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

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8 April, 2019

General Microbiome

Coevolutionary dynamics shape the structure of bacteria-phage infection networks. Fortuna MA.Evolution.

High proportions of bacteria are culturable across major biomes. Martiny AC. ISME Journal

The complexity of an optimal vaginal biome. Eschenbach DA. BJOG

The lung microbiome, vitamin D, and the tuberculous granuloma: A balance triangle. Balcells ME. Microbial Pathogenesis

Gut Microbiome

The parasitic worm product ES-62 normalises the gut microbiota bone marrow axis in inflammatory arthritis. Doonan J. Nature Communications

Culture-enriched human gut microbiomes reveal core and accessory resistance genes. Raymond F.Microbiome.

Plant, Soil, Water, and Air Microbiome

Temperature and soil moisture control microbial community composition in an arctic-alpine ecosystem along elevational and micro-topographic gradients.Frindte K. ISME Journal

Root traits and belowground herbivores relate to plant-soil feedback variation among congeners.Wilschut RA. Nature Communications

A Polyphasic Approach for Assessing Eco-System Connectivity Demonstrates that Perturbation Remodels Network Architecture in Soil Microcosms.Stamou GP. Microbial Ecology

Effect of stock density on the microbial community in biofloc water and Pacific white shrimp (Litopenaeus vannamei) gut microbiota.Deng Y. Applied Microbiology Biotechnology

Rapid and stable microbial community assembly in the headwaters of third-order stream. Teachey ME. Applied Environmental Microbiology

Comparative Metagenomics Reveals Enhanced Nutrient Cycling Potential After Two Years of Biochar Amendment in a Tropical Oxisol. Yu J. Applied Environmental Microbiology

Animal Experiments and Microbiome

Effect of a low protein diet on chicken ceca microbiome and productive performances. De Cesare A. Poultry Science

Impact of a probiotic-based cleaning product on the microbiological profile of broiler litters and chicken caeca microbiota.De Cesare P. Poultry Science

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. Grieco MB. Current Microbiology.

The hemolymph microbiome of insects. Blow F. Journal Of Insect Physiology

Musa basjoo regulates the gut microbiota in mice by rebalancing the abundance of probiotic and pathogen. Wei T. Microbial Pathogenesis

Investigating the influence of organic acid marinades, storage temperature and time on the survival/inactivation interface of Salmonella on chicken breast fillets.

Lytou AE. International Journal of Food Microbiology.

April 6, 2019

Highlights: Inferring absolute species concentration in vaginal microbiome, transcriptomics of Arctic Tundra soils, successional traits of prokaryotic communities in Tundra soil, Modulation of plant microbial community by fungal endophyte Epichloë and many more.

General microbiome

Microbial community design: methods, applications, and opportunities –  A Eng – Current Opinion in Biotechnology

Human vaginal microbiome

Comparative genomics of human Lactobacillus crispatus isolates reveals genes for glycosylation and glycogen degradation: implications for in vivo dominance of the vaginal microbiota – Charlotte van der Veer – Microbiome

Complementing 16S rRNA gene amplicon sequencing with estimates of total bacterial load to infer absolute species concentrations in the vaginal microbiome – Florencia Tettamanti Boshier – bioRxiv

Human gut microbiome

Perturbation of the human gut microbiome by a non-antibiotic drug contributes to the resolution of autoimmune disease – Renuka R Nayak – bioRxiv

Gut microbiota from high-risk men who have sex with men drive immune activation in gnotobiotic mice and in vitro HIV infection – SX Li – PLoS Pathogens

Distinct gut microbiota profile in antiretroviral therapy-treated perinatally HIV-infected patients associated with cardiac and inflammatory biomarkers – L Sessa – AIDS

The relationship between gastric microbiota and gastric disease – S Zhang – Scandinavian Journal of Gastroenterology

The Gut Microbiome Says NO to microRNA-Mediated Gene Silencing – Z Wei – Biochemistry

Functional diversity and metabolic profile of microbial community of mine soils with different levels of chromium contamination – SK Pradhan – International Journal of Environmental Health Research

16S rRNA/rRNA Gene Ratios and Cell Activity Staining Reveal Consistent Patterns of Microbial Activity in Plant-Associated Soil – AW Bowsher – mSystems

