June 13, 2018

Events and jobs

Computational scientists (from post-master to postdoc fellowships) in metagenomics and microbial genomics : Trento, Italy – The Laboratory of Computational Metagenomics

General microbiome

Meta-analysis of human genome-microbiome association studies: the MiBioGen consortium initiative – Jun Wang, Microbiome Announcement

Microbial ecology

Everything is not everywhere: a tale on the biogeography of cyanobacteria – Karine Felix Ribeiro, Hydrobiologia

A Meta‐Analysis of Temperature Sensitivity as a Microbial Trait – Charlotte J. Alster, Global Change Biology

Microbial island biogeography: isolation shapes the life history characteristics but not diversity of root-symbiotic fungal communities – John Davison, ISME

Bacillus thuringiensis produces the lipopeptide thumolycin to antagonize microbes and nematodes – Dehong Zheng, Microbiological Research

Qualitative analysis of biosurfactants from Bacillus species exhibiting antifungal activity – Ambrin Sarwar, Plos One

Antarctic cryptoendolithic fungal communities are highly adapted and dominated by Lecanoromycetes and Dothideomycetes – Claudia Coleine, Frontiers in Microbiology

Pregnancy and early life

The Microbiome and Metabolome of Preterm Infant Stool Are Personalized and Not Driven by Health Outcomes, Including Necrotizing Enterocolitis and Late-Onset Sepsis – Stephen Wandro, mSphere

The role of breast milk in the colonization of neonatal gut and skin with coagulase-negative staphylococci – Hiie Soeorg, Pediatric Research

Multisite human microbiome

Prion-like Propagation of α-synuclein in the gut-brain axis – Ying Chen, Brain Research Bulletin

Microbiome-Gut-Brain Axis and Toll-Like Receptors in Parkinson’s Disease – Valentina Caputi, International Journal of Molecular Sciences

Current Insights in Microbiome Shifts in Sjogren’s Syndrome and Possible Therapeutic Interventions – Christina Tsigalou, Frontiers in Immunology

Comparison of Infant Gut and Skin Microbiota, Resistome and Virulome between Neonatal Intensive Care Unit (NICU) Environments – Suchitra K. Hourigan, Frontiers in Microbiology

Human skin microbiome

Skin Microbiota in Obese Women at Risk for Surgical Site Infection After Cesarean Delivery – Kara M. Rood, Scientific Reports

Cutibacterium acnes (Propionibacterium acnes) and acne vulgaris: a brief look at the latest updates – B. Dréno, Journal of the European Academy of Dermatology and Venereology

Characterisation of Cutibacterium acnes phylotypes in acne and in vivo exploratory evaluation of Myrtacine® – S. Pécastaings, Journal of the European Academy of Dermatology and Venereology

Human oral microbiome

Analysis of the oral microbiome on the surface of modified dental polymers – Denise  Tornavoi de Castro, Archives of Oral Biology

Genetic Association with Subgingival Bacterial Colonization in Chronic Periodontitis – Franco Cavalla, Genes

Biological and cultural drivers of oral microbiota in Medieval and Post-Medieval London, UK – Andrew G Farrer, bioRxiv

Human gut microbiome

Breath methane concentrations and markers of obesity in patients with functional gastrointestinal disorders – Clive H. Wilder-Smith, United European Gastroenterology Journal

The Intersection Between Colonization Resistance, Antimicrobial Stewardship, and Clostridium difficile – Rossana Rosa, Current Infectious Disease Reports

Celiac Disease and Fecal Microbiota Transplantation: A New Beginning? – Shmuel Golfeyz MD, Correspondence

Gut microbiota metabolites, amino acid metabolites and improvements in insulin sensitivity and glucose metabolism: the POUNDS Lost trial – Yoriko Heianza, Nutrition

Cutting the Gordian Knot of the Microbiota – Kimberly S.Vasquez, Molecular Cell

Host: Microbiome co-metabolic processing of dietary polyphenols – An acute, single blinded, cross-over study with different doses of apple polyphenols in healthy subjects – Kajetan Trost, Food Research International

Clinical trials of kimchi intakes on the regulation of metabolic parameters and colon health in healthy Korean young adults – Hee-Young Kim, Journal of Functional Foods

Animal experiments

Propolis from Different Geographic Origins Suppress Intestinal Inflammation in a Model of DSS‐Induced Colitis is Associated with Decreased Bacteroides spp. in the Gut – Kai Wang, Molecular Nutrition and Food Research

