April 13, 2019

In today’s digest read about diverse population of bacteria and fungi on the International Space Station, how antidepressants affect gut microbiota, and check out a new framework for comparing and assessing taxonomic profilers (OPAL). Happy weekend!

Vaginal microbiome

Defining characteristics of genital health in South African adolescent girls and young women at high risk for HIV infection – Smritee Dabee – PlosOne

Detection of ureaplasmas and bacterial vaginosis associated bacteria and their association with non-gonococcal urethritis in men – Maria Frølund – PlosOne

Group B streptococcal screening, intrapartum antibiotic prophylaxis, and neonatal early-onset infection rates in an Australian local health district: 2006-2016 – Kathryn Braye – PlosOne

Gut microbiome

Long-term benefit of Microbiota Transfer Therapy on autism symptoms and gut microbiota – Dae-Wook Kang – Scientific Reports

The Prevotella copri complex comprises four distinct clades that are underrepresented in Westernised populations – Adrian Tett – bioRxiv

Fecal short-chain fatty acids are not predictive of colonic tumor status and cannot be predicted based on bacterial community structure – Marc A. Sze – bioRxiv

Evidence for a multi-level trophic organization of the human gut microbiome – Tong Wang – bioRxiv

Animal microbiome

Comparative analysis of amplicon and metagenomic sequencing methods reveals key features in the evolution of animal metaorganisms – Philipp Rausch – bioRxiv

Metagenomic Analysis of the Whole Gut Microbiota in Brazilian Termitidae Termites Cornitermes cumulans, Cyrilliotermes strictinasus, Syntermes dirus, Nasutitermes jaraguae, Nasutitermes aquilinus, Grigiotermes bequaerti, and Orthognathotermes mirim – Maria B. Grieco – Current Microbiolgy

The sponge microbiome within the greater coral reef microbial metacommunity – Daniel F. R. Cleary – Nature Communications

Insights into the intestinal microbiota of several aquatic organisms and association with the surrounding environment – Fulin Sun – Aquaculture

Animal experiments

*Antidepressants affect gut microbiota and Ruminococcus flavefaciens is able to abolish their effects on depressive-like behavior – Iva Lukić – Translational Psychiatry

Chronic paradoxical sleep deprivation-induced depression­like behavior, energy metabolism and microbial changes in rats – Weini Ma – Life Sciences

Ability of bifidobacteria to metabolize chitin-glucan and its impact on the gut microbiota – Giulia Alessandri – Scientific Reports

Probiotics

Fasting breath H2 and gut microbiota metabolic potential are associated with the response to a fermented milk product in irritable bowel syndrome – Boris Le Nevé – PlosOne

Lactobacillus fermentum and Lactobacillus plantarum increased gut microbiota diversity and functionality, and mitigated Enterobacteriaceae, in a mouse model – C. Linninge – Beneficial Microbes

Complex responses to inflammatory oxidants by the probiotic bacterium Lactobacillus reuteri – Poulami Basu Thaku – bioRxiv

Plant/root/soil microbiome

Urban traffic changes the biodiversity, abundance, and activity of phyllospheric nitrogen-fixing bacteria – Yang Li – Environmental Science and Pollution Research

Comparative analysis of the rhizomicrobiome of the wild versus cultivated crop: insights from rice and soybean – Shaohua Shi – Archives of Microbiology

Copper and zinc in rhizospheric soil of wild plants growing in long-term acid vineyard soils – C.Campillo-Cora – Science of The Total Environment

Review: Soil microbiome: a key player for conservation of soil health under changing climate – Anamika Dubey – Biodiversity and Conservation

Rhizosphere microbiota compositional changes reflect potato blackleg disease – Lutian Mao – Applied Soil Ecology

Pseudomonas urumqiensis sp. nov., isolated from rhizosphere soil of Alhagi sparsifolia – Yuanyuan Zou – International Journal of Systematic and Evolutionary Microbiology

Insights gained from metagenomic shotgun sequencing of apple fruit epiphytic microbiota – Dario Angeli – Postharvest Biology and Technology

Extremophile microbiome

*Characterization of the total and viable bacterial and fungal communities associated with the International Space Station surfaces – Aleksandra Checinska Sielaff – Microbiome

