17 October,​ 2018

General Microbiome

ESS: A Tool for Genome-Scale Quantification of Essentiality Score for Reaction/Genes in Constraint-Based Modeling.Zhang C. Frontiers in Physiology

Skin Microbiome

The emerging role of skin microbiome in atopic dermatitis and its clinical implication.Stalder JF. Journal of Dermatological Treatment

Oral Microbiome

Pleistocene dental calculus: Recovering information on Paleolithic food items, medicines, paleoenvironment and microbes.Hardy K. Environmental Anthropology

Gut Microbiome

Gut Microbial Product Predicts Cardiovascular Risk in Chronic Kidney Disease Patients.Jadoon A. American Journal of Nephrology

Interrogating gut bacterial genomes for discovery of novel carbohydrate degrading enzymes.Luis AS. Current Opinions in Chemical Biology

Vitamin D and the gut microbiome: a systematic review of in vivo studies.Waterhouse M. European Journal of Nutrition

A Review: The Fate of Bacteriocins in the Human Gastro-Intestinal Tract: Do They Cross the Gut-Blood Barrier?Dicks LMT. Frontier in Microbiology

Precision identification of diverse bloodstream pathogens in the gut microbiome.Tamburini FB. Nature Medicine

Animal Microbiome

Rickettsia diversity in southern Africa: A small mammal perspective.Essbauer S. Tick and Tick-Borne Disease

Response of Gut Microbiota to Dietary Fiber and Metabolic Interaction With SCFAs in Piglets.Liu B. Frontier in Microbiology

Precise Fecal Microbiome of the Herbivorous Tibetan Antelope Inhabiting High-Altitude Alpine Plateau.Bai X. Frontier in Microbiology

Microbiome-assisted carrion preservation aids larval development in a burying beetle.Shukla SP. PNAS

The gut microbiome: Relationships with disease and opportunities for therapy.Durack J. Journal of Experimental Medicine

Water Microbiome

Functional genera, potential pathogens and predicted antibiotic resistance genes in 16 full-scale wastewater treatment plants treating different types of wastewater.Fan XY. Bioresource Technology

Fine-scale spatial homogenization of microbial habitats: a multivariate index of headwater wetland complex condition.Moon JB. Ecological Applications

Functional and taxonomic classification of a greenhouse water drain metagenome.López-Leal G. Standards in Genomic Sciences

Plant and Soil Microbiome

Changes in the soil microbial communities of alpine steppe at Qinghai-Tibetan Plateau under different degradation levels.Zhou H. Science of the Total Environment

Long-term succession in a coal seam microbiome during in situ biostimulation of coalbed-methane generation.Beckmann S. ISME Journal

Advertisements

October 14, 2018

General microbiome

16S rRNA Gene Analysis with QIIME2 – Michael Hall, Microbiome Analysis

Predicting the Functional Potential of the Microbiome from Marker Genes Using PICRUSt – Gavin M. Douglas, Microbiome Analysis

Single-Cell Genomics of Microbial Dark Matter – Christian Rinke, Microbiome Analysis

An ecosystem framework for understanding and treating disease – Michael E. Hochberg, Foundation for Evolution, Medicine, and Public Health

Diet, Gut Microbes and Host Mate Choice – Philip T. Leftwich, BioEssays

Pregnancy and early life

Methods and Strategies to Examine the Human Breastmilk Microbiome – Lauren LeMay-Nedjelski, Microbiome Analysis

Multi-site human microbiome

Potential mechanisms linking gut microbiota and portal hypertension – Gyorgy Baffy, Liver International

Enlisting commensal microbes to resist antibiotic-resistant pathogens –  James W. Keith, Journal of Experimental Medicine

Human oral microbiome

Oral mucosa-on-a-chip to assess layer-specific responses to bacteria and dental materials – Christopher Rahimi, Biomicrofluidics

The effect of breastmilk and saliva combinations on the in vitro growth of oral pathogenic and commensal microorganisms – E. L. Sweeney, Scientific Reports

Human skin microbiome

A Natural History of Actinic Keratosis and Cutaneous Squamous Cell Carcinoma Microbiomes – David L. A. Wood, mBio

Human gut microbiome

The microbiome of Crohn’s disease aphthous ulcers – Claire L. O’Brien, Gut Pathogens

Gut microbiome can be restored without adverse events after Helicobacter pylori eradication therapy in teenagers – Takuji Gotoda, Helicobacter

Animal microbiome

Rethinking the Coral Microbiome: Simplicity Exists within a Diverse Microbial Biosphere – Alejandra Hernandez-Agreda, mBio

Host differentiation and compartmentalization of microbial communities in the azooxanthelate cupcorals Tubastrea coccinea and Rhizopsammia goesi in the Caribbean – Aschwin H. Engelen, Frontiers in Microbiology

Comparison of intestinal microbes in female and male Chinese concave‐eared frogs (Odorrana tormota) and effect of nematode infection on gut bacterial communities – Yilin Shu, Microbiology Open

