March 1, 2019

Today’s short digest covers articles on bacterial interaction with intestinal cells, semen microbiome and how microbiota affects insulin reactive immune cells.

General microbiome

The founder hypothesis: A basis for microbiota resistance, diversity in taxa carriage, and colonization resistance against pathogens – Yael Litvak -Plos Pathogens

Review : Impact of the gut microbiome on the genome and epigenome of colon epithelial cells: contributions to colorectal cancer development – Jawara Allen – Genome Medicine

Paneth cell granule dynamics on secretory responses to bacterial stimuli in enteroids – Yuki Yokoi – Scientific Reports

Human gut microbiome

Altered immunity and microbial dysbiosis in aged individuals with long-term controlled HIV infection – Nicholas S. Rhoades – Frontiers in Immunology

Bacterial viability in faecal transplants: Which bacteria survive? – Lito E. Papanicolas – EbioMedicine

Semen Microbiome Biogeography: An Analysis Based on a Chinese Population Study – Zhanshan Ma – Frontiers in Microbiology

Animal experiments

The effects of unfermented and fermented cow and sheep milk on the gut microbiota – Elizabeth Rettedal – Frontiers in Microbiology

Altered Gut Microbiota Activate and Expand Insulin B15-23-Reactive CD8+ T-Cells – James A. Pearson – Diabetes

Lactobacillus plantarum PFM 105 Promotes Intestinal Development Through Modulation of Gut Microbiota in Weaning Piglets – Tianwei Wang – Frontiers in Microbiology

Water microbiome and extremophiles

Microbial residence time is a controlling parameter of the taxonomic composition and functional profile of microbial communities – Cresten Mansfeldt – ISME Journal

Microbial community structure and functionality in the deep sea floor: evaluating the causes of spatial heterogeneity in a submarine canyon system (NW Mediterranean, Spain) – Sara Román – Frontiers in Marine Science

Non-microbiology picks

Dual AAV-mediated gene therapy restores hearing in a DFNB9 mouse model – Omar Akil – PNAS

February 26, 2019

Posted on February 26, 2019 by xinhuang7

Today’s Digest features a discovery of an intestinal archaea inversely associated with asthma, a tracking of surviving bacteria after FMT using 16s and a report on a bat species as a reservoir for antibiotic resistant determinants. Enjoy reading!

General microbiology

Sequence and cultivation study of Muribaculaceae reveals novel species, host preference, and functional potential of this yet undescribed family – Ilias Lagkouvardos et al. – Microbiome

Description of Janibacter massiliensis sp. nov., cultured from the vaginal discharge of a patient with bacterial vaginosis – Mossaab Maaloum et al. – Antonie van Leeuwenhoek

Preprint: Emergence of stable coexistence in a complex microbial community through metabolic cooperation and spatio-temporal niche partitioning – Sonja Blasche et al. – bioRxiv

Human oral microbiome

Streptococcus Salivarius: A Potential Salivary Biomarker for Orofacial Granulomatosis and Crohn’s Disease? – Rishi M Goel et al. – Inflammatory Bowel Diseases

Human respiratory microbiome

Changes in microbiome diversity following beta-lactam antibiotic treatment are associated with therapeutic versus subtherapeutic antibiotic exposure in cystic fibrosis – Andrea Hahn et al. – Scientific Reports

Human gut microbiome

** Intestinal archaea inversely associated with childhood asthma – David J.M. Barnett et al. – The Journal of Allergy and Clinical Immunology

Alterations in intestinal microbiota of colorectal cancer patients receiving radical surgery combined with adjuvant CapeOx therapy – Cheng Kong et al. – Science China Life Sciences

Immunity, microbiota and kidney disease – Felix Knauf et al. – Nature Reviews Nephrology

The human gut Firmicute Roseburia intestinalis is a primary degrader of dietary β-mannans – Sabina Leanti La Rosa et al. – Nature Communications

** Bacterial viability in faecal transplants: Which bacteria survive? – Lito E. Papanicolas et al. – EBioMedicine

Increased risk of chronic fatigue syndrome in patients with inflammatory bowel disease: a population-based retrospective cohort study – Shin-Yi Tsai et al. – Journal of Translational Medicine

Preprint: Necrotizing enterocolitis is preceded by increased gut bacterial replication, Klebsiella, and fimbriae-encoding bacteria that may stimulate TLR4 receptors – Matthew R Olm et al. – bioRxiv

Human gut-microbiome-brain axis

Review: Microbes and Monoamines: Potential Neuropsychiatric Consequences of Dysbiosis – Stephen D. Skolnick & Nigel H. Greig – Trends in Neurosciences