Techniques

Review: Untargeted LC/MS-based metabolic phenotyping (metabonomics/metabolomics): The state of the art – Helen Gika – Journal of Chromatography B

Bioinformatics

*Assessing taxonomic metagenome profilers with OPAL – Fernando Meyer – Genome Biology

Analysis of error profiles in deep next-generation sequencing data – Xiaotu Ma – Genome Biology

clonealign: statistical integration of independent single-cell RNA and DNA sequencing data from human cancers – Kieran R. Campbell – Genome Biology

RnBeads 2.0: comprehensive analysis of DNA methylation data – Fabian Müller – Genome Biology

Review: Big data analytics for personalized medicine – Davide Cirillo and Alfonso Valencia – Current Opinion in Biotechnology

Meta-network: optimized species-species network analysis for microbial communities – Pengshuo Yang – BMC Genomics

Advertisements

April 1, 2019

In today’s digest read about covert pathogenesis in urinary tract, microbial fuel cells in treatment of organic acid fermentation wastewater, gut microbial metabolism in weanling pigs, and more. Enjoy!

Urinary microbiome

*Covert pathogenesis: Transient exposures to microbes as triggers of disease – Nicole M. Gilbert, Amanda L. Lewis – PlosPathogens

Evaluation of antibacterial efficacy of sulfur nanoparticles alone and in combination with antibiotics against multidrug-resistant uropathogenic bacteria – Priti Paralikar – Journal of Environmental Science and Health, Part A

Review: A Comprehensive Review of Overactive Bladder Pathophysiology: On the Way to Tailored Treatment – Benoit Peyronnet – European Urology

Vaginal microbiome

Effect of progesterone on Candida albicans biofilm formation under acidic conditions: a transcriptomic analysis – Bruna Gonçalves – bioRxiv

Skin microbiome

Cutibacterium acnes antibiotic production shapes niche competition in the human skin microbiome – Jan Claesen – bioRxiv

Neutral Processes Drive Seasonal Assembly of the Skin Mycobiome – Xinzhao Tong – mSystems

Gut Microbiome

The Perturbation of Infant Gut Microbiota Caused by Cesarean Delivery Is Partially Restored by Exclusive Breastfeeding – Yu Liu – Frontiers in Microbiology

Gut Microbiome Functional and Taxonomic Diversity within an Amazonian semi-nomadic hunter-gatherer group – Liliane Costa Conteville – bioRxiv

Risk of inflammatory bowel disease after Campylobacter jejuni and Campylobacter concisus infection: a population-based cohort study – Hans Mittle Nielsen – Scandinavian Journal of Gastroenterology

Unilateral ureteral obstruction causes gut microbial dysbiosis and metabolome disorders contributing to tubulointerstitial fibrosis – Lin Chen – Experimental & Molecular Medicine

Oral microbiome

Polymicrobial synergy within oral biofilm promotes invasion of dendritic cells and survival of consortia members – Ahmed El-Awady – Biofilms and Microbiomes

Animal microbiome

*Metagenomic reconstructions of gut microbial metabolism in weanling pigs – Weilan Wang – Microbiome

Probiotics/Prebiotics

Strain-level diversity of commercial probiotic isolates of Bacillus, Lactobacillus, and Saccharomyces species illustrated by molecular identification and phenotypic profiling – Juliana M. Ansari – PlosOne

Biosurfactant Production by Lactic Acid Bacterium Pediococcus dextrinicus SHU1593 Grown on Different Carbon Sources: Strain Screening Followed by Product Characterization – Abouzar Ghasemi – Scientific Reports

Phages and viruses

Bacteriophage adherence to mucus mediates preventive protection against pathogenic bacteria – Gabriel MF Almeida – bioRxiv

Review: The gut virome: the ‘missing link’ between gut bacteria and host immunity? – Indrani Mukhopadhya – Therapeutic Advances in Gastroenterology

Soil microbiome

Shift of the microbial communities from exposed sandstone rocks to forest soils during pedogenesis – Yaping Liu – International Biodeterioration & Biodegradation