Change in the intestinal bacterial community structure associated with environmental microorganisms during the growth of Eriocheir sinensis – Chenhe Wang, Microbiology Open

Protective role of the vulture facial skin and gut microbiomes aid adaptation to scavenging – Marie Lisandra Zepeda Mendoza, Acta Veterinaria Scandinavica

Animal experiments 

Fecal Microbiota Transplantation Beneficially Regulates Intestinal Mucosal Autophagy and Alleviates Gut Barrier Injury – Saisai Cheng, mSystems

Host genetics and the rumen microbiome jointly associate with methane emissions in dairy cows – Gareth Frank Difford, Plos Genetics

Inhibitory effects of dietary soy isoflavone and gut microbiota on contact hypersensitivity in mice – Takao Nagano, Food Chemistry

Lichen microbiome

Plasticity of a holobiont: desiccation induces fasting-like metabolism within the lichen microbiota – Tomislav Cernava, ISME

Plant, root, and soil microbiome

Short-term effect of Eucalyptusplantations on soil microbial communities and soil-atmosphere methane and nitrous oxide exchange – Caroline A. Cuer, Scientific Reports

Microbial community structure and functional potential of lava-formed Gotjawal soils in Jeju, Korea – Jong-Shik Kim, Plos One

Diversity of fungi and bacteria in species-rich grasslands increases with plant diversity in shoots but not in roots and soil – Diana Navrátilová, FEMS Microbiology Ecology

Variation in ectomycorrhizal fungal communities associated with Silver linden (Tilia tomentosa) within and across urban areas – Maarten Van Geel, FEMS Microbiology Ecology

Influence of triazole pesticides on tillage soil microbial populations and metabolic changes – Praveen Satapute, Science of The Total Environment

Soil Nutrient Status and Microbial Communities as Influenced by Bio-Fuel Trees Plantation – Agnes Imoya P. O., Environment and Ecology

Various Phyllosphere and Soil Bacterial Communities of Natural Grasses and the Impact Factors in a Copper Tailings Dam – Tong Jia, Current Microbiology

Effects of wine-cap Strophariacultivation on soil nutrients and bacterial communities in forestlands of northern China – Sai Gong, PeerJ

Effect of pH and temperature on microbial community structure and carboxylic acid yield during the acidogenic digestion of duckweed – Ozgul Calicioglu, Biotechnology for Biofuels

Trichoderma harzianum T-22 and BOL-12QD inhibit lateral root development of Chenopodium quinoa in axenic co-culture – Oscar M. Rollano-Peñaloza, Cogent Biology

Water, wastewater, and extremophile microbiome

Microbial communities in the nepheloid layers and hypoxic zones of the Canary Current upwelling system – Stefan Thiele, Microbiology Open

The effects of litter quality and living plants on the home-field advantage of aquatic macrophyte decomposition in a eutrophic urban lake, China – Van Biak Luai, Science of The Total Environment

The microbiome and antibiotic resistance in integrated fishfarm water: Implications of environmental public health – Gary Klase, Science of The Total Environment

Changes in the drinking water microbiome: effects of water treatments along the flow of two drinking water treatment plants in a urbanized area, Milan (Italy) – Antonia Bruno, Frontiers in Microbiology

Organic particles: heterogeneous hubs for microbial interactions in aquatic ecosystems – Mina Bizic-Ionescu, Frontiers in Microbiology

Importance of denitrification driven by the relative abundances of microbial communities in coastal wetlands – Yan Zhang, Environmental Pollution

A nearly uniform distributional pattern of heterotrophic bacteria in the Mariana Trench interior – Jiwei Tian, Deep Sea Research Part I: Oceanographic Research Papers

Patterns of permissiveness towards broad host range plasmids in microbial communities across the urban water cycle in Europe – Arnaud Dechesne, Abstract from 17th International Symposium on Microbial Ecology

Biodegradation of sulfamethoxazole by a bacterial consortium of Achromobacter denitrificans PR1 and Leucobacter sp. GP – Ana C. Reis, Applied Microbiology and Biotechnology

Molecular and microbiological insights on the enrichment procedures for the isolation of petroleum degrading bacteria and fungi – Giulia Spini, Frontiers in Microbiology

Microbial Ecology of South Florida Surface Waters: Examining the Potential for Anthropogenic Influences – Chase P. Donnelly, HCNSO Student Theses and Dissertations

Antarctic heterotrophic bacterium Hymenobacter nivis P3Tdisplays light‐enhanced growth and expresses putative photoactive proteins – Mia Terashima, Environmental Microbiology Reports

Microbial genomics

Comprehensive analysis of intra- and interpatient evolution of enterovirus D68 by whole-genome deep sequencing – Robert Dyrdak, bioRxiv

Leveraging single-cell genomics to expand the fungal tree of life – Steven R. Ahrendt, Nature Microbiology

Microbes in space

Transcriptomic responses of Serratia liquefaciens cells grown under simulated Martian conditions of low temperature, low pressure, and CO2-enriched anoxic atmosphere – Patricia Fajardo-Cavazos, Scientific Reports