Metabolomics

Targeted metabolomics for the quantitative measurement of 9 gut microbiota–host co-metabolites in rat serum, urine and feces by liquid chromatography–tandem mass spectrometry – Yifeng Zeng et al. – Journal of Chromatography B

Untargeted Metabolomics and Inflammatory Markers Profiling in Children With Crohn’s Disease and Ulcerative Colitis—A Preliminary Study – Urszula Daniluk et al. – Inflammatory Bowel Diseases

Animal experiments

Effects of a Saccharomyces cerevisiae fermentation product on liver abscesses, fecal microbiome, and resistome in feedlot cattle raised without antibiotics – Katherine L. Huebner et al. – Scientific Reports

Mouse: Altered Gut Microbiota Activate and Expand Insulin B15-23-Reactive CD8+ T-Cells – James A. Pearson et al. – Diabetes

Xiaoyaosan improves depressive-like behavior in rats with chronic immobilization stress through modulation of the gut microbiota – Hui-Zheng Zhu et al. – Biomedicine & Pharmacotherapy
Animal microbiome

In-feed resin acids reduce matrix metalloproteinase activity in the ileal mucosa of healthy broilers without inducing major effects on the gut microbiota – Marisol Aguirre et al. – Veterinary Research

** Bats as reservoirs of antibiotic resistance determinants: A survey of class 1 integrons in Grey-headed Flying Foxes (Pteropus poliocephalus) – Fiona McDougall et al. – Infection, Genetics and Evolution

Plant, root and soil microbiome

Structural and functional responses of microbial community with respect to salinity levels in a coastal reclamation land – Kiyoon Kim et al. – Applied Soil Ecology

Biosolids and Tillage Practices Influence Soil Bacterial Communities in Dryland Wheat – Daniel C. Schlatter et al. – Microbial Ecology

Metabolic regulation of the maize rhizobiome by benzoxazinoids – T. E. Anne Cotton et al. – The ISME Journal

Above and belowground community strategies respond to different global change drivers – Karen L. Adair et al. – Scientific Reports

Utilization of actinobacteria to enhance the production and quality of date palm (Phoenix dactylifera L.) fruits in a semi-arid environment – Hamada AbdElgawad et al. – Science of The Total Environment

Protura are unique: first evidence of specialized feeding on ectomycorrhizal fungi in soil invertebrates – Sarah L. Bluhm et al. – BMC Ecology

Rotations with Indian Mustard and Wild Rocket Suppressed Cucumber Fusarium Wilt Disease and Changed Rhizosphere Bacterial Communities – Xue Jin et al. – Microorganisms

Water and extremophile microbiome

Change in the microbial community of saline geothermal fluids amended with a scaling inhibitor: effects of heat extraction and nitrate dosage – Anke Westphal et al. – Extremophiles

Genomic and metatranscriptomic analyses of carbon remineralization in an Antarctic polynya – So-Jeong Kim & Jong-Geol Kim et al. – Microbiome

Preprint: Extreme niche partitioning promotes a remarkably high diversity of soil microbiomes across eastern Antarctica – Eden Zhang et al. – bioRxiv

Phages and viruses

Viral metagenomics revealed novel betatorquevirus species in pediatric inpatients with encephalitis/meningoencephalitis from Ghana – Daniel Eibach et al. – Scientific Reports

February 23, 2019

Posted on February 23, 2019 by Kiran

Highlights: Today’s digest has articles on microbes associated with infants, vagina, gut, water and many more.

Events and jobs

Postdoctoral Researcher in mathematical modelling of the impact of host restriction on the transmission of bacteria – Amsterdam – Closing date: February 28, 2019

Pregnancy and early life

A role for the microbiome in mother–infant interaction and perinatal depression – Amanda Sanders – The International Review of Psychiatry

Multi-site human microbiome

Surgical site infections and the microbiome: An updated perspective – Richard P. Wenzel – Infection Control & Hospital Epidemiology

Human vaginal microbiome

The Endobiota Study: Comparison of Vaginal, Cervical and Gut Microbiota Between Women with Stage 3/4 Endometriosis and Healthy Controls – Baris Ata – Scientific Reports

Relationship between the Cervical Microbiome, HIV Status, and Precancerous Lesions – Cameron Klein – mBio

Human nearly-sterile sites

Microbiome-based body fluid identification of samples exposed to indoor conditions – Akos Dobay – FSI Genetics

Human gut microbiome

Arabinoxylan oligosaccharides and polyunsaturated fatty acid effects on gut microbiota and metabolic markers in overweight individuals with signs of metabolic syndrome: a randomized cross-over trial – Louise Kjølbæk – Clinical Nutrition

