October 22, 2018

Today’s digest features a novel fecal species [Prevotella rara sp. nov.], the virome in feces from healthy children from three Amerindian villages with minimal outside contact, a review of statistical challenges in the design and analysis of longitudinal microbiome studies, and more. Happy reading!

Gut microbiome

*Prevotella rara sp. nov., isolated from human faeces – Boris A. Efimov – International Journal of Systematic and Evolutionary Microbiology

Six-Week Endurance Exercise Alters Gut Metagenome That Is not Reflected in Systemic Metabolism in Over-weight Women – Eveliina Munukka – Frontiers in Microbiology

Association of serum bilirubin in newborns affected by jaundice with gut microbiota dysbiosis – Shaoming Zhou – The Journal of Nutritional Biochemistry

Review: Gut-microbiota-on-a-chip: an enabling field for physiological research – Grissel Trujillo-de Santiago – MicroPhysiological Systems

Review: Microbiome and diabetes: Where are we now? – Natalia G. Vallianou – Diabetes Research and Clinical Practice

Oral microbiome

Review: Biology of Oral Streptococci – Jacqueline Abranches – Microbiology Spectrum

Animal and plant microbiome

Review: How Can We Define “Optimal Microbiota?”: A Comparative Review of Structure and Functions of Microbiota of Animals, Fish, and Plants in Agriculture – Wakako Ikeda-Ohtsubo – Frontiers in Nutrition

Water microbiome

Temperature-controlled thermophilic bacterial communities in hot springs of western Sichuan, China – Jie Tang – BMC Microbiology

In situ production of core and intact bacterial and archaeal tetraether lipids in groundwater – Su Ding – Organic Geochemistry

Phages and viruses

*Complex virome in feces from Amerindian children in isolated Amazonian villages – Juliana D. Siqueira – Nature Communications

Bioinformatics

*Preprint Review: Statistical Considerations in the Design and Analysis of Longitudinal Microbiome Studies – Justin D Silverman – bioRxiv

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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 3, 2018

Enjoy Reading today’s Microbiome Digest blog focusing on the research articles covering the techniques, what and how treatments alter the microbiome, potential of mycobiome to produce fuels and chemicals, pathogenic functions, gut microbiome, animal microbiome, soil microbiome, Maternal Immune Activation(MIA) and its effect and probiotics from vaginal microbiome. 

TECHNIQUES:

Sequential Isolation of DNA, RNA, Protein, and Metabolite Fractions from Murine Organs and Intestinal Contents for Integrated Omics of Host–Microbiota Interactions – Pranjul Shah – Microbial Proteomics

A primer on investigating the role of the microbiome in brain and cognitive development – Caroline Kelsey – Developmental Psychobiology

TREATMENTS:

Roux-Y Gastric Bypass and Sleeve Gastrectomy directly change gut microbiota composition independent of operation type – Fernanda L. Paganelli – bioRxiv

Review – Systematic review on the first line treatment of amphotericin B in critically ill adults with candidemia or invasive candidiasis – Sean Keane – Expert Review of Anti-infective Therapy

Reconstitution of the gut microbiota of antibiotic-treated patients by autologous fecal microbiota transplant – Ying Taur – Gut Microbiota

Review – Reciprocal interactions between resveratrol and gut microbiota deepen our understanding of molecular mechanisms underlying its health benefits – LiangShen – Trends in Food Science & Technology

Synbiotics modulate gut microbiota and reduce enteritis and ventilator-associated pneumonia in patients with sepsis: a randomized controlled trial – Kentaro Shimizu – Critical Care

MICROBIAL ACTIVITY:

Relief from nitrogen starvation entails quick unexpected down-regulation of glycolytic/lipid metabolism genes in enological Saccharomyces cerevisiae– Catherine Tesnière – bioRxiv

ANTIMICROBIAL RESISTANCE:

Widespread Antibiotic, Biocide, and Metal Resistance in Microbial Communities Inhabiting a Municipal Waste Environment and Anthropogenically Impacted River – Aneisha M. Collins – Applied and Environmental Science

SOIL MICROBIOME:

Book Chapter – Paddy Soil Microbial Diversity and Enzymatic Activity in Relation to Pollution – Muhammad Afzaal – Environmental Pollution of Paddy Soils

Effect of Different Soil Phosphate Sources on the Active Bacterial Microbiota Is Greater in the Rhizosphere than in the Endorhiza of Barley (Hordeum vulgare L.) – Massimiliano Cardinale – Microbial Ecology

URINARY MICROBIOME:

Review – The Role of Urinary Microbiota in Lower Urinary Tract Dysfunction: A Systematic Review – TiagoAntunes-Lopes – European Urology Focus

ANIMAL MICROBIOME:

Ecological patterns in the skin microbiota of frogs from tropical Australia – Keith Christian – Ecology and Evolution

Oral Microbiota of the Snake Bothrops lanceolatus in Martinique – Dabor Résière – Int J Environ Res Public Health

MYCOBIOME:

Draft Genome Assemblies of Five Robust Yarrowia lipolytica Strains Exhibiting High Lipid Production, Pentose Sugar Utilization, and Sugar Alcohol Secretion from Undetoxified Lignocellulosic Biomass Hydrolysates – Caleb Walker – Genome Sequences

GENERAL MICROBIOME:

Book Chapter – The Role and Future Possibilities of Next-Generation Sequencing in Studying Microbial Diversity – VijayNema – Microbial Diversity in the Genomic Era

GUT MICROBIOME:

Review – Association of obesity, diabetes and linked complications with gut microbiota – Amina Arif – Pure and Applied Biology

Bifidobacterial Dominance of the Gut in Early Life and Acquisition of Antimicrobial Resistance – Diana H. Taft – Clinical Science and Epidemiology

The Gut Microbiota in the Pathogenesis and Therapeutics of Inflammatory Bowel Disease – Tao Zuo – Frontiers in Microbiology

Influence of maternal factors on the rumen microbiome and subsequent host performance – Hannah C. Cunningham – Translational Animal Science

Colorectal carcinogenesis: an archetype of gut microbiota–host interaction – James L Alexander – Ecancermedicalscience

ANIMAL MODELS MICROBIOME:

Maternal Immune Activation Alters Adult Behavior, Gut Microbiome and Juvenile Brain Oscillations in Ferrets – Yuhui Li – eNeuro

PROBIOTICS:
Bacteriocin production of the probiotic Lactobacillus acidophilus KS400 – C. Gaspar – AMB Express

September 18, 2018

Quite a few articles of interest today:

  1. Foods that are protective of the gut microbiome: Specific oligosaccharides in breast milk can compensate for the effects of C-section births, and cranberries can compensate for the effects of dietary changes in mice.
  2. A possible bi-directional relationship between the gut microbiome and high altitudes: Specific differences in the gut microbiome are associated with differences in tolerance to high altitudes in males, and exposure to high altitudes can alter the gut microbiome in mice.
  3. Microbes in Space: Nitrogen cycle nicroorganisms that may be able to produce food, water and O2 in space, and exposing desert extremophiles to Martian conditions to learn about the kinds of bacteria on other planets

Also: How smoking impacts the lung virome, the association between fecal microbiome profile and phylogeny in deer genera, and the development of the dust microbiome over time in a classroom

Pregnancy and early life

*Fucosylated oligosaccharides in mother’s milk alleviate the effects of caesarean birth on infant gut microbiota – Katri Korpela – Scientific Reports

The influence of maternal vaginal flora on the intestinal colonization in newborns and 3-month-old infants – Iwona Gabriel – The Journal of Maternal-Fetal & Neonatal Medicine

Fecal Volatile Organic Compounds in Preterm Infants Are Influenced by Enteral Feeding Composition – Sofia el Manouni el Hassani – Sensors

Multi-site human microbiome

Review: Talk to your gut: the oral-gut microbiome axis and its immunomodulatory role in the etiology of rheumatoid arthritis – Marines du Teil Espina – FEMS Microbiology Reviews

Human respiratory microbiome

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

Human anal microbiome

Anal microbial patterns and oncogenic HPV in a pilot study of Nigerian men who have sex with men at risk for or living with HIV – Rebecca G Nowak – AIDS Research and Human Retroviruses