Effect of direct-fed microbials on culturable gut microbiotas in broiler chickens: a meta-analysis of controlled trials – Chhaiden Heak, Asian-Australasian Journal of Animal Sciences

A dietary isothiocyanate-enriched moringa (Moringa oleifera) seed extract improves glucose tolerance in a high-fat-diet mouse model and modulates the gut microbiome – Asha Jaja-Chimedza, Journal of Functional Foods

The enteric microbiota regulates jejunal Paneth cell number and function without impacting intestinal stem cells – Alexi A. Schoenborn, Gut Microbes

Comprehensive longitudinal microbiome analysis of the chicken cecum reveals a shift from competitive to environmental drivers and a window of opportunity for Campylobacter – Umer Zeeshan Ijaz, bioRxiv

Microbial quantity impacts Drosophila nutrition, development, and lifespan – Erin S. Keebaugh, iScience

Absence of Gut Microbiota Reduces Emotional Reactivity in Japanese Quails (Coturnix japonica) – Narjis Kraimi, Frontiers in Physiology

Animal microbiome

Identification of circular single-stranded DNA viruses in faecal samples of Canada lynx (Lynx canadensis), moose (Alces alces) and snowshoe hare (Lepus americanus) inhabiting the Colorado San Juan Mountains – Simona Kraberger, Infection, Genetics and Evolution

Diverse novel resident Wolbachia strains in Culicine mosquitoes from Madagascar – Claire L Jeffries, bioRxiv

Sample treatment optimization for fish stool metabolomics – Takeshi Hano, Journal of Chromatography B

Plant, root, and soil microbiome

Two decades of altered snow cover does not affect soil microbial ability to catabolize carbon compounds in an oceanic alpine heath – E.R. Jasper Wubs, Soil Biology and Biochemistry

Grazing and resource availability control soil nematode body size and abundance‐mass relationship in semi‐arid grassland – W. S. Andriuzzi, Journal of Animal Ecology

Isolation and screening of antibiotic producing actinomycetes from rhizosphere and agricultural soils – Atsede Muleta, African Journal of Biotechnology

Responses of Bougainvillea spectabilis to elevated atmospheric CO2 under galaxolide (HHCB) pollution and the mechanisms of its rhizosphere metabolism – Minzhe Zhang, Journal of Soils and Sediments

Differential effect of the nitrogen form on the leaf gas exchange, amino acid composition, and antioxidant response of sweet pepper at elevated CO2 – María C. Piñero, Plant Growth Regulation

Viral metagenomics analysis and eight novel viral genomes identified from the Dushanzi mud volcanic soil in Xinjiang, China – Dan-Ting Yu, Journal of Soils and Sediments

Efficacy of Bacillus subtilis native strains for biocontrol of Phytophthora crown and root rot of pistachio in Iran – Mohammad Moradi, Tropical Plant Pathology

Modification of plant cell wall chemistry impacts metabolome and microbiome composition in Populus PdKOR1 RNAi plants – Allison M. Veach, Plant and Soil

Continuous application of different fertilizers induces distinct bulk and rhizosphere soil protist communities – Sai Guo, European Journal of Soil Biology

Microbial communities and natural fermentation of corn silages prepared with farm bunker-silo in Southwest China – Hao Guan, Bioresource Technology

Cultivated methanotrophs associated with rhizospheres of traditional rice landraces from Western India belong to Methylocaldum and Methylocystis – Monali C. Rahalkar, 3 Biotech

Metal(loid)-resistant bacteria reduce wheat Cd and As uptake in metal(loid)-contaminated soil – Xiao-Han Wang, Environmental Pollution

Enhanced removal of nitrate in the maize rhizosphere by plant growth-promoting Bacillus megaterium NCT-2, and its colonization pattern in response to nitrate – Shaohua Chu, Chemosphere

Bioactive luteoloside produced by Myroides odoratimimus, solvent-tolerant bacterium form the rhizosphere of Lonicera japonica –  Y. X. Zhao, Natural Product Research

Potential application of selected metal resistant phosphate solubilizing bacteria isolated from the gut of earthworm (Metaphire posthuma) in plant growth promotion – Jayanta  Kumar Biswas, Geoderma

Effects of Pseudomonas chenduensis and biochar on cadmium availability and microbial community in the paddy soil – Lingjuan Li, Science of The Total Environment