The human microbiota and infection prevention – R. Araos – Infection Control & Hospital Epidemiology

Gut pathobionts as triggers for liver diseases – Peter Fickert – Nature Microbiology

Man and the Microbiome: A New Theory of Everything? – Mary I. Butler – Annual Review of Clinical Psychology

Is it true that gut microbiota is considered as panacea in cancer therapy? – Amir Salek Farrokhi – Journal of Cellular Physiology

Composition of gut microbiota in patients with toxigenic Clostridioides (Clostridium) difficile: Comparison between subgroups according to clinical criteria and toxin gene load – Sung-Hee Han – PLoS ONE

Effects of dietary fat on gut microbiota and faecal metabolites, and their relationship with cardiometabolic risk factors: a 6-month randomised controlled-feeding trial – Yi Wan – Gut

The Intestinal Microbiome, Plasma Metabolome and Liver Transcriptome‐ A Conspiracy Driving Hepatic Steatosis – Wajahat Z Mehal – Hepatology

A possible link between polyunsaturated fatty acids and uremic toxins from the gut microbiota in hemodialysis patients: A hypothesis – Julie Ann Kemp – Hemodialysis International

Animal experiments

Alterations of the mice gut microbiome via Schistosoma japonicum ova-induced granuloma – Yanqing Zhao – Frontiers in Microbiology

The functional repertoire encoded within the native microbiome of the model nematode Caenorhabditis elegans – Johannes Zimmermann – bioRxiv

Helminth-Based Product and the Microbiome of Mice with Lupus – Hadar Neuman – mSystems

Gut microbiota regulates lacteal integrity by inducing VEGF-C in intestinal villus macrophages. – SH Suh – EMBO Reports

Animal microbiome

Gut Microbiome Analysis In Adult Tropical Gars (Atractosteus tropicus) – Roberto Mendez-Perez – bioRxiv

Moderate plant water stress improves larval development, and impacts immunity and gut microbiota of a specialist herbivore – Elena Rosa -PLoS ONE

Plant, root, and soil microbiome

Chinese white truffles shape the ectomycorrhizal microbial communities of Corylus avellana – Mei Yang – Annals of Microbiology

Narrow safety margin in the phyllosphere during thermal extremes – Sylvain Pincebourde – PNAS

Nitrogen- and phosphorus-starved Triticum aestivum show distinct belowground microbiome profiles – Antoine P. Pagé – PLoS ONE

Water and extremophile microbiome

Community ecology across bacteria, archaea and microbial eukaryotes in the sediment and seawater of coastal Puerto Nuevo, Baja California – Sabah Ul-Hasan – PLoS ONE

Editorial: Thermophilic and Halophilic Extremophiles in Eurasian Environments – Hongchen Jiang – Frontiers in Microbiology

Marine deep biosphere microbial communities assemble in near-surface sediments in Aarhus Bay – Caitlin Petro – bioRxiv

Quantifying population-specific growth in benthic bacterial communities under low oxygen using H218O – Ömer K. Coskun – The ISME Journal

Bacterial community pattern along the sediment seafloor of the Arctic fjorden (Kongsfjorden, Svalbard) – Xiao-Mei Fang – Antonie van Leeuwenhoek

Sources and selection of snow-specific microbial communities in a Greenlandic sea ice snow cover – Lorrie Maccario – Scientific Reports

Bacterial community composition shaped by water chemistry and geographic distance in an anthropogenically disturbed river – Peng Wang – Science of The Total Environment

Built environment

Cell factories converting lactate and acetate to butyrate: Clostridium butyricum and microbial communities from dark fermentation bioreactors – Anna Detman – Microbial Cell Factories

Phages and viruses

Discovery of several thousand highly diverse circular DNA viruses – Michael J Tisza – bioRxiv

Techniques

Spatial metabolomics of in situ, host-microbe interactions – Benedikt K Geier – bioRxiv

Performance of Microbiome Sequence Inference Methods in Environments with Varying Biomass – Vincent Caruso – mSystems

February 19, 2019

Posted on February 19, 2019 by Kiran

Highlights: Microbial colonization in infants, prokaryotes of oxygen depleted water in Bay of Bengal, biodegradation of petroleum hydrocarbons, microbial communities across a range of saline soils, trait based approaches in wastewater treatment bioreactors to understand the changes in bacterial community composition. You can also read a handful of career based news in today’s non-microbe picks.