Food microbiology

Metagenomic analysis and the functional profiles of traditional fermented pork fat ‘sa-um’ of Northeast India – Surajit De Mandal, AMB Express

Probiotics / prebiotics

Gut microbiome modulation during treatment of mucositis with the dairy bacterium Lactococcus lactis and recombinant strain secreting human antimicrobial PAP – Rodrigo Carvalho, Scientific Reports

In Vitro Fermentation of Selected Prebiotics and Their Effects on the Composition and Activity of the Adult Gut Microbiota – Sophie Fehlbaum, International Journal of Molecular Sciences

Techniques

Assessing the ratio of Bacillus spores and vegetative cells by shotgun proteomics – Charlotte Mappa, Environmental Science and Pollution Research

 

October 10, 2018

Microbiota conservation and diversity in butterfly species, air and waterborne microbiota of a pharmaceutical plant, the a study on the oral microbiota of rugby players.

General microbiome

Preserving microbial diversity – Maria G Dominguez Bello – Science

Pregnancy and early life

Evaluation of patient- versus provider-collected vaginal swabs for microbiome analysis during pregnancy – Kristine M Wylie – BMC Research Notes

Human skin microbiome

The microbiome of the “sterile” pustules in palmoplantar pustulosis – Kana Masuda-Kuroki – Experimental Dermatology

Human oral microbiome

Oral health and microbiota status in professional rugby players: A case-control study – Matthieu Minty – Journal of Dentistry

Oral Bacteriome Compositions Identified by 16S rRNA Metagenomics in a Randomly Selected “Healthy” Nigerian Male and Female Subjects – Kingsley C Anukam – International Journal of Research and Reports in Dentistry

Human gut microbiome

Review: The Gut-Brain Axis and the Microbiome: Mechanisms and Clinical Implications – Vadim Osadchiy – Clinical Gastroenterology and Hepatology

Animal experiments

Replication Study: Intestinal inflammation targets cancer-inducing activity of the microbiota – Kathryn Eaton – eLIFE

Animal microbiome

Pre-print: Conserved microbiota among young Heliconius butterfly species – Bas van Schooten – PeerJ

Gastrointestinal Microbial Flora in Wild and Captive Olive Baboons (Papio anubis) – Senelwa Davis Lugano – American Journal of Infectious Diseases and Microbiology

Plant, root, and soil microbiome

Rhizosphere microbiome structure alters to enable wilt resistance in tomato – Min-Jung Kwak – Nature Biotechnology

Apple rootstocks of different nitrogen tolerance affect the rhizosphere bacterial community composition – Xiaofen Chai – Journal of Applied Microbiology

Effects of consecutive monoculture of sweet potato on soil bacterial community as determined by pyrosequencing – Huan Li – Journal of Basic Microbiology

Ectomycorrhizal fungi may not act as a barrier inhibiting host plant absorption of heavy metals – Yangze Tang – Chemosphere

Pre-print: Co-occurrence patterns of litter decomposing communities in mangroves indicate a robust community resistant to disturbances – Rodrigo G Taketani – PeerJ

Water and extremophile microbiome

Structure of Microbial Mats in the Mramornaya Bay (Crimea) Coastal Areas – NV Pimenov – Microbiology

Pangenomic comparison of globally distributed Poribacteria associated with sponge hosts and marine particles – Sheila Powell – The ISME Journal

High diversity of thermophilic cyanobacteria in Rupite hot spring identified by microscopy, cultivation, single-cell PCR and amplicon sequencing – Otakar Strunecky – Extremophiles

Built environment

Air and waterborne microbiome of a pharmaceutical plant provide insights on spatiotemporal variations and community resilience after disturbance – Filippo Pacchioni – BMC Microbiology

Food microbiology

Review: The Effect of Gluten-Free Diet on Health and the Gut Microbiota Cannot Be Extrapolated from One Population to Others – Jose F Garcia-Marzcorro – Nutrients

Phages and viruses

Characterization of dog serum virome from Northeastern Brazil – MN Weber – Virology

Bioinformatics

‘NetShift’: a methodology for understanding ‘driver microbes’ from healthy and disease microbiome datasets – Bhusan K Kuntal – The ISME Journal

Techniques

A Simple In Vitro Gut Model for Studying the Interaction between Escherichia coli and the Intestinal Commensal Microbiota in Cecal Mucus – Matthew E Mokszycki – Applied and Environmental Microbiology

Science, career, and publishing

Inoculating science against potential pandemics and information hazards – Kevin M Esvelt – PLOS Pathogens

October 9, 2018

 

Pregnancy and early life

Gut Microbiota and Body Weight in School‐Aged Children: The KOALA Birth Cohort Study – Catherine A. Mbakwa – Obesity

Multi-site human microbiome

Grow With the Challenge – Microbial Effects on Epithelial Proliferation, Carcinogenesis, and Cancer Therapy – Jakob von Frieling – Frontiers in Microbiology

