota for immunotherapies, non-digestible carbohydrates for infant microbiota and contribution of marine microbiota in reactive oxygen species; research articles on how gluten sensitivity is affected by duodenal microbiota and how ginger intake affects mouse microbiota.

General microbiome

Review: Mining the microbiota for microbial and metabolite-based immunotherapies – Ashwin N. Skelly – Nature Reviews Immunology

Pregnancy and early life microbiome

Relationship between vitamin D status and the vaginal microbiome during pregnancy – Kimberly K. Jefferson – Journal of Perinatology

Review: Shaping the Infant Microbiome With Non-Digestible Carbohydrates – Stella A. Verkhnyatskaya – Frontiers in Microbiology

Variations in early gut microbiome are associated with childhood eczema – Yu Zhang – FEMS Microbiology Letters

Human gut microbiome

Gut microbiota in HIV–pneumonia patients is related to peripheral CD4 counts, lung microbiota, and in vitro macrophage dysfunction – Meera K. Shenoy – Microbiome

Effects of bowel preparation on the human gut microbiome and metabolome – Naoyoshi Nagata – Scientific Reports

Human colon mucosal biofilms from healthy or colon cancer hosts are carcinogenic – Sarah Tomkovich – The Journal of Clinical Investigation

Animal experiments

Host NLRP6 exacerbates graft-versus-host disease independent of gut microbial composition – Tomomi Toubai – Nature Microbiology

Duodenal bacterial proteolytic activity determines sensitivity to dietary antigen through protease-activated receptor-2 – Alberto Caminero – Nature Communications

The dynamics of the antibiotic resistome in the feces of freshly weaned pigs following therapeutic administration of oxytetracycline – Mahdi Ghanbari – Scientific Reports

Beneficial effects of ginger on prevention of obesity through modulation of gut microbiota in mice – Jing Wang – European Journal of Nutrition

Six‐Week High‐Fat Diet Alters the Gut Microbiome and Promotes Cecal Inflammation, Endotoxin Production, and Simple Steatosis without Obesity in Male Rats – Melisa Crawford – Lipids

Gut microbiome structure and adrenocortical activity in dogs with aggressive and phobic behavioral disorders – Elisabetta Mondo – BioRxiv

The gut microbiota regulates mouse biliary regenerative responses – Wenli Liu – BioRxiv

Plant, root, soil microbiome

Consistent bacterial selection by date palm root system across heterogeneous desert oasis agroecosystems – Maria J. Mosqueira – Scientific Reports

Bacterial fermentation and respiration processes are uncoupled in anoxic permeable sediments – Adam J. Kessler – Nature Microbiology

Effects of graphene oxide and graphite on soil bacterial and fungal diversity – Christian Forstner – BioRxiv

Water microbiome and extremophiles

Review: The microbial contribution to reactive oxygen species dynamics in marine ecosystems – Erik R. Zinser – Environmental Microbiology Reports

Non-microbiology picks

Nano-bot can probe inside human cells – Science Daily

March 12, 2019

Today’s Digest casts a wide net with focuses on antibiotic resistance , human gut microbiome and microbiome in extreme environments. Highlights include a review on fungi in the marine environment, a report on gut mucosal virome alterations in ulcerative colitis and finally, sleep well!

General microbiology

Review: Transcription in cyanobacteria: a distinctive machinery and putative mechanisms – Amber Riaz-Bradley – Biochemical Society Transactions

Preprint: How sample heterogeneity can obscure the signal of microbial interactions – David W. Armitage & Stuart E. Jones – bioRxiv

Behavioral heterogeneity in quorum sensing can stabilize social cooperation in microbial populations – Kelei Zhao et al. – BMC Biology

Antibiotic resistance

Antimicrobial photodynamic activity of toluidine blue encapsulated in mesoporous silica nanoparticles against Pseudomonas aeruginosa and Staphylococcus aureus – Paramanantham Parasuraman et al. – Biofouling

Metaphire guillelmi gut as hospitable micro-environment for the potential transmission of antibiotic resistance genes – Huizhen Chao et al. – Science of The Total Environment