General microbiome

Petroleum Microbiology Under Extreme Conditions – Oluwadara Oluwaseun Alegbeleye –Microbial Action on Hydrocarbons

Pregnancy and early life

Genome-resolved metagenomics of eukaryotic populations during early colonization of premature infants and in hospital rooms – Matthew R Olm – Microbiome

Review: Establishment of an ideal gut microbiota to boost healthy growth of neonates – Thi Thanh Binh Nguyen – Critical Reviews in Microbiology

Necrotizing Enterocolitis Pathophysiology: How Microbiome Data Alter Our Understanding – Christina S. Kim MD – Clinics in Perinatology

Human skin microbiome

Rapid discrimination of fungal strains isolated from human skin based on microbial volatile organic profiles – Joao Raul Belinato – Journal of Chromatography B

Human gut microbiome

A pilot study on clinicopathological features and intestinal microflora changes in colorectal cancer patients born over a nine-year period encompassing three years before and after the Great Chinese famine – Jiante Li – Cancer Epidemiology

Animal experiments

Ameliorating gut microenvironment through staphylococcal nuclease-mediated intestinal NETs degradation for prevention of type 1 diabetes in NOD mice – Yixuan Liang – Life Sciences

Oral administration of antibiotics increased the potential mobility of bacterial resistance genes in the gut of the fish Piaractus mesopotamicus – Johan S. Sáenz – Microbiome

Animal microbiome

Effects of a Saccharomyces cerevisiae fermentation product on fecal characteristics, nutrient digestibility, fecal fermentative end-products, fecal microbial populations, immune function, and diet palatability in adult dogs – Ching-Yen Lin – Journal of Animal Science

Bacterial community analysis for investigating bacterial transfer from tonsils to the pig carcass – Anne Mette Jakobsen – International Journal of Food Microbiology

Plant, root, and soil microbiome

Spatial distribution of prokaryotic communities in hypersaline soils – Blanca Vera-Gargallo – Scientific Reports

Comparative Genomics, Siderophore Production, and Iron Scavenging Potential of Root Zone Soil Bacteria Isolated from ‘Concord’ Grape Vineyards – Ricky W. Lewis – Microbial Ecology

Dynamics of soil microbial communities following vegetation succession in a karst mountain ecosystem, Southwest China – Chang Zhao – Scientific Reports

Diversity and Functionality of Culturable Endophytic Bacterial Communities in Chickpea Plants – Clarisse Brígido – MDPI

Robust archaeal and bacterial communities inhabit shallow subsurface sediments of the Bonneville Salt Flats – Julia M. McGonigle – bioRxiv

Impact of intercropping on the coupling between soil microbial community structure, activity, and nutrient-use efficiencies – Tengxiang Lian – PeerJ

Alteration of Crop Rotation in Continuous Pinellia ternate Cropping Soils Profiled via ITS Amplicon Sequencing – Zhigui He – Letters in Applied Microbiology

Assessment of the Diversity of Fungal Community Composition Associated With Vachellia pachyceras and Its Rhizosphere Soil From Kuwait Desert – Majda K. Suleiman – Frontiers in Microbiology

Water and extremophile microbiome

Prokaryotic Diversity in Oxygen Depleted Waters of the Bay of Bengal Inferred Using Culture-Dependent and -Independent Methods – Genevieve L. Fernandes – Indian Journal of Microbiology

Enrichment of anaerobic heterotrophic thermophiles from four Azorean hot springs revealed different community composition and genera abundances using recalcitrant substrates – Marcel Suleiman – Extremophiles

Microbial Consortia and Biodegradation of Petroleum Hydrocarbons in Marine Environments – J. Paniagua-Michel – Microbial Action on Hydrocarbons

Built environment

Trait-based life-history strategies explain succession scenario for complex bacterial communities under varying disturbance – Ezequiel Santillan – bioRxiv

Non-Microbiology picks

To move research from quantity to quality, go beyond good intentions – Nature

How business-savvy scientists can find success in the risky start-up world – Nature

A disadvantaged background doesn’t have to be a barrier to success – Nature

Announcing the 2019 ScientistAtWork photo competition – Nature

Huge variations in US postdoc salaries point to undervalued workforce – Nature

February 16, 2019

Posted on February 16, 2019 by Tulika Arora

Today’s digest is full of interesting articles about virome and phages, sinonasal microbiome and human milk microbiota. Enjoy weekend reading!