Continuous application of different fertilizers induces distinct bulk and rhizosphere soil protist communities – Sai Guo, European Journal of Soil Biology

Analysis on metabolic functions of stored rice microbial communities by BIOLOG ECO microplates – Zhiwen Ge, Frontiers in Microbiology

Effects of discrete bioactive microbial volatiles on plants and fungi – Birgit Piechulla, Plant, Cell, and Environment

Phylogenetic-scale disparities in the soil microbial diversity–ecosystem functioning relationship – Marta Goberna, ISME

Similar soil microbial community structure across different environments after long‐term succession: evidence from volcanoes of different ages – Shangqi Xu, Journal of Basic Microbiology

Water and extremophile microbiome

Comparison among the microbial communities in the lake, lake wetland, and estuary sediments of a plain river network – Wei Huang, Microbiology Open

The distinctive microbial community improves composting efficiency in a full-scale hyperthermophilic composting plant – Zhen Yu, Bioresource Technology

Co-occurrence Networks Among Bacteria and Microbial Eukaryotes of Lake Baikal During a Spring Phytoplankton Bloom – Ivan S. Mikhailov, Microbial Ecology

The Legacy Effects of Winter Climate on Microbial Functioning After Snowmelt in a Subarctic Tundra – Maria Väisänen, Microbial Ecology

Characterization of phototrophic microorganisms and description of new cyanobacteria isolated from the saline-alkaline crater-lake Dziani Dzaha (Mayotte, Indian Ocean) – M. Cellamare, FEMS Microbiology Ecology

Methanogens in the Antarctic Dry Valley Permafrost – Tatiana A. Vishnivetskaya, FEMS Microbiology Ecology

Bacterial Diversity in an Alpine Debris-Free and Debris-Cover Accumulation Zone Glacier Ice, North Sikkim, India – Mingma Thundu Sherpa, Indian Journal of Microbiology

Culturing the ubiquitous freshwater actinobacterial acI lineage by supplying a biochemical ‘helper’ catalase – Suhyun Kim, bioRxiv

Assessing the effect of pretreatments on the structure and functionality of microbial communities for the bioconversion of microalgae to biogas – Olivia Córdova, Frontiers in Microbiology

Great Salt Lake microbiology: a historical perspective – Bonnie K. Baxter, International Microbiology

Life from the ashes: survival of dry bacterial spores after very high temperature exposure – Lynda Beladjal, Extremophiles

Microbial and geochemical controls on waste rock weathering and drainage quality – Sharon Blackmore, Science of The Total Environment

Characterization and high-throughput sequencing of a trichlorophenol-dechlorinating microbial community acclimated from sewage sludge – Jiaxiu Song, Journal of Cleaner Production

Impacts of surface-applied residues on N-cycling soil microbial communities in miscanthus and switchgrass cropping systems – Karen A. Thompson, Applied Soil Ecology

Water is a critical factor in evaluating and assessing microbial colonization and destruction of Angkor sandstone monuments – Xiaobo Liu, International Biodeterioration & Biodegradation

Methanogenic community shifts during the transition from sewage mono-digestion to co-digestion of grass biomass – Justus Hardegen, Bioresource Technology

Bacterial lineages putatively associated with the dissemination of antibiotic resistance genes in a full-scale urban wastewater treatment plant – Carlos Narciso-da-Rocha, Environment International

Impact of organic waste composition on life cycle energy production, global warming and Water use for treatment by anaerobic digestion followed by composting – Sara A. Pace, Resources, Conservation and Recycling

1H NMR metabolomics of microbial metabolites in the four MW agricultural biogas plant reactors: A case study of inhibition mirroring the acute rumen acidosis symptoms – Boštjan Murovec, Journal of Environmental Management

Comparative Metagenomics Provides Insight into the Ecosystem Functioning of the Shark Bay Stromatolites, Western Australia – Joany Babilonia, Frontiers in Microbiology

Assessing the abundance of fungal populations in a full-scale membrane bioreactor (MBR) treating urban wastewater by using quantitative PCR (qPCR) – P. Maza-Márquez, Journal of Environmental Management

Food microbiology

Occurrence of lactic acid bacteria and yeasts at species and strain level during spontaneous fermentation of mawè, a cereal dough produced in West Africa – Marcel Houngbédji, Food Microbiology

Probiotics / prebiotics

Probiotics in IBD: Combining in vitro and in vivomodels for selecting strains with both anti-inflammatory potential as well as a capacity to restore the gut epithelial barrier – Mazen Zaylaa, Journal of Functional Foods