Abundance of antibiotic resistance genes and their association with bacterial communities in activated sludge of wastewater treatment plants: Geographical distribution and network analysis – Haihan Zhang et al. – Journal of Environmental Sciences

Cationic Intrinsically Disordered Antimicrobial Peptides (CIDAMPs) Represent a New Paradigm of Innate Defense with a Potential for Novel Anti-Infectives – Ties Latendorf et al. – Scientific Reports

Preprint: Bacterial interspecies interactions modulate pH-mediated antibiotic tolerance in a model gut microbiota – Andres Aranda-Diaz et al. – bioRxiv

Human oral microbiome

** Sleep deprivation and a non–24-h working schedule lead to extensive alterations in physiology and behavior – Huan Ma et al. – FASEB J

Human gut microbiome

Review: Microbe-metabolite-host axis, two-way action in the pathogenesis and treatment of human autoimmunity – Xiang Meng et al. – Autoimmunity Reviews

Pearls: Bile salt hydrolases: Gatekeepers of bile acid metabolism and host-microbiome crosstalk in the gastrointestinal tract – Matthew H. Foley et al. – PLoS Pathogens

Review: Biomarkers for Immune Therapy in Gastrointestinal Cancers – Benjamin A. Weinberg et al. – Clinical Advances in Hematology & Oncology

Microbiota Diversity in Human Colorectal Cancer Tissues Is Associated with Clinicopathological Features – Yaxin Wu et al. – Nutrition and Cancer

Review: The microbiome, cancer, and cancer therapy – Beth A. Helmink et al. – Nature Medicine

Correlations of the Gastric and Duodenal Microbiota with Histological, Endoscopic, and Symptomatic Gastritis – Hye Seung Han et al. – Journal of Clinical Medicine

Gut-microbe-braint axis

Research Highlight: Depression linked to the microbiome – Hannah Stower – Nature Medicine

Animal experiments

Differential Sensitivity to Plasmodium yoelii Infection in C57BL/6 Mice Impacts Gut-Liver Axis Homeostasis – Joshua E. Denny et al. – Scientific Reports

Metabolic footprint and intestinal microbial changes in response to dietary proteins in a pig model – Alexandra Schutkowski et al. – Journal of Nutritional Biochemistry

Alterations of Bile Acids and Gut Microbiota in Obesity Induced by High Fat Diet in Rat Model – Hong Lin et al. – Journal of Agricultural and Food Chemistry

Effects of lifelong intake of lemon polyphenols on aging and intestinal microbiome in the senescence-accelerated mouse prone 1 (SAMP1) – Chikako Shimizu et al. – Scientific Reports

Effect of green tea and mulberry leaf powders on the gut microbiota of chicken – Yuan Chen et al. – BMC Veterinary Research

Animal microbiome

Fiddler crab bioturbation determines consistent changes in bacterial communities across contrasting environmental conditions – Jenny Marie Booth & Marco Fusi et al. – Scientific Reports

Plant, root and soil microbiome

Hypotheses: Application of filamentous phages in environment: A tectonic shift in the science and practice of ecorestoration – Radhey Shyam Sharma et al. – Ecology and Evolution

Native and Invading Yellow Starthistle (Centaurea solstitialis) Microbiomes Differ in Composition and Diversity of Bacteria – Patricia Lu-Irving et al. – mSphere

Small molecule reaction networks that model the ROS dynamics of the rhizosphere – Olga Taran et al. – Chemical Communications

Soil HONO emissions at high moisture content are driven by microbial nitrate reduction to nitrite: tackling the HONO puzzle – Dianming Wu et al. – The ISME Journal

Evidence of within-species specialization by soil microbes and the implications for plant community diversity – Jenalle L. Eck et al. – PNAS

Effects of four years of elevated ozone on microbial biomass and extracellular enzyme activities in a semi-natural grassland – Jinyang Wang et al. – Science of The Total Environment