General microbiome

Bacteria and archaea on Earth and their abundance in biofilms – Hans-Curt Flemming – Nature Reviews Microbiology

The Impact of Low-FODMAPs, Gluten-Free, and Ketogenic Diets on Gut Microbiota Modulation in Pathological Conditions – Sofia Reddel – Nutrients

Impact of Gut Microbiota on Host Glycemic Control – Celine Gérard – Frontiers in Endocrinology

Intestinal Microbiota as a Host Defense Mechanism to Infectious Threats – Simona Iacob – Frontiers in Microbiology

Pregnancy and early life

Composition and Variation of the Human Milk Microbiota Are Influenced by Maternal and Early-Life Factors – Shirin Mossavi – Cell Host and Microbe

Human microbiome

Gut microbiota diversity associates with cardiorespiratory fitness in post-primary treatment breast cancer survivors – Stephen J. Carter – Experimental Physiology

Alterations in fecal short-chain fatty acids in patients with irritable bowel syndrome: A systematic review and meta-analysis – Qinghua Sun – Medicine

Mucosa-associated microbiota drives pathogenic functions in IBD-derived intestinal iNKT cells – Claudia Burrello – Life Science Alliance

The international sinonasal microbiome study (ISMS): a multi-centre, international characterization of sinonasal bacterial ecology – Sathish Paramasivan – BioRxiv

Microbiotyping the sinonasal microbiome – Ahmed Bassiouni – BioRxiv

Prevotella copri in individuals at risk for rheumatoid arthritis – Deshire Alpizar-Rodriguez – Annals of Rheumatic Diseases

Gut Microbiota Dysbiosis Is Not Independently Associated With Neurocognitive Impairment in People Living With HIV – Fengdi Zhang – Frontiers in Microbiology

Animal experiments

Gut microbiota signatures and lipids metabolism profiles by exposure to polyene phosphatidylcholine – Haining Yu – Biofactors

Exploring the Fecal Microbial Composition and Metagenomic Functional Capacities Associated With Feed Efficiency in Commercial DLY Pigs – Jianping Quan – Frontiers in Microbiology

Plant root soil microbiome

Successive phytoextraction alters ammonia oxidation and associated microbial communities in heavy metal contaminated agricultural soils – Jipeng Luo – Science of The Total Environment

Water microbiome and extremophiles

Low concentrations of copper oxide nanoparticles alter microbial community structure and function of sediment biofilms – Lingzhan Miao – Science of the Total Environment

Characterizing the microbiome in petroleum reservoir flooded by different water sources – Xiaotong Wang – Science of the Total Environment

Baseline characterisation of aerobic hydrocarbon degrading microbial communities in deep‐sea sediments of the Great Australian Bight, Australia – Jodie van de Kamp – Environmental Microbiology

Viruses and phages

Expansion of Bacteriophages Is Linked to Aggravated Intestinal Inflammation and Colitis – Lasha Gogokhia – Cell Host and Microbe

Virome Diversity Correlates with Intestinal Microbiome Diversity in Adult Monozygotic Twins – J. Leonardo Moreno-Gallego – Cell Host and Microbe

Bacteriophages of the Human Gut: The “Known Unknown” of the Microbiome – Andrey N. Shkoporov – Cell Host and Microbe

Non-microbiology picks

Function and mechanisms of enteroendocrine cells and gut hormones in metabolism – Fiona M. Gribble – Nature Reviews Endocrinology

February 12, 2019

Posted on February 12, 2019 by xinhuang7

Today’s Digest features a major effect to tackle the dark matter in the human gut microbiome, comparison of 8 methods to extract DNA from the oral cavity that yielded an unexpected result, and the investigation on whether we can predict sex/age by our gut microbiota. Enjoy!

General microbiology

Perspective: Bridging the Holistic-Reductionist Divide in Microbial Ecology – Robin Tecon et al. – mSystems

Microbioime sister journal: Welcome to Animal Microbiome – Sharon A. Huws

Engineering microbial consortia by division of labor – Garrett W. Roell et al. – Microbial Cell Factories

Preprint: Revisiting the evolution and taxonomy of Clostridia, a phylogenomic update – Pablo Cruz-Morales et al. – bioRxiv

Human skin microbiome

Skin Microbiota in Contact Sports Athletes and Selection of Antiseptics for Professional Hygiene – Dilyara S. Martykanova et al. – BioMed Research International

Human oral microbiome

Qualitative and quantitative differences in the subgingival microbiome of the restored and unrestored teeth – Steven W. H. Rademacher et al. – Journal of Periodontal Research

Human respiratory microbiome

Comparison of Subtyping Approaches and the Underlying Drivers of Microbial Signatures for Chronic Rhinosinusitis – Kristi Biswas et al. – mSphere

Human gut microbiome

** 1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses – Yuanqiang Zou et al. – Nature Biotechnology

Genomic insights from Monoglobus pectinilyticus: a pectin-degrading specialist bacterium in the human colon – Caroline C. Kim et al. – The ISME Journal