Human gut microbiome

*Associations between the gut microbiota and host responses to high altitude – J. Philip Karl – American Journal of Physiology

Intestinal barrier integrity in patients with plaque psoriasis – Mariusz Sikora – The Journal of Dermatology

Review: Mechanisms by which gut microorganisms influence food sensitivities
– Alberto Caminero – Nature Reviews Gastroenterology & Hepatology

Review: Selective sensitivity of the gut microbiome to iron chelators in polybacterial abdominal sepsis – Kayle Dickson – Medical Hypotheses

Review: ADHD-originating in the gut? The emergence of a new explanatory model – Anna M. Sandgren – Medical Hypotheses

Review: Guideline for the Management of Clostridium Difficile Infection in Children and Adolescents With Cancer and Pediatric Hematopoietic Stem-Cell Transplantation Recipients – Caroline Diorio – Journal of Clinical Oncology

Review: Altered Gut Microbiota in Type 2 Diabetes: Just a Coincidence? – Antonio Sircana – Current Diabetes Reports

Review: Bowel Biofilms: Tipping Points between a Healthy and Compromised Gut? – Hanne L.P. Tytgat – Trends in Microbiology

Review: Fecal microbiota transplant – a new frontier in inflammatory bowel disease – Sunkara T – Dove Press

Review: Gut microbiota, cognitive frailty and dementia in older individuals: a systematic review –  Ticinesi A – Dove Press

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Animal experiments

Deletion of poly(ADP‑ribose) polymerase-1 changes the composition of the microbiome in the gut – András Vida – Molecular Medicine Reports

Lactobacillus reuteri F‐9‐35 Prevents DSS‐Induced Colitis by Inhibiting Proinflammatory Gene Expression and Restoring the Gut Microbiota in Mice – Mao‐cheng Sun – Journal of Food Science

*Cranberries attenuate animal-based diet-induced changes in microbiota composition and functionality: A randomized crossover controlled feeding trial – Jose Rodríguez-Morató – The Journal of Nutritional Biochemistry

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

The Effects of Berberine on the Gut Microbiota in Apc min/+ Mice Fed with a High Fat Diet – Huan Wang – Molecules

The influence of gut microbiota dysbiosis to the efficacy of 5-Fluorouracil treatment on colorectal cancer – Lu Yuan – Biomedicine & Pharmacotherapy

Protein deficiency reduces efficacy of oral attenuated human rotavirus vaccine in a human infant fecal microbiota transplanted gnotobiotic pig model – Ayako Miyazaki – Vaccine

In vitro experiments

Butyrate upregulates the TLR4 expression and the phosphorylation of MAPKs and NK‑κB in colon cancer cell in vitro – Tengfei Xiao – Oncology Letters

Animal microbiome

Comparison of the gut microbiota of captive common bottlenose dolphins, Tursiops truncatus in three aquaria – Akihiko Suzuki – Journal of Applied Microbiology

Bacteria richness and antibiotic-resistance in bats from a protected area in the Atlantic Forest of Southeastern Brazil – Vinícius C. Cláudio – PLOS ONE

*Divergence of Fecal Microbiota and Their Associations With Host Phylogeny in Cervinae – Jiaying Li – Frontiers in Microbiology

Probiotics modify body weight together with anxiety states via pro-inflammatory factors in HFD-treated Syrian golden hamster – Ennio Avolio – Behavioural Brain Research

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

The rumen microbiome: a crucial consideration when optimising milk and meat production and nitrogen utilisation efficiency – Chloe Matthews – Gut

MicrobesEvaluation of conjunctival microbiota in clinically normal persian squirrels (Sciurus Anomalus) – Houman Faghihi – Journal of Zoo and Wildlife Medicine

Plant, root, and soil microbiome

Trichoderma gamsii affected herbivore feeding behaviour on Arabidopsis thaliana by modifying the leaf metabolome and phytohormones – Dongmei Zhou – Microbial Biotechnology

Responses of soil biological traits and bacterial communities to nitrogen fertilization mediate maize yields across three soil types – Hailing Yu – Soil and Tillage Research