Human respiratory microbiome

Microbiome dataset from the upper respiratory tract of patients living with HIV, HIV/TB and TB from Myanmar – Kyaw SoeHtuna – Data in Brief

Human skin microbiome

The microbiome of the “sterile” pustules in palmoplantar pustulosis – Kana Masuda‐Kuroki – Experimental Dermatology

Human vaginal microbiome

Evaluation of patient- versus provider-collected vaginal swabs for microbiome analysis during pregnancy – Kristine M. Wylie – BMC Research Notes

*****************************

Animal experiments

Protective effects of a triple-fermented barley extract (FBe) against HCl/EtOH-induced gastric mucosa damage in mice – Jong‐Min Lim – Food Science & Nutrition

Guarana (Paullinia cupana Mart.) alters gut microbiota and modulates redox status, partially via caffeine in Wistar rats – Alexandre Kleber Silveira – Phytotherapy Research

Gut microbiota–dependent modulation of innate immunity and lymph node remodeling affects cardiac allograft outcomes – Jonathan S. Bromberg – JCI Insight

Prokaryotic communities of Indo-Pacific giant barrel sponges are more strongly influenced by geography than host phylogeny – T Swierts – FEMS Microbiology Ecology

In vitro experiments

A Simple In Vitro Gut Model for Studying the Interaction between Escherichia coli and the Intestinal Commensal Microbiota in Cecal Mucus – Matthew E Mokszycki – Applied and Environmental Microbiology

Animal microbiome

Tissue-specific immune responses to Vibrio sp. infection in mussels (Perna canaliculus): A metabolomics approach – Thao V. Nguyen – Aquaculture

Conserved microbiota among young Heliconius butterfly species – Bas van Schooten – Peer J

Microbial community composition of nest-carton and adjoining soil of the ant Lasius fuliginosus and the role of host secretions in structuring microbial communities – Pina Brinker – Fungal Ecology

Comparative metagenomics of the gut microbiota in wild greylag geese (Anser anser) and ruddy shelducks (Tadorna ferruginea) – Wen Wang – Microbiology Open

Microbiome and Blood Analyte Differences Point to Community and Metabolic Signatures in Lean and Obese Horses – Amy S. Biddle – Frontiers in Veterinary Science

Plant, root, and soil microbiome

Determinants of Deadwood-Inhabiting Fungal Communities in Temperate Forests: Molecular Evidence From a Large Scale Deadwood Decomposition Experiment – Witoon Purahong –

Induction of defense mechanisms involved in disease resistance of onion blight disease caused by Botrytis allii – Mohamed M A Hussein – Egyptian Journal of Biological Pest Control

Ectomycorrhizal fungi may not act as a barrier inhibiting host plant absorption of heavy metals – Yangze Tang – Chemosphere

The impacts of deglaciation and human activity on the taxonomic structure of prokaryotic communities in Antarctic soils on King George Island – E.V. Pershina – Antarctic Science

Fungal, Bacterial, and Archaeal Diversity in Soils Beneath Native and Introduced Plants in Fiji, South Pacific – Gian Maria Niccolò Benucci – Microbial Ecology

Mangrove Sediment Microbiome: Adaptive Microbial Assemblages and Their Routed Biogeochemical Processes in Yunxiao Mangrove National Nature Reserve, China – Xiaolan Lin – Microbial Ecology

Draft Genome Sequence of Burkholderia reimsis BE51, a Plant-Associated Bacterium Isolated from Agricultural Rhizosphere – Qassim Esmaeel – Microbiology Resource Announcements

Rhizosphere microbial response to multiple metal(loid)s in different contaminated arable soils indicates crop-specific metal-microbe interactions – Weimin Sun – Applied and Environmental Microbiology

Draft Genome Sequence of Burkholderia reimsis BE51, a Plant-Associated Bacterium Isolated from Agricultural Rhizosphere – Qassim Esmaeel – Microbiology Resource Announcements

Rhizosphere microbial response to multiple metal(loid)s in different contaminated arable soils indicates crop-specific metal-microbe interactions – Weimin Sun – Applied and Environmental Microbiology

Apple rootstocks of different nitrogen tolerance affect the rhizosphere bacterial community composition – Xiaofen Chai – Journal of Applied Microbiology

Draft Genome Sequence of Pseudomonas sp. Strain MWU13-2860, Isolated from a Wild Cranberry Bog in Truro, Massachusetts – Ghazal Ebadzadsahrai – Microbiology Resource Announcements

Biotechnological potential of plant growth-promoting bacteria from the roots and rhizospheres of endemic plants in ironstone vegetation in southeastern Brazil – Érica Barbosa Felestrino – World Journal of Microbiology and Biotechnology

Effects of consecutive monoculture of sweet potato on soil bacterial community as determined by pyrosequencing – Huan Li – Journal of Basic Microbiology

Air and waterborne microbiome of a pharmaceutical plant provide insights on spatiotemporal variations and community resilience after disturbance – Filippo Pacchioni – BMC Microbiology

Spatial variability of microbial communities in a fractured sedimentary rock matrix impacted by a mixed organics plume – Gláucia da P. Lima – Journal of Contaminant Hydrology