Pinning down the role of common luminal intestinal parasitic protists in human health and disease – status and challenges – Christen Rune Stensvold – Parasitology

Dynamics of the Gut Microbiota in Children Receiving Selective or Total Gut Decontamination Treatment During Hematopoietic Stem Cell Transplantation – Vincent Bekker & Romy D. Zwittink et al. – Biology of Blood and Marrow Transplantation

Fecal Microbiota Transplantation in Patients With Primary Sclerosing Cholangitis: A Pilot Clinical Trial – Jessica Allegretti et al. – The American Journal of Gastroenterology

** Preprint: Age and sex-dependent patterns of gut microbial diversity in human adults – Jacobo de la Cuesta-Zuluaga et al. – bioRxiv

Human reproductive tract microbiome

Cervical microbiota in women with cervical intra-epithelial neoplasia, prior to and after local excisional treatment, a Norwegian cohort study – Johanna Wiik – BMC Women’s Health

Built environment microbiome

Spatial and seasonal variation of the airborne microbiome in a rapidly developing city of China – Hu Li et al. – Science of the Total Environment

Animal experiments

Synbiotic-driven improvement of metabolic disturbances is associated with changes in the gut microbiome in diet-induced obese mice – Xinxin Ke et al. – Molecular Metabolism

The gut microbiota is largely independent of host genetics in regulating fat deposition in chickens – Chaoliang Wen et al. – The ISME Journal

The Glucoamylase Inhibitor Acarbose Has a Diet-Dependent and Reversible Effect on the Murine Gut Microbiome – Nielsen T. Baxter et al. – mSphere

Animal microbiome

Effects of polyethylene microplastics on the gut microbial community, reproduction and avoidance behaviors of the soil springtail, Folsomia candida – Hui Ju et al. – Environmental Pollution

Effects of host blood meal source on reproductive output, nutrient reserves and gut microbiome of West Nile virus vector Culex quinquefasciatus – Aparna Telang & Jessica Skinner – Journal of Insect Physiology

Plant, root and soil microbiome

Soil microbes alter plant fitness under competition and drought – Connor R. Fitzpatrick et al. – Journal of Evolutionary Biology

Multi-resistant plant growth-promoting actinobacteria and plant root exudates influence Cr(VI) and lindane dissipation – María ZoleicaSimón Solá et al. – Chemosphere

Interactions between Pseudomonas spp. and their role in improving the red pepper plant growth under salinity stress – Sandipan Samaddar et al. – Microbiological Research

Plant Defense by VOC-Induced Microbial Priming – Hongwei Liu & Laura E. Brettell – Trends in Plant Science

Water and extremophile microbiome

Microbial ecology of the cryosphere (glacial and permafrost habitats): current knowledge – Rosa Margesin & Tony Collins – Applied Microbiology and Biotechnology

Unique Patterns and Biogeochemical Relevance of Two-Component Sensing in Marine Bacteria – Noelle A. Held et al. – mSystems

Oil-Spill Triggered Shift in Indigenous Microbial Structure and Functional Dynamics in Different Marine Environmental Matrices – C. S. Neethu et al. – Scientific Reports

An integrated meta-omics approach reveals substrates involved in synergistic interactions in a bisphenol A (BPA)-degrading microbial community – Ke Yu et al. – Microbiome

Effects of biomass pyrolysis derived wood vinegar on microbial activity and communities of activated sludge – Fang Zhang et al. – Bioresource Technology

Anti-seasonal submergence dominates the structure and composition of prokaryotic communities in the riparian zone of the Three Gorges Reservoir, China – Yan Fang et al. – Science of The Total Environment

Phages and viruses

Cobaviruses – a new globally distributed phage group infecting Rhodobacteraceae in marine ecosystems – Vera Bischoff et al. – The ISME Journal

In plaque-mass spectrometry imaging of a bloom-forming alga during viral infection reveals a metabolic shift towards odd-chain fatty acid lipids – Guy Schleyer et al. – Nature Microbiology

Technology

The mucosal–luminal interface: an ideal sample to study the mucosa-associated microbiota and the intestinal microbial biogeography – Walid Mottawea et al. – Pediatric Research

Development and application of a HILIC UHPLC-MS method for polar fecal metabolome profiling – Nina Sillner et al. – Journal of Chromatography B

** Evaluation of Oral Cavity DNA Extraction Methods on Bacterial and Fungal Microbiota – Jennifer Rosenbaum et al. – Scientific Reports

Xin’s Non-microbiology pick

Preprint: Where do our graduates go? A toolkit for retrospective and ongoing career outcomes data collection for biomedical PhD students and postdoctoral scholars – Elizabeth A. Silva et al. – bioRxiv

February 8, 2019

Posted on February 8, 2019 by korinalbert

Happy Friday! Today’s digest includes the sea cucumber gut microbiome, bacterial diversity of volcano steam vents, and the impacts of arsenic and antimony on microbes in river sediment. Enjoy!