Can prebiotics assist in the management of cognition and weight gain in schizophrenia? – Amy Chia-Ching Kao, Psychoneuroendocrinology

Probiotic potentials of Lactobacillus plantarum isolated from fermented durian (Tempoyak), a Malaysian traditional condiment – Asmariah Ahmad, Food Science and Nutrition

Bioinformatics

Identifying Heritable Communities of Microbiome by Root-Unifrac and Wishart Distribution – Yunfan Tang, bioRxiv

PARTIE: a partition engine to separate metagenomic and amplicon projects in the Sequence Read Archive – Pedro J. Torres, Bioinformatics

Techniques

Dead or Alive? Molecular life-dead distinction in human stool samples reveals significantly different composition of the microbial community – Alexandra Perras, bioRxiv

Critical Assessment of Methods to Quantify Biofilm Growth and Evaluate Antibiofilm Activity of Host Defence Peptides – Evan F. Haney, Biomolecules

Advertisements

June 3, 2018

Today’s digest full of great and fun studies including a fungal survey of the atmosphere and links between gut microbiome and MS.

General Microbiome

RNA-based stable isotope probing (RNA-SIP) to unravel intestinal host-microbe interactions. Egert M. Methods

Environmental Sources of Bacteria Differentially Influence Host-Associated Microbial Dynamics.Cardona C. mSystems

Biohydrogen production from space crew’s waste simulants using thermophilic consolidated bioprocessing.Wang J. Bioresource Technology

Prevalence of <i>Trichomonas vaginalis</i> infection and protozoan load in South African women: a cross-sectional study.de Waaij DJ.BMJ Open

Time course metabolome of Roux-en-Y gastric bypass confirms correlation between leptin, body weight and the microbiome.Seridi L. PLoS One

Gut Microbiome

A gut feeling about multiple sclerosis.Quintana FJ. Proceedings of the National Academy of Sciences

Dietary fat and gut microbiota: mechanisms involved in obesity control.Coelho OGL. Critical Reviews in Food Science and Nutrition

Probiotic Species in the Modulation of Gut Microbiota: An Overview.Azad MAK J. Biomedical Research International.

The Relationship between Frequently Used Glucose-Lowering Agents and Gut Microbiota in Type 2 Diabetes Mellitus.Lv Y. Journal of Diabetes Research

The Gut Microbiome Profile in Obesity: A Systematic Review.Castaner O. International Journal of Endocrinology.

The <i>Lactobacillus</i> Bile Salt Hydrolase Repertoire Reveals Niche-Specific Adaptation.O’Flaherty S. mSphere

Skin Microbiome

Early-life skin microbiota in hospitalized preterm and full-term infants.Younge NE. Microbiome.

Oral Microbiome

Stimulated and unstimulated saliva samples have significantly different bacterial profiles.Gomar-Vercher S. PLoS

Alterations in the oral microbiome in HIV-infected participants after antiretroviral therapy administration are influenced by immune status.Presti RM. AIDS

Oral microbiota in youth with perinatally acquired HIV infection. Starr JR. Microbiome

Air and Water Microbiome

Biogeochemical probing of microbial communities in a basalt-hosted hot spring at Kverkfjöll volcano, Iceland.Cousins CR. Geobiology

Taxonomic diversity of fungi deposited from the atmosphere.Woo C. ISME Journal.

Model Communities Hint at Promiscuous Metabolic Linkages between Ubiquitous Free-Living Freshwater Bacteria.Garcia SL. mSphere.

Animal Experiments and Microbiome

Thermal processing of food reduces gut microbiota diversity of the host and triggers adaptation of the microbiota: evidence from two vertebrates.Zhang Z. Microbiome

Longevity extension in Drosophila through gut-brain communication.Westfall S. Scientific Reports

Exploring the diversity-stability paradigm using sponge microbial communities.Glasl B. Scientific Reports

Exploring the Microbiome of Callinectes sapidus (Maryland Blue Crab).Ramachandran P. Genome Announcements

Effect of different types of olive oil pomace dietary supplementation on the rumen microbial community profile in Comisana ewes.Mannelli F. Scientific Reports

Variation in faecal microbiota in a group of horses managed at pasture over a 12-month period.Salem SE. Scientific Reports

Intestinal microbiota composition is altered according to nutritional biorhythms in the leopard coral grouper (Plectropomus leopardus).Mekuchi M. PLoS One

Characterization of the fecal and mucosa-associated microbiota in dogs with colorectal epithelial tumors.Herstad KMV.PLoS One

Fungal, Bacterial, and Archaeal Diversity in the Digestive Tract of Several Beetle Larvae (Coleoptera). Ziganshina EE. Biomedical Research International.