Modeling microbial communities from atrazine contaminated soils promotes the development of biostimulation solutions – Xihui Xu – The ISME Journal

Root growth, function and rhizosphere microbiome analyses show local rather than systemic effects in apple plant response to replant disease soil – Maik Lucas – PLOS One

Rhizosphere microbiome structure alters to enable wilt resistance in tomato – Min-Jung Kwak – Nature Biotechnology

Soil microbial community structure in the rhizosphere of Robinia pseudoacacia L. seedlings exposed to elevated air temperature and cadmium-contaminated soils for 4 years – X.Jia – Science of the Total Environment

Water and extremophile microbiome

Desiccation- and Saline-Tolerant Bacteria and Archaea in Kalahari Pan Sediments – Steffi Genderjahn – Frontiers in Microbiology

Air and waterborne microbiome of a pharmaceutical plant provide insights on spatiotemporal variations and community resilience after disturbance – Filippo Pacchioni – BMC Microbiology

High diversity of thermophilic cyanobacteria in Rupite hot spring identified by microscopy, cultivation, single-cell PCR and amplicon sequencing – Otakar Strunecký – Extremophiles

Structure of Microbial Mats in the Mramornaya Bay (Crimea) Coastal Areas – N. V. Pimenov – Microbiology

Characterization of a novel bacteriophage specific to Exiguobacterium indicum isolated from a plateau eutrophic lake – Shiying Zhang – Journal of Basic Biology

Pangenomic comparison of globally distributed Poribacteria associated with sponge hosts and marine particles – Sheila Podell – The ISME Journal

The impact of iron nanoparticles on technetium-contaminated groundwater and sediment microbial communities – Laura Newsome – Journal of Hazardous Materials

Microbial diversity and antibiotic resistance in a final effluent-receiving lake – Kinga Bondarczuk – Science of the Total Environment

Reduced chlorine in drinking water distribution systems impacts bacterial biodiversity in biofilms – Claire Bertelli – Frontiers in Microbiology

Microbial Ecology

A Microbial Saga: How to Study an Unexpected Hot Spot of Microbial Biodiversity from Scratch? – Valeria Souza – Cuatro Ciénegas Ecology, Natural History and Microbiology

How Divergent Is the Cuatro Ciénegas Oasis? Genomic Studies of Microbial Populations and Niche Differentiation – Zulema Gomez-Lunar – Cuatro Ciénegas Ecology, Natural History and Microbiology

Trace metals supplementation enhanced microbiota and biohythane production by two-stage thermophilic fermentation – Chonticha Mamimin – International Journal of Hydrogen Energy

Microcosms and Mesocosms: A Way to Test the Resilience of Microbial Communities in Cuatro Ciénegas – Nguyen E. López-Lozano – Cuatro Ciénegas Ecology, Natural History and Microbiology

Resistome

Candida albicans biofilm–induced vesicles confer drug resistance through matrix biogenesis – Robert Zarnowski – PLOS One

Microbes in space

Comparing Spore Resistance of Bacillus Strains Isolated from Hydrothermal Vents and Spacecraft Assembly Facilities to Environmental Stressors and Decontamination Treatments – Vincenzo Zammuto – Mary Ann Liebert Publishers

*****************************

Probiotics / prebiotics

Understanding mode of action can drive the translational pipeline towards more reliable health benefits for probiotics – Michiel Kleerebezem – Current Opinion in Biotechnology

Systematic review with meta‐analysis: the efficacy of prebiotics, probiotics, synbiotics and antibiotics in irritable bowel syndrome – Alexander C. Ford – Alimentary Pharmacology and Therapeutics

Phages and viruses

Characterization of dog serum virome from Northeastern Brazil – M.N.Weber – Virology

Hyperdiverse Viral Communities in an Oligotrophic Oasis (Cuatro Ciénegas): Marine Affinities and Microgeographic Differentiation – P. Isa – Cuatro Ciénegas Ecology, Natural History and Microbiology

Bioinformatics

IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes – I-Min A Chen – Nucleic Acids Research

Strain-GeMS: Optimized subspecies identification from microbiome data based on accurate variant modeling – Chongyang Tan – Bioinformatics

Strain-GeMS: Optimized subspecies identification from microbiome data based on accurate variant modeling – Chongyang Tan – Bioinformatics

 

 

October 02, 2018

Today’s digest features a study on altered gut microbial composition in persons with chronic schizophrenia, a review of different approaches for discovering radical-dependent enzymes in the human gut microbiota and Nature podcast with the latest science news. Happy reading/listening!