Human gut microbiome

Use of shotgun metagenomics for the identification of protozoa in the gut microbiota of healthy individuals from worldwide populations with various industrialization levels – Lokmer – PLoS ONE

Age-associated Impairment of the Mucus Barrier Function is Associated with Profound Changes in Microbiota and Immunity – Sovran – Scientific Reports

A single alcohol binge impacts on neutrophil function without changes in gut barrier function and gut microbiome composition in healthy volunteers – Stadlbauer – PLoS ONE

Animal experiments

TGFβ/BMP immune signaling affects abundance and function of C. elegans gut commensals – Berg – Nature Communications

Animal microbiome

Distinct microbiotas of anatomical gut regions display idiosyncratic seasonal variation in an avian folivore – Drovetski – Animal Microbiome

Characterization of the intestinal microbiota of the sea cucumber Holothuria glaberrima – Pagán-Jiménez – PLoS ONE

Dynamic distribution of gallbladder microbiota in rabbit at different ages and health states – Xing – PLoS ONE

Dietary-induced modulation of the hindgut microbiota is related to behavioral responses during stressful events in horses – Destrez – Physiology & Behavior

Review: Host-Microbe Coevolution: Applying Evidence from Model Systems to Complex Marine Invertebrate Holobionts – O’Brien – mBio

Plant, root, and soil microbiome

Environmental filtering drives distinct continental atlases of soil archaea between dryland and wetland agricultural ecosystems – Jiao – Microbiome

The occurrence of potato common scab correlates with the community composition and function of the geocaulosphere soil microbiome – Shi -Microbiome

Enterobacteriaceae dominate the core microbiome and contribute to the resistome of arugula (Eruca sativa Mill.) – Cernava – Microbiome

Unlocking a high bacterial diversity in the coralloid root microbiome from the cycad genus Dioon – Suárez-Moo – PLoS ONE

Characterization of iron-metabolizing communities in soils contaminated by acid mine drainage from an abandoned coal mine in Southwest China – Gao – Environmental Science and Pollution Research

Water and extremophile microbiome

Impacts of Arsenic and Antimony Co-Contamination on Sedimentary Microbial Communities in Rivers with Different Pollution Gradients – Sun – Microbial Ecology

The bacterial diversity on steam vents from Paricutín and Sapichu volcanoes – Souza Brito – Extremophiles

Food microbiology

Spent coffee grounds extract rich in manooligosaccharides promote a healthier gut microbial community in a dose dependent manner – Pérez-Burillo – Journal of Agricultural and Food Chemistry

Impact of routine sanitation on the microbiomes in a fresh produce processing facility – Gu – International Journal of Food Microbiology

February 1, 2019

Posted on January 31, 2019 by Svetlana Ugarcina Perovic

Today’s digest is quite diverse: the respiratory microbiome networks in cystic fibrosis patients, ketogenic diet effects on the gut microbiota in children with severe epilepsy, and insect-associated Streptomyces (spoiler: inhibit antimicrobial-resistant pathogens more than soil Streptomyces). Happy reading!

General microbiome

Minireview: The signatures of microorganisms and of human and environmental biomes can now be used to provide evidence in legal cases – A H Bishop – FEMS Microbiology Letters

Transforming medicine with the microbiome – Niv Zmora – Science Translational Medicine

Gut microbiome

Gut intraepithelial T cells calibrate metabolism and accelerate cardiovascular disease – Shun He – Nature

*The ketogenic diet influences taxonomic and functional composition of the gut microbiota in children with severe epilepsy – Marie Lindefeldt – npj Biofilms and Microbiomes

Vaginal microbiome

Association between vaginal washing and vaginal bacterial concentrations – Michelle C. Sabo – PlosOne

Skin microbiome

Investigation of the Skin Microbiome: Swabs vs Biopsies – S. Prast‐Nielsen – British Journal of Dermatology

Oral microbiome

Carbonic Anhydrase 6 Gene Variation influences Oral Microbiota Composition and Caries Risk in Swedish adolescents – A. Esberg – Scientific Reports

Respiratory microbiome

*Microbiome networks and change-point analysis reveal key community changes associated with cystic fibrosis pulmonary exacerbations – Mehdi Layeghifard – npj Biofilms and Microbiomes

Plant/root/soil microbiome

Effects of long-term fertilization on soil organic carbon mineralization and microbial community structure – Zhen Guo – PlosOne