Water and extremophile microbiome

Startup, performance, and microbial communities of an anammox reactor inoculated with indigenous sludge for the treatment of high-salinity and mesophilic underground brine – Nobuyuki Yokota – Clean Technologies and Environmental Policy

*Power generation and microbial community analysis in microbial fuel cells: A promising system to treat organic acid fermentation wastewater – Tian Xia – Bioresource Technology

Techniques

Cultivating in situ triggers growth of previously uncultivated microorganisms via a growth initiation factor in nature – Dawoon Jung – bioRxiv

Bioinformatics

Library preparation and sequencing platform introduce bias in metagenomics characterisation of microbial communities – Casper S. Poulse – bioRxiv

March 27, 2019

Happy Wednesday! Today’s digest includes spider endosymbionts, microbes shared between family members, and the effects of plastic on the microbiome of compost. Enjoy!

General microbiome

Transmission of human-associated microbiota along family and social networks – Brito – Nature Microbiology

Diversity-disease relationships and shared species analyses for human microbiome-associated diseases – Ma – ISME

Dispersal homogenizes communities via immigration even at low rates in a simplified synthetic bacterial metacommunity – Fodelianakis – Nature Communications

Preprint: Exploring the archaeome: detection of archaeal signatures in the human body – Pausan – bioRxiv

Human gut microbiome

Sucrose 6F-phosphate phosphorylase: a novel insight in the human gut microbiome – Tauzin – Microbial Genomics

Human skin microbiome

Preprint: Moving microbes: the dynamics of transient microbial residence on human skin – Vandegrift – bioRxiv

Animal experiments

Effects of phycocyanin in modulating the intestinal microbiota of mice – Xie – MicrobiologyOpen

Animal microbiome

Preprint: Endosymbiotic bacteria are prevalent and diverse in agricultural spiders – White – bioRxiv

Plant, root, and soil microbiome

Litter Quality Modulates Effects of Dissolved Nitrogen on Leaf Decomposition by Stream Microbial Communities – Jabiol – Microbial Ecology

Additions of sugar and nitrogenous fertiliser affect plant nitrogen status and soil microbial communities – Morrow – Applied Soil Ecology

Characterizing differences in microbial community composition and function between Fusarium wilt diseased and healthy soils under watermelon cultivation – Wang – Plant and Soil

Meta-analysis shows positive effects of plant diversity on microbial biomass and respiration – Chen – Nature Communications

Effects of transgenic glufosinate-tolerant rapeseed (Brassica napus L.) and the associated herbicide application on rhizospheric bacterial communities – Tang – Physiological and Molecular Plant Pathology

Structure and Diversity of Soil Bacterial Communities in Offshore Islands – Lin – Scientific Reports

The effect of environment on the microbiome associated with the roots of a native woody plant under different climate types in China – Chen – Applied Microbiology and Biotechnology

Variation in rhizosphere priming and microbial growth and carbon use efficiency caused by wheat genotypes and temperatures – Yin – Soil Biology and Biochemistry

Using a soil bacterial species balance index to estimate potato crop productivity – Jeanne – PLoS One

Limited effect of planting transgenic rice on the soil microbiome studied by continuous 13CO2 labeling combined with high-throughput sequencing – Wang – Applied Microbiology and Biotechnology

Range-expansion effects on the belowground plant microbiome – Ramirez – Nature Ecology and Evolution

Water and extremophile microbiome

Environmental filtering determines family-level structure of sulfate-reducing microbial communities in subsurface marine sediments – Marshall – ISME

Built environment

Exploring the long-term effect of plastic on compost microbiome – Esan – PLoS One

An integrated microbiological and electrochemical approach to determine distributions of Fe metabolism in acid mine drainage-induced “iron mound” sediments – Leitholf – PLoS One

Probiotics/prebiotics

Strain-level diversity of commercial probiotic isolates of Bacillus, Lactobacillus, and Saccharomyces species illustrated by molecular identification and phenotypic profiling – Ansari – PLoS One

Review: Importance of probiotics in the prevention and treatment of colorectal cancer – Eslami – Journal of Cellular Physiology

Techniques

Robust sampling and preservation of DNA for microbial community profiling in field experiments – Groenenboom – BMC Research Notes

March 21, 2019

Happy Spring! Today’s Digest features a megaphylogeny of mushrooms, new papers about the respiratory microbiome, fecal microbiome and metatranscriptomic analysis from nonhuman primates, and the microbial ecology of snow. Bonus: a pick about the first woman to win the Abel Prize.