Gut microbiome

*Differences in gut microbiome composition between persons with chronic schizophrenia and healthy comparison subjects – Tanya T. Nguyen – Schizophrenia Research

*Review: Discovering radical-dependent enzymes in the human gut microbiota – Benjamin J Levin and Emily P Balskus – Current Opinion in Chemical Biology

Review: Air Pollution, Early Life Microbiome, and Development – Yvonne Vallès and M. Pilar Francino – Current Environmental Health Reports

Review: The implementation of omics technologies in cancer microbiome research – Benjamin H Mullish – Ecancermedicalscience

Skin microbiome

Skin microbiome modulation induced by probiotic solutions – Bernhard Paetzold – bioRxiv

Vaginal microbiome

Review: Alternative and complementary therapies for vulvovaginal candidiasis – Thais Chimati Felix – Folia Microbiologica

Animal microbiome

Review: Fish Gut Microbiome: Current Approaches and Future Perspectives – Chandni Talwar – Indian Journal of Microbiology

Review: The application of omics to rumen microbiota function – Stuart E Denman – Animal

Animal experiments

The circadian clock regulates the diurnal levels of microbial short‐chain fatty acids and their rhythmic effects on colon contractility in mice – Anneleen Segers – Acta Physiologie

Bioinformatics

Dynamic interaction network inference from longitudinal microbiome data – Jose Lugo-Martinez – bioRxiv

Microbes in the news

6 Artificial Sweeteners That Can Hurt Your Microbiome Revealed in New Study – By Emma Betuel – Inverse

Study: Measuring Artificial Sweeteners Toxicity Using a Bioluminescent Bacterial Panel – Dorin Harpaz – Molecules

Podcast

*A wearable biosensor and a metamaterial’s strange behaviour – Benjamin Thompson and Shamini Bundell – Nature Podcast

September 15, 2018

Have a nice weekend! Today, we have several papers, covering different aspects of the microbiome! Some highlights (in bold): the role of microbiota in cancer immunotherapy success; interesting study about the lung microbiota and smoking; changes in gut microbiota in asthma patients, microbiota changes in high-salt feces; an interesting article about the potential effect of dogs in veteran rehabilitation; a review about periodontitis and the microbiome; a ecophylogenetic study about mammalian microbiome, and more!

 

Human and General Microbiome

Metagenomic Approaches for Understanding New Concepts in Microbial Science – Luana de Fátima Alves – International Journal of Genomics

Review: Epigenetic Mechanisms Link Maternal Diets and Gut Microbiome to Obesity in the Offspring – Yuanyuan Li – Frontiers in Genetics

Review: NLRP3 inflammasome in colitis and colitis-associated colorectal cancer – Agampodi Promoda Perera – Mammalian Genome

Oral Microbiome Shifts From Caries-Free to Caries-Affected Status in 3-Year-Old Chinese Children: A Longitudinal Study – He Xu – Frontiers in Microbiology

Review: Roles of intestinal microbiota in response to cancer immunotherapy – Jing Cong – European Journal of Clinical Microbiology & Infectious Diseases

Intestinal dysbiosis and hormonal neuroendocrine secretion in the fibromyalgic patient: Relationship and correlations – Giovanni Tomasello – Biomedical Papers

Macroecology to Unite All Life, Large and Small – Ashley Shade – Trends in Ecology and Evolution

Dichotomous development of the gut microbiome in preterm infants – Thao T. B. Ho – Microbiome

Smoking is associated with quantifiable differences in the human lung DNA virome and metabolome – Ann C. Gregory – Respiratory Research

A metagenome-wide association study of gut microbiota in asthma in UK adults – Qi Wang – BMC Microbiology

The Cutaneous Microbiome and Wounds: New Molecular Targets to Promote Wound Healing – Taylor R. Johnson – International Journal of Molecular Sciences

Phthalate Exposure and Odds of Bacterial Vaginosis Among U.S. Reproductive-Aged Women, NHANES 2001-2004 – Ruth J.Geller – Reproductive Toxicology

Para-cresol production by Clostridium difficile affects microbial diversity and membrane integrity of Gram-negative bacteria – Ian J. Passmore – PLoS Pathogens

Salt in stools is associated with obesity, gut halophilic microbiota and Akkermansia muciniphila depletion in humans – E. H. Seck – International Journal of Obesity

The local microbiome after pediatric bladder augmentation: intestinal segments and the native urinary bladder host similar mucosal microbiota – Z.F. Kispal – Journal of Pediatric Urology

The Gut-Brain Axis in Alzheimer’s Disease and Omega-3. A Critical Overview of Clinical Trials – Francesca La Rosa – Nutrients

Associations between Flavonoid Intakes and Gut Microbiota in a Group of Adults with Cystic Fibrosis – Li Li – Nutrients

Review: Insights into the Human Virome Using CRISPR Spacers from Microbiomes – Claudio Hidalgo-Cantabrana – Viruses

Review: Probiotics in the Treatment of Colorectal Cancer –  Robert Hendler – Medicines

Airway Microbiota Dynamics Uncover a Critical Window for Interplay of Pathogenic Bacteria and Allergy in Childhood Respiratory Disease – Shu Mei Teo – Cell Host and Microbe

Human skin volatiles: Passive sampling and GC × GC-ToFMS analysis as a tool to investigate the skin microbiome and interactions with anthropophilic mosquito disease vectors – Alexis P. Roodt – Journal of Chromatography B