Plant and Soil Microbiomes

Antibiotic Resistance in Plant-Pathogenic Bacteria. Sundin GW. Annual Review of Phytopathology

Characterization of Microbial Communities in Pilot-Scale Constructed Wetlands with <i>Salicornia</i> for Treatment of Marine Aquaculture Effluents.Ma X. Archaea.

Fall Armyworm-Associated Gut Bacteria Modulate Plant Defense Responses.Acevedo FE. Molecular Plant-Microbe Interactions

Multifunctional potential of endophytic and rhizospheric microbial isolates associated with Butia purpurascens roots for promoting plant growth.da Silva CF. Antonie Van Leeuwenhoek

Rapid Microbial Community Changes During Initial Stages of Pine Litter Decomposition.Gołębiewski M. Microbial Ecology

In situ relationships between microbiota and potential pathobiota in Arabidopsis thaliana.Bartoli C. ISME Journal.

 

May 15, 2018

Comparison of the cottage cheese and artisanal cheese microbiota, no microbes found in amniotic fluid from healthy term pregnancies, impacts of ocean warming on the oyster microbiome.

General microbiome

Molecular (Me)micry? – Orly Avni – Cell Host & Microbe

Pregnancy and early life

Amniotic fluid from healthy term pregnancies does not harbor a detectable microbial community – Efrem S Lim – Microbiome

Multi-site human microbiome

Data on the gut and saliva microbiota from a cohort of atherosclerosis patients determined by 16S rRNA gene sequencing – Gregory B Gloor – Data in Brief

Human skin microbiome

Antiseptic Agents Elicit Short-Term, Personalized and Body Site-Specific Shifts in Resident Skin Bacterial Communities – Adam J SanMiguel – The Journal of Investigative Dermatology

Human gut microbiome

Review: Systematic review assessing the effectiveness of dietary intervention on gut microbiota in adults with type 2 diabetes – David Houghton – Diabetologia

Animal experiments

Increased butyrate priming in the gut stalls microbiome associated-gastrointestinal inflammation and hepatic metabolic reprogramming in a mouse model of Gulf War Illness – Ratanesh Kumar Seth – Toxicology and Applied Pharmacology

Light exposure influences the diurnal oscillation of gut microbiota in mice – Guangyan Wu – Biochemical and Biophysical Research Communications

Early-Life Antibiotic-Driven Dysbiosis Leads to Dysregulated Vaccine Immune Responses in Mice – Miriam Anne Lynn – Cell Host & Microbe

The effect of the timing of exposure to Campylobacter jejuni on the gut microbiome and inflammatory responses of broiler chickens – Phillippa L Connerton – Microbiome

Animal microbiome

Potential impacts of hypoxia and a warming ocean on oyster microbiomes – Bushra Khan – Marine Environmental Research

Mixed-Mode Transmission Shapes Termite Gut Community Assemblies – Rafael R da Costa – Trends in Microbiology

Plant, root, and soil microbiome

Effect of compost application on the dynamics of carbon in a nectarine orchard ecosystem – E Baldi – Science of the Total Environment

Review: Current research trends on plastic pollution and ecological impacts on the soil ecosystem: A review – Yooeun Chae – Environmental Pollution

Community structure and plant growth-promoting potential of cultivable bacteria isolated from Cameroon soil – Gylaine Vanissa Tchuisseu Tchakounté – Microbiological Research

Characterisation of antagonistic yeasts for biocontrol applications on apples or in soil by quantitative analyses of synthetic yeast communities – Simon Gross – Yeast

Water and extremophile microbiome

Microbial ecology of two hot springs of Sikkim: Predominate population and geochemistry – Ishfaq Nabi Najar – Science of the Total Environment

Exploring abundance, diversity and variation of a widespread antibiotic resistance gene in wastewater treatment plants – Ziyan Wei – Environment International

Antimicrobial resistance and potential virulence of Vibrio parahaemolyticus isolated from water and bivalve mollusks from Bahia, Brazil – Irana Paim Silva – Marine Pollution Bulletin