Water and extremophile microbiome

Surveying of acid-tolerant thermophilic lignocellulolytic fungi in Vietnam reveals surprisingly high genetic diversity – Vu Nguyen Thanh et al. – Scientific Reports

Radioactive environment adapted bacterial communities constituting the biofilms of hydrothermal spring caves (Budapest, Hungary) – Nóra Tünde Enyedi et al. – Journal of Environmental Radioactivity

COD/sulfate ratio does not affect the methane yield and microbial diversity in anaerobic digesters – Zeynep Cetecioglu et al. – Water Research

** Review: Fungi in the Marine Environment: Open Questions and Unsolved Problems – Anthony Amend et al. – mBio

Holocene paleodepositional changes reflected in the sedimentary microbiome of the Black Sea – Kuldeep D. More et al. – Geobiology

Fluid geochemistry, local hydrology, and metabolic activity define methanogen community size and composition in deep-sea hydrothermal vents – Lucy C. Stewart et al. – The ISME Journal

Prebiotics, probiotics and synbiotics

Review: Potential prebiotics and their transmission mechanisms: Recent approaches – Ishu Khangwal & Pratyoosh Shukla – Journal of Food and Drug Analysis

A Preventive Prebiotic Supplementation Improves the Sweet Taste Perception in Diet-Induced Obese Mice – Arnaud Bernard et al. – Nutrients

Phages and viruses

Pancreas of coxsackie virus infected dams and their challenged pups: A complex issue – Sona Sarmirova et al. – Virulence

Preprint: Clades of huge phage from across Earth’s ecosystems – Basem Al-Shayeb et al. – bioRxiv

** Gut mucosal virome alterations in ulcerative colitis – Tao Zuo et al. – Gut

Bioinformatics

MetaCHIP: community-level horizontal gene transfer identification through the combination of best-match and phylogenetic approaches – Weizhi Song et al. – Microbiome

Scientific Communication and Education

Preprint: The life of P.I. – Transitions to Independence in Academia – Sophie E Acton et al. – bioRxiv

March 11, 2019

To start off the week, here’s a rundown of new papers, including how symbiotic Vibrio signals drive squid gene expression, the intergenerational fur seal microbiome, and a few food microbiology studies on kimchi and pasta. Happy reading!

Pregnancy and Early Life
Review: Neonatal microbiome – a brief review – Anchala Singh – The Journal of Maternal-Fetal & Neonatal Medicine

Feeding practice influences gut microbiome composition in very low birth weight preterm infants and the association with oxidative stress: A prospective cohort study – Chenxi Cai – Free Radical Biology and Medicine

Human Skin Microbiome
Commensal Staphylococci Influence Staphylococcus aureus Skin Colonization and Disease – Corey P. Parlet – Trends in Microbiology

Human Oral Microbiome
No differences in microbiome changes between anti-adhesive and antibacterial ingredients in toothpastes during periodontal therapy – Daniel Hagenfeld – Journal of Periodontal Research

Human Gut Microbiome
Endocytosis of commensal antigens by intestinal epithelial cells regulates mucosal T cell homeostasis – Mark S. Ladinsky – Science

Review: Mendelian randomization reveals causal effects of the gut microbiota – Hugh Thomas – Nature Reviews Gastroenterology & Hepatology

Association Between Antibiotics in the First Year of Life and Celiac Disease – Stine Dydensborg Sander – Gastroenterology

Daiokanzoto (Da-Huang-Gan-Cao-Tang) is an effective laxative in gut microbiota associated with constipation – Kento Takayama – Scientific Reports

Dietary raisin intake has limited effect on gut microbiota composition in adult volunteers – Akemi T. Wijayabahu – Nutrition Journal

Early gut microbiota signature of aGvHD in children given allogeneic hematopoietic cell transplantation for hematological disorders – Elena Biagi – BMC Medical Genomics

Fecal Calprotectin and Fecal Indole Predicts Outcome of Fecal Microbiota Transplantation in Subjects with Recurrent Clostridium difficile Infection – J. Hibbard – Anaerobe