Commentary: Regulating stool for microbiota transplantation – Pilar N. Ossorio – Gut Microbes

Associations between the gut microbiota and host responses to high altitude – J. Philip Karl – Gastrointestinal and Liver Physiology

Exploring service dogs for rehabilitation of veterans with PTSD: A microbiome perspective – Andrew J.,Billera Hoisington – Rehabilitation Psychology

Mucosal associated invariant T cells from human breast ducts mediate a Th17-skewed response to bacterially exposed breast carcinoma cells – Nicholas A. Zumwalde – Breast Cancer Research

Periodontitis and the microbiome: a systematic review and meta-analysis – Fabrizio Guerra – Minerva Stomatologica

Formal Comment: The microbiome and the human: A reply to Parke and colleagues – Tobias Rees – PLoS Biology

Microbiota-gut-brain research: a critical analysis – Katarzyna B. Hooks – Behavioral and Brain Sciences

 

Animal Microbiome

Ecophylogenetics Clarifies the Evolutionary Association between Mammals and Their Gut Microbiota – Christopher A. Gaulke – mBio

The Inhibitory Innate Immune Sensor NLRP12 Maintains a Threshold against Obesity by Regulating Gut Microbiota Homeostasis – Agnieszka D. Truax – Cell Host and Microbe

American ginseng microbial metabolites attenuate DSS-induced colitis and abdominal pain – Chong-Zhi Wang – International Immunopharmacology

Impact of violacein from Chromobacterium violaceum on the mammalian gut microbiome – Heidi Pauer – PLoS ONE

Bacterial community composition in the salivary glands of triatomines (Hemiptera: Reduviidae) – Michele Souza Lima – PLoS Neglected Tropical Diseases

Postnatal Administration of Lactobacillus rhamnosus HN001 Ameliorates Perinatal Broad-Spectrum Antibiotic-Induced Reduction in Myelopoiesis and T cell Activation in Mouse Pups – Eva Fuglsang – Molecular Nutrition and Food Research

Absorption of Codonopsis pilosula Saponins by Coexisting Polysaccharides Alleviates Gut Microbial Dysbiosis with Dextran Sulfate Sodium-Induced Colitis in Model Mice – Yaping Jing – BioMed Research International

Tributyrin Supplementation Protects Immune Responses and Vasculature and Reduces Oxidative Stress in the Proximal Colon of Mice Exposed to Chronic-Binge Ethanol Feeding – B. Glueck – Journal of Immunology Research

Fecal Hyodeoxycholic Acid Is Correlated With Tylosin-Induced Microbiome Changes in Growing Pigs – Michaela P. Trudeau – Frontiers in Veterinary Science

Yeast Probiotics Shape the Gut Microbiome and Improve the Health of Early-Weaned Piglets – Jinqiang Xu – Frontiers in Microbiology

Probiotic Bacillus amyloliquefaciens C-1 Improves Growth Performance, Stimulates GH/IGF-1, and Regulates the Gut Microbiota of Growth-Retarded Beef Calves – Renjia Du – Frontiers in Microbiology

The Microbiome of the Gastrointestinal Tract of a Range-Shifting Marine Herbivorous Fish – Jacquelyn Jones – Frontiers in Microbiology

Intestinal Microbiome-Metabolome Responses to Essential Oils in Piglets – Yuan Li – Frontiers in Microbiology

Review: Managing the Microbial Community of Marine Fish Larvae: A Holistic Perspective for Larviculture – Olav Vadstein – Frontiers in Microbiology

Functional modulation of caecal fermentation and microbiota in rat by feeding bean husk as a dietary fibre supplement – H. Myint – Beneficial Microbes

Effects of short-term fasting on in vivo rumen microbiota and in vitro rumen fermentation characteristics – Jong Nam Kim – Asian-Australian Journal of Animal Sciences

The effect of exposure to high altitude and low oxygen on intestinal microbial communities in mice – Wei Zhang – PLoS ONE

 

Food Microbiome

Lactic Acid Bacterium Population Dynamics in Artisan Sourdoughs Over One Year of Daily Propagations Is Mainly Driven by Flour Microbiota and Nutrients – Fabio Minervini – Frontiers in Microbiology

Effect of Pressure, Reconstituted RTE Meat Microbiota, and Antimicrobials on Survival and Post-pressure Growth of Listeria monocytogenes on Ham – Januana S. Teixeira – Frontiers in Microbiology

 

Plant Microbiome

G3 PhyloChip Analysis Confirms the Promise of Plant-Based Culture Media for Unlocking the Composition and Diversity of the Maize Root Microbiome and for Recovering Unculturable Candidate Divisions/Phyla – Mohamed S. Sarhan – Microbes and Environments

Root exudates drive the soil-borne legacy of aboveground pathogen infection – Jun Yuan – Microbiome

Review: Mycorrhizal microbiomes – Mika T. Tarkka – Mycorrhiza

 

Bioinformatics

GePMI: A statistical model for personal intestinal microbiome identification – Zicheng Wang – npj Biofilms and Microbiomes