Water microbiome

Functional screening for triclosan resistance in a wastewater metagenome and isolates of Escherichia coli and Enterococcus spp. from a large Canadian healthcare region – Andrew Camero – PlosOne

Animal experiments

Cream Cheese-Derived Lactococcus chungangensis CAU 28 Modulates the Gut Microbiota and Alleviates Atopic Dermatitis in BALB/c Mice – Jong-Hwa Kim – Scientific Reports

Animal Microbiome

*The antimicrobial potential of Streptomyces from insect microbiomes – Marc G. Chevrette – Nature Communications

January 31, 2019

Posted on January 31, 2019 by Tulika Arora

Today’s digest covers articles describing sphingolipids in host-microbiome interaction, unique microbiome and metabolome of Indian population, selection and stabilization of soil microbiome and effect of probiotics on early sepsis in patients and immune response in children. Enjoy reading!

General microbiome

Metabolic Modeling of Human Gut Microbiota on a Genome Scale: An Overview – Partho Sen – Metabolites

Altered composition and function of intestinal microbiota in autism spectrum disorders: a systematic review – Feitong Liu – Translational Psychiatry

Sphingolipids in host–microbial interactions – Stacey L. Heaver – Current Opinion in Microbiology

Pregnancy and early life

Mixed Viral-Bacterial Infections and Their Effects on Gut Microbiota and Clinical Illnesses in Children – Shilu Mathew – Scientific Reports

Pathways linking caesarean delivery to early health in a dual burden context: Immune development and the gut microbiome in infants and children from Galápagos, Ecuador – Amanda L. Thompson – American Journal of Human Biology

Human gut microbiome

The vagino-cervical microbiome as a woman’s life history – Zhuye Jie – BioRxiv

Dynamics of Human Gut Microbiota and Short-Chain Fatty Acids in Response to Dietary Interventions with Three Fermentable Fibers – Nielson T. Baxter – mBio

The unique composition of Indian gut microbiome, gene catalogue and associated faecal metabolome deciphered using multi-omics approaches – D.B. Dhakan – Gigascience

Animal experiments

Oral neonatal antibiotic treatment perturbs gut microbiota and aggravates central nervous system autoimmunity in Dark Agouti rats – Suzana Stanisavljević – Scientific Reports

Intestinal epithelial N-acylphosphatidylethanolamine phospholipase D links dietary fat to metabolic adaptations in obesity and steatosis – Amandine Everard – Nature Communications

Mutual interplay between IL-17–producing γδT cells and microbiota orchestrates oral mucosal homeostasis – Anneke Wilharm – PNAS

Plant, root and soil microbiome

Selection, succession and stabilization of soil microbial consortia – Elias K. Zegeye – BioRxiv

Comparison of the bacterial and methanotrophic diversities between an Italian paddy field and its neighboring meadow – Mohammad Ghashghavi – BioRxiv

Quality of Irrigation Water Affects Soil Functionality and Bacterial Community Stability in Response to Heat Disturbance – Sammy Frenk – Applied and Environmental Microbiology

Water and extremophiles microbiome

Archaea dominate the microbial community in an ecosystem with low-to-moderate temperature and extreme acidity – Aleksei A. Korzhenkov – Microbiome

Antibiotic disturbance affects aquatic microbial community composition and foodweb interactions but not community resilience – Ester M. Eckert – Molecular Ecology

Phages and viruses

Megaphages infect Prevotella and variants are widespread in gut microbiomes – Audra E. Devoto – Nature Microbiology

Probiotics / prebiotics

Dysbiosis in early sepsis can be modulated by a multispecies probiotic: a randomised controlled pilot trial – V. Stadlbauer – Beneficial Microbes

Lactobacillus plantarum IS-10506 supplementation increases faecal sIgA and immune response in children younger than two years – P.D. Kusumo – Beneficial Microbes

Supplementation with Lactobacillus kefiranofaciens ZW3 from Tibetan Kefir improves depression-like behavior in stressed mice by modulating the gut microbiota – Ye Sun – Food and Function

Non-microbiology picks

Identification of Enteroendocrine Regulators by Real-Time Single-Cell Differentiation Mapping – Helmuth Gehart – Cell

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Microbiome Digest – Bik's Picks

A daily digest of scientific microbiome papers, by the MD team. Founded by Elisabeth Bik, microbiome and science integrity consultant. Twitter: @microbiomdigest

Category Archives: Water microbiome

March 1, 2019

February 27, 2019

February 26, 2019

February 23, 2019

February 19, 2019

February 16, 2019

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February 1, 2019

January 31, 2019