Gut microbiota-stimulated cathepsin K secretion mediates TLR4-dependent M2 macrophage polarization and promotes tumor metastasis in colorectal cancer – Rui Li – Cell Death & Differentiation

Alterations in bacterial communities, SCFA and biomarkers in an elderly HIV-positive and HIV-negative population in western Mexico – Luz A. González-Hernández – BMC Infectious Diseases

RA and the microbiome: do host genetic factors provide the link? – Philippa M. Wells – Journal of Autoimmunity

The Gut Microbiota in Causation, Detection, and Treatment of Cancer – Clodagh Murphy – The American Journal of Gastroenterology

Gut-Brain Axis
From Infection to the Microbiome: An Evolving Role of Microbes in Schizophrenia – Emily G. Severance – Current Topics in Behavioral Neurosciences

Animal Experiments
Critical symbiont signals drive both local and systemic changes in diel and developmental host gene expression – Silvia Moriano-Gutierrez – PNAS

Different host-specific responses in thyroid function and gut microbiota modulation between diet-induced obese and normal mice given the same dose of iodine – Huiting Shen – Applied Microbiology and Biotechnology

Antibiotic treatment affects the expression levels of copper transporters and the isotopic composition of copper in the colon of mice – Kerri A. Miller – PNAS

Protective effect of prebiotic and exercise intervention on knee health in a rat model of diet-induced obesity – Jaqueline Lourdes Rios – Scientific Reports

Chlorogenic acid alleviates obesity and modulates gut microbiota in high-fat-fed mice – Zhengyu Wang – Food Science & Nutrition

Crucial Role of Microbiota in Experimental Psoriasis Revealed by a Gnotobiotic Mouse Model – Zuzana Stehlikova – Frontiers in Microbiology

Parasitoid envenomation alters the Galleria mellonella midgut microbiota and immunity, thereby promoting fungal infection – Olga V. Polenogova – Scientific Reports

Nutritional Interventions Improved Rumen Functions and Promoted Compensatory Growth of Growth-Retarded Yaks as Revealed by Integrated Transcripts and Microbiome Analyses – Rui Hu – Frontiers in Microbiology

Animal Microbiome
Fur seal microbiota are shaped by the social and physical environment, show mother-offspring similarities and are associated with host genetic quality – Stefanie Grosser – Molecular Ecology

Intensity of Nosema ceranae infection is associated with specific honey bee gut bacteria and weakly associated with gut microbiome structure – Andrey Rubanov – Scientific Reports

Characterizing the microbiota in gastrointestinal tract segments of Rhabdophis subminiatus: Dynamic changes and functional predictions – Wenjiao Tang – MicrobiologyOpen

Studying the microbiota of bats: Accuracy of direct and indirect samplings – Muriel Dietrich – Ecology and Evolution

A cellulolytic fungal biofilm enhances the consolidated bioconversion of cellulose to short chain fatty acids by the rumen microbiome – Charilaos Xiros – Applied Microbiology and Biotechnology

Plant, Root, and Soil Microbiome
Changes in the soil microbial community are associated with the occurrence of Panax quinquefolius L. root rot diseases – Jinglong Jiang – Plant and Soil

Metagenomic analysis reveals distinct patterns of denitrification gene abundance across soil moisture, nitrate gradients – Sarah A. Nadeau – Environmental Microbiology

Divergent national-scale trends of microbial and animal biodiversity revealed across diverse temperate soil ecosystems – Paul B. L. George – Nature Communications

Impact of Wuyiencin Application on the Soil Microbial Community and Fate of Typical Antibiotic Resistance Genes – Liming Shi – Scientific Reports

Airborne microbial transport limitation to isolated Antarctic soil habitats – Stephen D. J. Archer – Nature Microbiology

Agricultural intensification reduces microbial network complexity and the abundance of keystone taxa in roots – Samiran Banerjee – ISMEJ

Biochars reduced the bioaccessibility and (bio)uptake of organochlorine pesticides and changed the microbial community dynamics in agricultural soils -Neelum Ali – Chemosphere

Molecular identification and biocontrol activity of sugarcane rhizosphere bacteria against red rot pathogen Colletotrichum falcatum – Prittesh Patel – Biotechnology Reports