Diversity and distribution of Archaea in global estuarine ecosystems – Xiaobo Liu – Science of the Total Environment

Microbes in space

Acute exposure to space flight results in evidence of reduced lymph Transport, tissue fluid Shifts, and immune alterations in the rat gastrointestinal system – W E Cromer – Life Sciences in Space Research

Food microbiology

Using PacBio sequencing to investigate the bacterial microbiota of traditional Buryatian cottage cheese and comparison with Italian and Kazakhstan artisanal cheeses – Hao Jin – Journal of Dairy Science

Salmonella Cold Stress Response: Mechanisms and Occurrence in Foods – Steven C Ricke – Advances in Applied Microbiology

Probiotics/prebiotics

Strategies to improve the functionality of probiotics in supplements and foods – Claude P Champagne – Current Opinion in Food Science

Phages and viruses

Pre-print: Diversity of active viral infections within the Sphagnum microbiome – Joshua M A Stough – bioRxiv

Review: Composition of gut microbiota and its influence on the immunogenicity of oral rotavirus vaccines – Cliff A Magwira – Vaccines

Metabolomics

Review: A Review on Human Fecal Metabolomics: Methods, Applications and the Human Fecal Metabolome Database – Naama Karu – Analytica Chimica Acta

More microbes

Critical knowledge gaps and research needs related to the environmental dimensions of antibiotic resistance – D G Joakim Larsson – Environment International

May 10, 2018

Today we have quite a few interesting papers in “Water microbiome”, there you can read about: drift in the community structuring of bacteria and microbial eukaryotes by R.Logares; phylogeny‐based database “EukRef–Ciliophora” by V. Boscaro;  diverse bacterial and viral populations in agricultural freshwater pond by J. Chopyk. In a “Bioinformatics” section you can read about “MIMOSA: Algorithms for Microbial Profiling” (by O. U. Nalbantoglu) and about use of SplinectomeR package in longitudinal microbiome studies by R.R. Shields- Cutler. Enjoy!

Jobs

PhD position for anaerobic microbiology of the Black Sea, Netherlands

General microbiome

Cargo Transport Shapes the Spatial Organization of a Microbial Community – Abhishek Shrivastava – bioRxiv

The Effect of Berberine on the Transcriptome and Proteome of E. coli – Zhang Shilei – bioRxiv

Predator-by-Environment Interactions Mediate Bacterial Competition in the Dictyostelium discoideum Microbiome – R. Fredrik Inglis – Frontiers in Microbiology / Evolutionary and Genomic Microbiology

Diversity time-period and diversity-time-area relationships exemplified by the human microbiome – Zhanshan (Sam) Ma – Scientific Reports

Pregnancy and early life

Microbial Biomarkers of Intestinal Barrier Maturation in Preterm Infants – Bing Ma – bioRxiv

Influence of human milk oligosaccharides on adherence of bifidobacteria and clostridia to cell lines – Musilova Sarka  – Acta Microbiologica et Immunologica Hungarica

 

Oral microbiome

Research on oral microbiota of monozygotic twins with discordant caries experience – in vitro and in vivo study – Hongle Wu – Scientific Reports

Glycemic Status Affects the Subgingival Microbiome of Diabetic Patients – Priscila Larcher Longo – Journal of Clinical Periodontology

Research on oral microbiota of monozygotic twins with discordant caries experience – in vitro and in vivo study – Hongle Wu – Scientific Reports

Human gut microbiome

Fecal microbiota transplantation in experimental ulcerative colitis reveals associated gut microbial and host metabolic reprogramming – Zhixiang Yan – Applied and Environmental Microbiology

Fecal microbiota transplantation treatment for refractory ulcerative colitis with allergy to 5-aminosalicylic acid: A case report – Hong-Gang Wang – Medicine

Review: Influence of Commensal Microbiota on the Enteric Nervous System and Its Role in Neurodegenerative Diseases – Endres K. – Journal of Innate Immunology

Loss of Ethanolamine Utilization in Enterococcus faecalis Increases Gastrointestinal Tract Colonization – Karan Gautam Kavala – mBio

Compositional and Functional Differences in the Human Gut Microbiome Correlate with Clinical Outcome following Infection with Wild-Type Salmonella enterica Serovar Typhi – Yan Zhang – mBio

Animal experiments

Effects of gut microbiota and time of treatment on tissue levels of green tea polyphenols in mice – Anna B. Liu – BioFactors