General Microbiome
Megaphylogeny resolves global patterns of mushroom evolution – Torda Varga – Nature Ecology and Evolution

Fate of CMY-2-encoding plasmids introduced into the human fecal microbiota by exogenous Escherichia coli – Mehreen Anjum – Antimicrobial Agents and Chemotherapy

Review: The impact of indigenous microbes on Parkinson’s disease – Timothy Sampson – Neurobiology of Disease

Pregnancy and Early Life
Michigan cohorts to determine associations of maternal pre-pregnancy body mass index with pregnancy and infant gastrointestinal microbial communities: Late pregnancy and early infancy – Kameron Y. Sugino – PLOS One

Human Respiratory Microbiome
Bacterial and viral respiratory tract microbiota and host characteristics in children with lower respiratory tract infections: a matched case-control study – Wing Ho Man – The Lancet Respiratory Medicine

The Yin and Yang of Streptococcus Lung Infections in Cystic Fibrosis: A Model for Studying Polymicrobial Interactions – Jessie E. Scott – Journal of Bacteriology

The nasal and oropharyngeal microbiomes of healthy livestock workers – Ashley E. Kates – PLOS One

Human Gut Microbiome
Review: Role of SCFAs in gut microbiome and glycolysis for colorectal cancer therapy – Gang Wang – Journal of Cellular Physiology

Review: Obesity, Motility, Diet, and Intestinal Microbiota—Connecting the Dots – Maya Fayfman – Current Gastroenterology Reports

Review: The gut microbiome and response to immune checkpoint inhibitors: preclinical and clinical strategies – Jun Gong – Clinical and Translational Medicine

The exosome secretion inhibitor neticonazole suppresses intestinal dysbacteriosis-induced tumorigenesis of colorectal cancer – Lei Gu – Investigational New Drugs

Glutamate interactions with obesity, insulin resistance, cognition and gut microbiota composition – María Encarnación Palomo-Buitrago – Acta Diabetologica

Understanding the gut–kidney axis among biopsy-proven diabetic nephropathy, type 2 diabetes mellitus and healthy controls: an analysis of the gut microbiota composition – Sibei Tao – Acta Diabetologica

Identification of the microbial diversity after fecal microbiota transplantation therapy for chronic intractable constipation using 16s rRNA amplicon sequencing – Tadashi Ohara – PLOS One

Animal Experiments
Gut microbiota from infant with Cow’s Milk Allergy promotes clinical and immune features of atopy in a murine model – A. Mauras – Allergy

N-(1-carbamoyl-2-phenylethyl) butyramide reduces antibiotic-induced intestinal injury, innate immune activation and modulates microbiota composition – Adriano Lama – Scientific Reports

Immunosuppression-induced alterations in fish gut microbiota may increase the susceptibility to pathogens – Xiao-Zhou Qi – Fish & Shellfish Immunology

Rifaximin Alters Intestinal Microbiota and Prevents Progression of Ankylosing Spondylitis in Mice – Lianjun Yang – Frontiers in Cellular and Infection Microbiology

Hydroxytyrosol Improves Obesity and Insulin Resistance by Modulating Gut Microbiota in High-Fat Diet-Induced Obese Mice – Zhuoqun Liu – Frontiers in Microbiology

Review: Dietary Fiber and Intestinal Health of Monogastric Animals – Rajesh Jha – Frontiers in Veterinary Science

Circadian disruption and divergent microbiota acquisition under extended photoperiod regimens in chicken – Anne-Sophie Charlotte Hieke – PeerJ

Animal Microbiome
Fecal metatranscriptomics of macaques with idiopathic chronic diarrhea reveals altered mucin degradation and fucose utilization – Samuel T. Westreich – Microbiome

Microbiome Profiles of Ligature-Induced Periodontitis in Nonhuman Primates Across the Lifespan – Sreenatha Kirakodu – Infection and Immunity

Diabetic cats have decreased gut microbial diversity and a lack of butyrate producing bacteria – Ida Nordang Kieler – Scientific Reports