Natural and assisted dissipation of polycyclic aromatic hydrocarbons in a long-term co-contaminated soil with creosote and potentially toxic elements
F.Madrid – Science of The Total Environment

Horizontal gene transfer and shifts in linked bacterial community composition are associated with maintenance of antibiotic resistance genes during food waste composting – Hanpeng Liao – Science of The Total Environment

Sedimentary Marl mudstone as a substrate in a xeric environment revealed by microbiome analysis – Oksana Koryachenko – Extremophiles

Water and Extremophile Microbiome
Drivers of Regional Bacterial Community Structure and Diversity in the Northwest Atlantic Ocean – Jackie Zorz – Frontiers in Microbiology

Microbial community composition in alpine lake sediments from the Hengduan Mountains – Binqiang Liao – MicrobiologyOpen

Stepwise pH control to promote synergy of chemical and biological processes for augmenting short-chain fatty acid production from anaerobic sludge fermentation – Xu Wang – Water Research

Food Microbiology
Effects of the supplementation of plant-based formulations on microbial fermentation and predicted metabolic function in vitro – Renée Maxine Petri – Anaerobe

Effects of functional pasta ingredients on different gut microbiota as revealed by TIM-2 in vitro model of the proximal colon – A. Martina – Beneficial Microbes

Effect of pasteurization on delayed kimchi ripening and regression analysis for shelf life estimation of kimchi – Hyun‐Gyu Lee – Food Science & Nutrition

Optimization on production of konjac oligo‐glucomannan and their effect on the gut microbiota – Catarina Aprilia Ariestanti – Food Science & Nutrition

Probiotics
Mechanisms and immunomodulatory properties of pre- and probiotics – V.B.M. Peters – Beneficial Microbes

Wild bacterial probiotics fed to larvae of mass-reared Queensland fruit fly [Bactrocera tryoni (Froggatt)] do not impact long-term survival, mate selection or locomotor activity – Lucas A. Shuttleworth – Insect Science

Bioinformatics
Web-gLV: A Web Based Platform for Lotka-Volterra Based Modeling and Simulation of Microbial Populations – Bhusan K. Kuntal – Frontiers in Microbiology

Techniques
PCR effects of melting temperature adjustment of individual primers in degenerate primer pools – Ankur Naqib -PeerJ

Review: Combinatory biotechnological intervention for gut microbiota – Ishu Khangwal – Applied Microbiology and Biotechnology

March 8, 2019

Happy Friday! Read on for insights into the relationship between the oral microbiome and taste perception, how earthworms interact with pathogens during vermicomposting, the use of phages against drug resistant bacterial pathogens, and how microbiota depletion affects brown adipose tissue thermogenesis. Plus, two new techniques for shotgun metagenomes.

General microbiome
Quorum Sensing Signal Selectivity and the Potential for Interspecies Cross Talk – Samantha Wellington – mBio

Streptomyces Volatile Compounds Influence Exploration and Microbial Community Dynamics by Altering Iron Availability – Stephanie E. Jones – mBio

Microbiome Imbalances: An Overlooked Potential Mechanism in Chronic Nonhealing Wounds – Mengru Pang – The International Journal of Lower Extremity Wounds

Human oral microbiome
New insights into the relationship between taste perception and oral microbiota composition – Camilla Cattaneo – Scientific Reports

The Supragingival Biofilm in Early Childhood Caries: Clinical and Laboratory Protocols and Bioinformatics Pipelines Supporting Metagenomics, Metatranscriptomics, and Metabolomics Studies of the Oral Microbiome – Kimon Divaris – Odontogenesis

Human vaginal microbiome
Comparison of the Vaginal Microbiomes of Premenopausal and Postmenopausal Women – Karol Gliniewicz – Frontiers in Microbiology

Pregnancy and early life
Dose-interval study of a dual probiotic in preterm infants – Claire Watkins – Archives of Disease in Childhood – Fetal and Neonatal Edition