Gastrointestinal microbiota and mucosal immune gene expression in neonatal pigs reared in a cross-fostering model – Nidia Maradiaga – Microbial Pathogenesis

Prolonged restraint stressor exposure in outbred CD-1 mice impacts microbiota, colonic inflammation, and short chain fatty acids – Ross M. Maltz – PLOS One

Review: Biomarkers for monitoring intestinal health in poultry: present status and future perspective – Richard Ducatelle – Veterinary Research

Animal microbiome 

Near full-length 16S rRNA gene next-generation sequencing revealed Asaia as a common midgut bacterium of wild and domesticated Queensland fruit fly larvae – Ania T. Deutscher – Microbiome

Crown-of-thorns sea star, Acanthaster cf. solaris, have tissue-characteristic microbiomes with potential roles in health and reproduction – Lone Høja – Applied and Environmental Microbiology

Multilevel social structure and diet shape the gut microbiota of the gelada monkey, the only grazing primate – Pål Trosvik – Microbiome

Antimicrobial activity in culturable gut microbial communities of springtails – Valeria Agamennone  – Journal of Applied Microbiology

Diversity and antimicrobial potential in sea anemone and holothurian microbiomes – Elizabeth León-Palmero  – PLOS One

Plant, root, and soil microbiome

Niche partition of phenanthrene-degrading bacteria along a Phragmites australis rhizosphere gradient – Xiaofei Lv – Biology and Fertility of Soils

Core microbiomes for sustainable agroecosystems – Toju H -Nature Plants

Determination of agricultural impact on soil microbial activity using δ18OP HCl and respiration experiments – Katherine Polain – ACS Earth and Space Chemistry

Seasonal dynamics of bacterial communities in a Betula albosinensis forest – C. Du – European Journal of Soil Science

Niche partition of phenanthrene-degrading bacteria along a Phragmites australis rhizosphere gradient – Xiaofei Lv – Biology and Fertility of Soils

Water and extremophile microbiome

Effects of Xiantao sewage treatment on microbial community structure of shallow groundwater in wetland – Shu-Fen Song – bioRxiv

Unexpected versatility in the metabolism and ecophysiology of globally relevant nitrite-oxidizing Nitrotoga bacteria – Andrew Boddicker – bioRxiv

Long-term seasonality of marine photoheterotrophic bacteria reveals low cohesiveness within the different phylogroups – Adrià Auladell – bioRxiv

Molecular cloning of glutathione peroxidase gene of Antarctic ice microalga Chlamydomonas sp. ICE‐L and its expression changes under temperature and salinity stress – Jin Hui Wang – Phycological Research

Contrasting prevalence of selection and drift in the community structuring of bacteria and microbial eukaryotes – Ramiro Logares – Environmental Microbiology

EukRef–Ciliophora: A manually curated, phylogeny‐based database of small subunit rRNA gene sequences of ciliates – Vittorio Boscaro – Environmental Microbiology

Novel human-associated Lachnospiraceae genetic markers improve detection of fecal pollution sources in urban waters – Shuchen Feng – Applied and Environmental Microbiology

Municipal wastewater treatment potential and metal accumulation strategies of Colocasia esculenta (L.) Schott and Typha latifolia L. in a constructed wetland – Vivek Rana – Environmental Monitoring and Assessment

Agricultural Freshwater Pond Supports Diverse and Dynamic Bacterial and Viral Populations – Jessica Chopyk – Frontiers in Microbiology / Aquatic Microbiology

Characterization of a Highly Enriched Microbial Consortium Reductively Dechlorinating 2,3-Dichlorophenol and 2,4,6-Trichlorophenol and the Corresponding cprA Genes from River Sediment – Wael S. El-Sayed – Polish Journal of Microbiology

Built environment

Characterization of fungi in office dust: comparing results of microbial secondary metabolites, fungal ITS region sequencing, viable culture, and other microbial indices – Ju Hyeong Park – Indoor Air

Investigation of the Active Biofilm Communities on Polypropylene Filter Media in a Fixed Biofilm Reactor for Wastewater Treatment – Iffat Naz – Journal of Chemical Technology and Biotechnology

Food microbiology

Characterization of the contaminant bacterial communities in sugarcane first-generation industrial ethanol production – Maria L. Bonatelli – FEMS Microbiology Letters