Exploring the bacteriome in anthropophilic ticks: To investigate the vectors for diagnosis – Aránzazu Portillo – PLOS One

Plant, Root, and Soil Microbiome
Microbiota in Non-flooded and Flooded Rice Culms – Hui-Ling Cui – FEMS Microbiology Ecology

Microbial community structure in full scale anaerobic mono-and co-digesters treating food waste and animal waste – Taewoan Koo – Bioresource Technology

Variations in pH significantly affect cadmium uptake in grafted muskmelon (Cucumis melo L.) plants and drive the diversity of bacterial communities in a seedling substrate – Jian Zhang – Plant Physiology and Biochemistry

Divergent microbial communities in groundwater and overlying soils exhibit functional redundancy for plant-polysaccharide degradation – Martin Taubert – PLOS One

Microbial diversity and soil physiochemical characteristic of higher altitude – Saurabh Kumar – PLOS One

Water and Extremophile Microbiome
Microbial Ecology of Snow Reveals Taxa-Specific Biogeographical Structure – Shawn P. Brown – Microbial Ecology

Bacterial community in cold and alkaline environments of Hoh Xil basin in Qinghai–Tibet Plateau and isolation of potential sources of microbiota – Rui Xing – Annals of Microbiology

Bacterial communities of the microbial mats of Chokrak sulfide springs – Ekaterina I. Burganskaya – Archives of Microbiology

Dynamics of microbial community in the bioreactor for bisphenol S removal – Wen-Cong Huang – Science of the Total Environment

High-throughput DNA sequencing reveals the dominance of pico- and other filamentous cyanobacteria in an urban freshwater Lake – Hanyan Li – Science of the Total Environment

A novel phenol and ammonia recovery process for coal gasification wastewater altering the bacterial community and increasing pollutants removal in anaerobic/anoxic/aerobic system – Xuefei Gui – Science of the Total Environment

Built Environment
Biodeterioration of mortar coating in historical buildings: Microclimatic characterization, material, and fungal community – Fernanda L. Guerra – Building and Environment

A different suite: The assemblage of distinct fungal communities in water-damaged units of a poorly-maintained public housing building – Iman A. Sylvain – PLOS One

Microbes in Space
Subsurface Microbial Habitats in an Extreme Desert Mars-Analog Environment – Kimberley A. Warren-Rhodes – Frontiers in Microbiology

Food Microbiology
Microbiome patterns reveal the transmission of pathogenic bacteria in hilsa fish (Tenualosa ilisha) marketed for human consumption in Bangladesh – Md Javed Foysal – Journal of Applied Microbiology

Impact of turning, pod storage and fermentation time on microbial ecology and volatile composition of cocoa beans – Yasmine Hamdouche – Food Research International

Probiotic potential of a Lactobacillus rhamnosus cheese isolate and its effect on the fecal microbiota of healthy volunteers – Joaquin Bautista-Gallego – Food Research International

Dynamics of biogenic amines and bacterial communities in a Thai fermented pork product Nham – Pannita Santiyanont – Food Research International

Probiotics/Prebiotics
16S rRNA gene profiling and genome reconstruction reveal community metabolic interactions and prebiotic potential of medicinal herbs used in neurodegenerative disease and as nootropics – Christine Tara Peterson – PLOS One

Phages and Viruses
Review: Phage therapy: What factors shape phage pharmacokinetics and bioavailability? Systematic and critical review – Krystyna Dąbrowska – Medicinal Research Reviews

Bioinformatics
MetaPheno: A Critical Evaluation of Deep Learning and Machine Learning in Metagenome-Based Disease Prediction – Nathan LaPierre – Methods

Assessing alignment-based taxonomic classification of ancient microbial DNA – Raphael Eisenhofer – PeerJ

Techniques
A comparison of storage methods for gut microbiome studies in teleosts: Insights from rainbow trout (Oncorhynchus mykiss) – Mathis Hildonen – Journal of Microbiological Methods

Alyson’s Non-Microbiology Picks
Soap-bubble pioneer is first woman to win prestigious maths prize

Girls who share a womb with boys tend to make less money than those with twin sisters

 

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 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