Review: The Relationship Between Perinatal Mental Health and Stress: a Review of the Microbiome – Nusiebeh Redpath – Current Psychiatry Reports

Multi-site human microbiome
Preprint: Functional metagenomics-guided discovery of potent Cas9 inhibitors in the human microbiome – Kevin J Forsberg – bioRxiv

Human gut microbiome
Infectious Complications Are Associated With Alterations in the Gut Microbiome in Pediatric Patients With Acute Lymphoblastic Leukemia – Jacob T Nearing – Frontiers in Cellular and Infection Microbiology

Preprint: HLA alleles associated with risk of ankylosing spondylitis and rheumatoid arthritis influence the gut microbiome – Mark Asquith – bioRxiv

Preprint: Gut feelings begin in childhood: how the gut metagenome links to early environment, caregiving, and behavior – Jessica Flannery – bioRxiv

Review: From gut microbiota dysfunction to obesity: could short-chain fatty acids stop this dangerous course? – Luigi Barrea – Hormones

Animal microbiome
Microbial communities in hummingbird feeders are distinct from floral nectar and influenced by bird visitation – Casie Lee – Proceedings of the Royal Society B

High individual variability in the transcriptomic response of Mediterranean mussels to Vibrio reveals the involvement of myticins in tissue injury – Magalí Rey-Campos – Scientific Reports

The Bos taurus maternal microbiome: Role in determining the progeny early-life upper respiratory tract microbiome and health – Svetlana Ferreira Lima – PLoS One

Contact with adult hen affects development of caecal microbiota in newly hatched chicks – Tereza Kubasova – PLoS One

Examination of the temporal and spatial dynamics of the gut microbiome in newborn piglets reveals distinct microbial communities in six intestinal segments – Ying Liu – Scientific Reports

Microbial diversity in the tick Argas japonicus (Acari: Argasidae) with a focus on Rickettsia pathogens – P. Yan – Medical and Veterinary Entomology

Mutual interactions of E. andrei earthworm and pathogens during the process of vermicomposting – Radka Roubalová – Environmental Science and Pollution Research

Animal experiments
Microbiota Depletion Impairs Thermogenesis of Brown Adipose Tissue and Browning of White Adipose Tissue – Baoguo Li – Cell Reports

Fasting-Mimicking Diet Modulates Microbiota and Promotes Intestinal Regeneration to Reduce Inflammatory Bowel Disease Pathology – Priya Rangan – Cell Reports

Linseed oil and heated linseed grain supplements have different effects on rumen bacterial community structures and fatty acid profiles in cashmere kids – Xue Wang – Journal of Animal Science

Sodium butyrate supplementation in high-soybean meal diets for turbot (Scophthalmus maximus L.): Effects on inflammatory status, mucosal barriers and microbiota in the intestine – Yang Liu – Fish and Shellfish Immunology

The gut microbiota composition affects dietary polyphenols-mediated cognitive resilience in mice by modulating the bioavailability of phenolic acids – Tal Frolinger – Scientific Reports

Dietary lysozyme supplementation contributes to enhanced intestinal functions and gut microflora of piglets – Xia Xiong – Food and Function

Plant, root, and soil microbiome
Potential role of weather, soil and plant microbial communities in rapid decline of apple trees – Jugpreet Singh – PLoS One

The structure of denitrifying microbial communities in constructed mangrove wetlands in response to fluctuating salinities – Guiping Fu – Journal of Environmental Management

Exploring the links between bacterial communities and magnetic susceptibility in bulk soil and rhizosphere of beech (Fagus sylvatica L.) – Carolina Chiellini – Applied Soil Ecology

Impact of Fabricated Nanoparticles on the Rhizospheric Microorganisms and Soil Environment – Mokula Mohammed Raffi – Nanomaterials and Plant Potential

Variation in soil fungal community structure during successive rotations of Casuarina equisetifolia plantations as determined by high-throughput sequencing analysis – Zhou Liuting – Plant Growth Regulation

Water and extremophile microbiome
Microbial responses to anthropogenic dissolved organic carbon in Arctic and Antarctic coastal seawaters – Elena Cerro‐Gálvez – Environmental Microbiology