Web of microbes (WoM): a curated microbial exometabolomics database for linking chemistry and microbes – Suzanne M. Kosina – BMC Microbiology

 

Other

Temporal variability and stability of the fecal microbiome: the Multiethnic Cohort Study – Benjamin C Fu – Cancer Epidemiology, Biomarkers & Prevention

A flavin-based extracellular electron transfer mechanism in diverse Gram-positive bacteria – Samuel H. Light – Nature

 

September 8, 2018

Have a nice weekend! Today, in Microbiome Digest: an interesting study remarking the importance of personalization in the efficient use of probiotics, given their individualized impact in gut microbiota (Zmora et al., Cell); another interesting paper about the application of autologous FMT in patients in Post-Antibiotic use and a worsening effect of Probiotics (Suez et al., Cell). Today, we have also papers about the dysbiosis in coronary artery disease, a metagenome of the female reproductive tract, a trial about the role of antibiotics in IBS risk and more!

Human and General Microbiome

Post-Antibiotic Gut Mucosal Microbiome Reconstitution Is Impaired by Probiotics and Improved by Autologous FMT – Jotham Suez – Cell

Personalized Gut Mucosal Colonization Resistance to Empiric Probiotics Is Associated with Unique Host and Microbiome Features – Niv Zmora – Cell

The metagenome of the female upper reproductive tract – Chen Chen – GigaScience

Dysbiosis signatures of gut microbiota in coronary artery disease – Qi Zhu – Physiological Genomics

Review: The immunomodulatory role of probiotics in allergy therapy – Jafar Hajavi – Journal of Cellular Physiology

Efficient isolation and observation of the most complex human commensal, Demodex spp. – B. M. Clanner-Engelshofen – Experimental and Applied Acarology

Research Highlight: Boost microbiota studies – Wenjie Sun – Nature Nanotechnology

Reliability of a participant-friendly fecal collection method for microbiome analyses: a step towards large sample size investigation – Joanna W. Szopinska – BMC Microbiology

Alterations and structural resilience of the gut microbiota under dietary fat perturbations – Cong Liu – The Journal of Nutritional Biochemistry

Antibiotics: a risk factor for irritable bowel syndrome in a population-based cohort – Laura Rindom Krogsgaard – Scandinavian Journal of Gastroenterology

Inter-relationship between diet, lifestyle habits, gut microflora, and the equol-producer phenotype: baseline findings from a placebo-controlled intervention trial – Remi Yoshikata – Menopause

Review: Effects of Sourdough on FODMAPs in Bread and Potential Outcomes on Irritable Bowel Syndrome Patients and Healthy Subjects – Leidiane A. A. Menezes – Frontiers in Microbiology

Alteration of the cutaneous microbiome in psoriasis and potential role in Th17 polarization – Hsin-Wen Chang – Microbiome

 

Animal Microbiome / Animal Experiments

Early-life exposure to gut microbiota from disease protected mice does not impact disease outcome in type 1 diabetes susceptible NOD mice – Jane A. Mullaney – Immunology and Cell Biology

Shifts in the Skin-Associated Microbiota of Hatchery-Reared Common Snook Centropomus undecimalis During Acclimation to the Wild – Andrea M. Tarnecki – Microbial Ecology

Habitat environments impacted the gut microbiome of long-distance migratory swan geese but central species conserved – Yueni Wu – Scientific Reports

Effects of mixed lactic acid bacteria on intestinal microbiota of mice infected with Staphylococcus aureus – Dayong Ren – BMC Microbiology

Green tea polyphenols modify gut-microbiota dependent metabolisms of energy, bile constituents and micronutrients in female Sprague-Dawley rats – Jun Zhou – The Journal of Nutritional Biochemistry

Time-restricted feeding causes irreversible metabolic disorders and gut microbiota shift in pediatric mice – Dandan Hu – Pediatric Research

Compositional and predicted functional analysis of the gut microbiota of Radix auricularia (Linnaeus) via high-throughput Illumina sequencing – Zongfu Hu – PeerJ

The Effect of Co-infection of Food-Borne Pathogenic Bacteria on the Progression of Campylobacter jejuni Infection in Mice – Gang Wang – Frontiers in Microbiology

Structural and Functional Alterations in the Microbial Community and Immunological Consequences in a Mouse Model of Antibiotic-Induced Dysbiosis – Ying Shi – Frontiers in Microbiology

 

Plant Microbiome

Endophytic Bacterial Community Structure and Function of Herbaceous Plants From Petroleum Hydrocarbon Contaminated and Non-contaminated Sites – Rhea Lumactud – Frontiers in Microbiology

 

Environmental Microbiome

The effects of emerging environmental contaminants on Stenotrophomonas maltophilia isolated from drinking water in planktonic and sessile states – Inês B.Gomes – Science of The Total Environment

Genetic and Functional Diversity of Bacterial Microbiome in Soils With Long Term Impacts of Petroleum Hydrocarbons – Anna Gałązka – Frontiers in Microbiology