Spatial segregation of the biological soil crust microbiome around its foundational cyanobacterium, Microcoleus vaginatus, and the formation of a nitrogen-fixing cyanosphere – E Couradeau – Microbiome

 

Plant, root, and soil microbiome

A long-term field experiment demonstrates the influence of tillage on the bacterial potential to produce soil structure-stabilizing agents such as exopolysaccharides and lipopolysaccharides – Barbara Cania – Environmental Microbiome

Heritable Epichloë symbiosis shapes fungal but not bacterial communities of plant leaves – Riitta Nissinen – Scientific Reports

Prokaryotic community shifts during soil formation on sands in the tundra zone – Alena Zhelezova – PLoS ONE

The epiphytic microbiota of sour rot-affected grapes differs minimally from that of healthy grapes, indicating causal organisms are already present on healthy berries – Megan E Hall – PLoS ONE

Transcriptomic responses to warming and cooling of an Arctic tundra soil microbiome – Morten Dencker Schostag – bioRxiv

Metatranscriptomic reconstruction reveals RNA viruses with the potential to shape carbon cycling in soil – Evan P. Starr – bioRxiv

Comparison of prokaryotic communities between the fields showing different disinfestation effects by anaerobic soil disinfestation – Chol Gyu Lee – bioRxiv

Long-term urea fertilization alters the composition and increases the abundance of soil ureolytic bacterial communities in an upland soil – R Sun – FEMS Microbial Ecology

Water and extremophile microbiome 

Diversity and shifts of the bacterial community associated with Baikal sponge mass mortalities – Sergei Belikov – PLoS ONE

Temporal covariation of epibacterial community and surface metabolome in the Mediterranean seaweed holobiont Taonia atomaria – B Paix – Environmental Microbiology

Monitoring Microbial Communities in the Marine Environment – Ger van den Engh – Cytometry Part A

Microbes in the news

Evidence for link between ‘leaky gut’ and autoantibody production in HIV-positive patients – Science Daily

Eden Project hosts bacteria filled art exhibition – The Packet

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 20, 2019

Today’s digest features a longitudinal survey of maternal anti-viral antibodies in newborns that provides a blueprint for understanding infectious disease susceptibility, a detailed overview of antimicrobial resistance identification and characterization methods (from traditional antimicrobial susceptibility testing to recent deep-learning methods), and more. Happy reading!

Gut microbiome

Gut microbiota plasticity is correlated with sustained weight loss on a low-carb or low-fat dietary intervention – Jessica A Grembi – bioRxiv

The intestinal microbiota programs diurnal rhythms in host metabolism through histone deacetylase 3 – Zheng Kuang – bioRxiv

*Neuronal programming by microbiota enables environmental regulation of intestinal motility – Yuuki Obata – bioRxiv

Probiotics

Growth Mode and Carbon Source Impact the Surfaceome Dynamics of Lactobacillus rhamnosus GG – Kirsi Savijoki – bioRxiv

Nasal microbiome

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

Vaginal microbiome

Mini review: Vaginal microbiota transplantation for the treatment of bacterial vaginosis: a conceptual analysis – Dongwen Ma – FEMS Microbiology Letters

Comparative study of vulva and abdominal skin microbiota of healthy females with high and average BMI – Rebecca Vongsa – BMC Microbiology

Plant/root/soil microbiome

Biosurfactant production by a rhizosphere bacteria Bacillus altitudinis MS16 and its promising emulsification and antifungal activity – Madhurankhi Goswami & Suresh Deka – Colloids and Surfaces B: Biointerfaces

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

Water microbiome

Ecological processes underpinning microbial community structure during exposure to subinhibitory level of triclosan – Seungdae Oh – Scientific Reports

Microbial Ecology of Snow Reveals Taxa-Specific Biogeographical Structure – Shawn P. Brown & Ari Jumpponen – Microbial Ecology

Phages and viruses

*The repertoire of maternal anti-viral antibodies in human newborns – Christian Pou – Nature Medicine

Methods

*Review: Sequencing-based methods and resources to study antimicrobial resistance – Manish Boolchandani – Nature Reviews Genetics

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 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