Microbes in Space
A Low-Diversity Microbiota Inhabits Extreme Terrestrial Basaltic Terrains and Their Fumaroles: Implications for the Exploration of Mars – Charles S. Cockell – Astrobiolgy

Phages and Viruses
Targeting antibiotic resistant bacteria with phage reduces bacterial density in an insect host – Lauri Mikonranta – Biology Letters

Bioinformatics
Autometa: automated extraction of microbial genomes from individual shotgun metagenomes – Ian J Miller – Nucleic Acids Research

Preprint: Toward perfect reads: short reads correction via mapping on compacted de Bruijn graphs – Antoine Limasset – bioRxiv

 

March 7, 2019

Happy Thursday! Today’s digest includes the tree shrew gut virome, microbial communities in hummingbird feeders, and the relationship between oral microbes and taste. Enjoy!

Human gut microbiome

Human Gut Microbiome Response Induced by Fermented Dairy Product Intake in Healthy Volunteers – Volokh – Nutrients

Human oral microbiome

New insights into the relationship between taste perception and oral microbiota composition – Cattaneo – Scientific Reports

Animal experiments

Linseed oil and heated linseed grain supplements have different effects on rumen bacterial community structures and fatty acid profiles in cashmere kids – Wang – Journal of Animal Science

Microbiota Depletion Impairs Thermogenesis of Brown Adipose Tissue and Browning of White Adipose Tissue – Li – Cell Reports

Fasting-Mimicking Diet Modulates Microbiota and Promotes Intestinal Regeneration to Reduce Inflammatory Bowel Disease Pathology – Rangan – Cell Reports

The gut microbiota composition affects dietary polyphenols-mediated cognitive resilience in mice by modulating the bioavailability of phenolic acids – Frolinger – Scientific Reports

Animal microbiome

Characteristics of the tree shrew gut virome – Chen – PLoS One

Contact with adult hen affects development of caecal microbiota in newly hatched chicks – Kubasova – PLoS One

The Bos taurus maternal microbiome: Role in determining the progeny early-life upper respiratory tract microbiome and health – Ferreira Lima – PLoS One

Microbial diversity in the tick Argas japonicus (Acari: Argasidae) with a focus on Rickettsia pathogens – Yan – medical and Veterinary Entomology

Microbial communities in hummingbird feeders are distinct from floral nectar and influenced by bird visitation – Lee – Proceedings of the Royal Society B: Biological Sciences

Examination of the temporal and spatial dynamics of the gut microbiome in newborn piglets reveals distinct microbial communities in six intestinal segments – Liu – Scientific Reports

Plant, root, and soil microbiome

Potential role of weather, soil and plant microbial communities in rapid decline of apple trees – Singh – PLoS One

Plant Materials are Sustainable Substrates Supporting New Technologies of Plant-Only-Based Culture Media for in vitro Culturing of the Plant Microbiota – Mourad – Microbes and Environments

Variation in soil fungal community structure during successive rotations of Casuarina equisetifolia plantations as determined by high-throughput sequencing analysis – Liuting – Plant Growth Regulation

Exploring the links between bacterial communities and magnetic susceptibility in bulk soil and rhizosphere of beech (Fagus sylvatica L.) – Chiellini – Applied Soil Ecology

The structure of denitrifying microbial communities in constructed mangrove wetlands in response to fluctuating salinities – Fu – Journal of Environmental Management

Water and extremophile microbiome

A Low-Diversity Microbiota Inhabits Extreme Terrestrial Basaltic Terrains and Their Fumaroles: Implications for the Exploration of Mars – Cockell – Astrobiology

Microbial responses to anthropogenic dissolved organic carbon in Arctic and Antarctic coastal seawaters – Cerro‐Gálvez – Environmental Microbiology

Techniques

Introducing THOR, a Model Microbiome for Genetic Dissection of Community Behavior – Lozano – MBio

A theoretical framework for controlling complex microbial communities – Tulio Angulo – Nature Communications