Soil microbial response to Rhododendron understory removal in southern Appalachian forests: Effects on extracellular enzymes – Ernest D. Osburn – Soil Biology and Biochemistry

Insight into Bacterial Community Diversity and Monthly Fluctuations of Medicago sativa Rhizosphere Soil in Response to Hydrogen Gas Using Illumina High-Throughput Sequencing – Zhiying Li – Current Microbiology

Bacterial diversity in rhizosphere of Paspalum scrobiculatum L. (kodo millet) is revealed with shotgun metagenome sequencing and data analysis – Ratna Prabha – Data in Brief

Responses of soil biological traits and bacterial communities to nitrogen fertilization mediate maize yields across three soil types – Hailing Yu – Soil and Tillage Research

Microbial Ecology

Effects of Cd, Cu, Zn and their combined action on microbial biomass and bacterial community structure – Jiuwei Song – Environmental Pollution

Effects of graphene oxides and silver-graphene oxides on aquatic microbial activity – Kwanyoung Ko – Science of The Total Environment

Built environment

*Longitudinal development of the dust microbiome in a newly opened Norwegian kindergarten – Anders B. Nygaard – Microbiome

Microbiological analysis of contact lens cases: impact of the hospital environment – Vinicius Targa Villas Bôas – Arquivos Brasileiros de Oftalmologia

Microbes in space

*Nitrogen cycle microorganisms can be reactivated after Space exposure – Ralph E. F. Lindeboom – Scientific Reports

*Desert cyanobacteria under space and planetary simulations: a tool for searching for life beyond Earth and supporting human space exploration – Daniela Billi – International Journal of Astrobiology

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Bioinformatics

MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis – Gherman V. Uritskiy – Microbiome

Approximate, simultaneous comparison of microbial genome architectures via syntenic anchoring of quiver representations  – Alex N Salazar – Bioinformatics

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Microbes in the news

The electrifying energy of gut microbes – Laty A. Cahoon – Nature News and Views

Bacteria and Art

How Anicka Yi’s Science Experiments Are Expanding the Boundaries of Art – Andrew Russeth – W

 

 

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

 

August 27, 2018

Highlights: how microbes influence the system they inhabit, maternal microbial metabolism, gut microbiota in pancreatic disease and other metabolic disorders, core and staphylococcal microbiota in skin & nose of pigs, wheat head microbiome bacteria,  abundant & rare biospheres of hot springs, antibiotic degradation by microbes, virome.

General microbiome

Review: Understanding how microbiomes influence the systems they inhabit – Ed K. Hall – Nature Microbiology

Male Bladder Microbiome Relates to Lower Urinary Tract Symptoms – Petar Bajic – European Urology Focus

Pregnancy and early life

Is maternal microbial metabolism an early-life determinant of health? – Kymberleigh A. Romano – LabAnimal

Human oral microbiome

The oral microbiome in oral lichen planus during a one‐year randomized clinical trial – Camilla Kragelund – Oral Diseases

Human respiratory microbiome

Interaction between the microbiome and TP53 in human lung cancer – K. Leigh Greathouse – Genome Biology

Human gut microbiome

The Gut Microbiome in Pancreatic Disease – Venkata S. Akshintala – Clinical Gastroenterology and Hepatology

FXR-Dependent Modulation of the Human Small Intestinal Microbiome by the Bile Acid Derivative Obeticholic Acid – Elliot S. Friedman – Gastroenterology

Review: Role of gut microbiota in chronic low‐grade inflammation as potential driver for atherosclerotic cardiovascular disease: a systematic review of human studies – I. C. L. van den Munckhof – Obesity Reviews

Bile acid homeostasis and intestinal dysbiosis in alcoholic hepatitis – Dragos Ciocan – Alimentary Pharmacology & Therapeutics

Characterization and induction of prophages in human gut-associated Bifidobacterium hosts – Travis N. Mavrich – Scientific Reports

In Vitro Ecological Response of the Human Gut Microbiome to Bioactive Extracts from Edible Wild Mushrooms – Emanuel Vamanu – Molecules

Review: The journey of gut microbiome – An introduction and its influence on metabolic disorders – Ankita Chattopadhyay -Frontiers in Biology

Animal experiments 

Sulfated polysaccharide from sea cucumber modulates the gut microbiota and its metabolites in normal mice – Zhenjun Zhu – International Journal of Biological Macromolecules

Chitin-based barrier immunity and its loss predated mucus-colonization by indigenous gut microbiota – Keisuke Nakashima – Nature Communications

Reduced particle size wheat bran is efficiently colonized by lactic acid producing community and reduces Enterobacteriaceae levels in the cecal microbiota of broilers – Karen Vermeulen – Applied and Environmental Microbiology

A High Salt Diet Modulates the Gut Microbiota and Short Chain Fatty Acids Production in a Salt-Sensitive Hypertension Rat Model – Ariel Bier – Nutrients

Animal microbiome 

A detailed investigation of the porcine skin and nose microbiome using universal and Staphylococcus specific primers – Mikael Lenz Strube – Scientific Reports

Characterization of bacterial microbiota compositions along the intestinal tract in pigs and their interactions and functions – Daniel Crespo-Piazuelo – Scientific Reports

Cnidarian Interaction with Microbial Communities: From Aid to Animal’s Health to Rejection Responses – Loredana Stabili – Marine Drugs

Plant, root, and soil microbiome

Wheat microbiome bacteria can reduce virulence of a plant pathogenic fungus by altering histone acetylation – Yun Chen – Nature Communications

Biodegradation of oxytetracycline and enrofloxacin by autochthonous microbial communities from estuarine sediments – Malek Harrabi – Science of The Total Environment

Soil micro-food web interactions and rhizosphere priming effectSoil micro-food web interactions and rhizosphere priming effect – Xinchang Kou – Plant and Soil

Burkholderia pseudomallei-absent soil bacterial community results in secondary metabolites that kill this pathogen – Chotima Potisap – AMB Express

Variation in the leaf and root microbiome of sugar maple (Acer saccharum) at an elevational range limit – Jessica Wallace – PeerJ

Contrasting responses of the bacterial communities in ectomycorrhizal roots and rhizosphere soils to defoliation or winter hardening – Hironari Izumi – Rhizosphere

Water and extremophile microbiome 

Abundant and rare microbial biospheres respond differently to environmental and spatial factors in Tibetan hot springs – Yanmin Zhang – Frontiers in Microbiology

Built environment 

Review: Microbiology of the built environment – Jack A Gilbert – Nature Reviews

Application of hybrid anaerobic reactor: Treatment of increasing cyanide containing effluents and microbial composition identification – Pragya Gupta – Journal of Environmental Management

A little breath of fresh air into an anaerobic system: How microaeration facilitates anaerobic digestion process – Duc Nguyen – Biotechnology Advances

Managing microbial communities in membrane biofilm reactors – A. Ontiveros-Valencia – Applied Microbiology and Biotechnology

Phages and viruses

Preprint: May the phage be with you? Prophage-like elements in the genomes of Soft Rot Pectobacteriaceae (Pectobacterium spp. and Dickeya spp.) – Robert Czajkowski – bioRxiv

Occurrence, integrity and functionality of AcaML1–like viruses infecting extreme acidophiles of the Acidithiobacillus species complex – Paulo C. Covarrubias – Research in Microbiology

Chapter: Robust Analysis of Time Series in Virome Metagenomics – Jose Manuel Martí – The Human Virome

Chapter: A Method for Isolation of the Virome from Plasma Samples – Pilar Domingo-Calap – The Human Virome

Chapter: Virome Sequencing of Stool Samples – Lenka Kramná – The Human Virome

Chapter: Protocol for Generating Infectious RNA Viromes from Complex Biological Samples – Sonia Monteil-Bouchard – The Human Virome

Techniques

Review: Transcriptome Sequencing Approaches to Elucidate Host–Microbe Interactions in Opportunistic Human Fungal Pathogens – Hrant Hovhannisyan – Current Topics in Microbiology and Immunology 

Chapter: Flow Cytometry and Direct Sequencing of Viruses – Mária Džunková – The Human Virome