Probiotics / prebiotics

Phylotype-level profiling of lactobacilli in highly complex environments by means of an ITS-based metagenomic approach – Christian Milani – Applied and Environmental Microbiology

Comparative Genomics Reveals the Regulatory Complexity of Bifidobacterial Arabinose and Arabino-Oligosaccharide Utilization – Aleksandr A. Arzamasov – Frontiers in Microbiology /Evolutionary and Genomic Microbiology

 

Bioinformatics

MIMOSA: Algorithms for Microbial Profiling – Ozkan Ufuk Nalbantoglu – IEEE/ACM Transactions on Computational Biology and Bioinformatics

SplinectomeR Enables Group Comparisons in Longitudinal Microbiome Studies – Robin R. Shields-Cutler – Frontiers in Microbiology / Systems Microbiology

Metagenome enrichment approach used for selection of oil-degrading bacteria consortia for drill cutting residue bioremediation – Alaine B.Guerra – Environmental Pollution

Biotechnology

Microbial co-culturing systems: butanol production from organic wastes through consolidated bioprocessing – Yujia Jiang – Applied Microbiology and Biotechnology

Techniques

Sensitive detection of Live Escherichia coli by bacteriophage amplification-coupled immunoassay on the Luminex® MAGPIX instrument – Tomotaka Mido – bioRxiv

Microbes in the news

Scientists use dietary seaweed to manipulate gut bacteria in mice

Microbes are savvy investors when contributing to the common good

 

May 4, 2018

Today we have many interesting news and many papers in “Plant, root, and soil microbiome” section. Enjoy your friday read!

General microbiome

Uncovering the drivers of host-associated microbiota with joint species distribution modeling – Johannes R. Björk – bioRxiv

Competence Inhibition by the XrpA Peptide Encoded Within the comX Gene of Streptococcus mutans – Justin Kaspar – bioRxiv

Microbiota and metabolic diseases – Alessia Pascale – Endocrine

Human respiratory microbiome

The Gut-Lung Axis and Pulmonary Responses to Ozone – Judith A Voynow – American Journal of Respiratory and Molecular Biology

 

Human skin microbiome

Microbial host interactions and impaired wound healing in mice and humans: defining a role for BD14 and NOD2 – Helen Williams – Journal of Investigative Dermatology

Human nearly-sterile sites

The Role of Microbiota in Retinal Disease – Sheldon Rowan – Retinal Degenerative Diseases

Human gut microbiome

Immune Cells and Microbiota Response to Iron Starvation – Marcello Chieppa – Frontiers in Medicine / Gastroenterology

The Role of the Gut Microbiome in Colorectal Cancer – Grace Y. Chen – Clinics in Colon and Rectal Surgery

Enterococcus faecalis AHG0090 is a Genetically Tractable Bacterium and Produces a Secreted Peptidic Bioactive that Suppresses Nuclear Factor Kappa B Activation in Human Gut Epithelial Cells – Páraic Ó Cuív – Frontiers in Immunology /  Microbial Immunology

Animal experiments

Core gut microbiota in Jinhua pigs and its correlation with strain, farm and weaning age – Hua Yang – Journal of Microbiology

Animal microbiome 

Gut microbiomes of wild great apes fluctuate seasonally in response to diet – Allison L. Hicks – Nature Communications

Stochastic processes govern bacterial communities from the blood of pikas and from their arthropod vectors – Huan Li – FEMS Microbiology Ecology

An in vitro evaluation of browser and grazer fermentation efficiency and microbiota using European moose spring and summer foods – Sophie J. Krizsan – Ecology & Evolution

The effect of gut microbiota elimination in Drosophila melanogaster: A how-to guide for host–microbiota studies – Chloe Heys  – Ecology & Evolution

Urea hydrolysis by gut bacteria in a hibernating frog: evidence for urea-nitrogen recycling in Amphibia – James M. Wiebler – Proceedings of the Royal Society B

Plant, root, and soil microbiome

Highly diverse endophytes in roots of Cycas bifida (Cycadaceae), an ancient but endangered gymnosperm – Ying Zheng – Journal of Microbiology

Soil metabarcoding identifies season indicators and differentiators of pig and Agrostis/Festuca spp. decomposition – Ayodeji O.Olakanye – Forensic Science International

Modulation of plant chemistry by beneficial root microbiota – Desalegn W. Etalo  –  Natural Product Reports

Highly diverse endophytes in roots of Cycas bifida (Cycadaceae), an ancient but endangered gymnosperm – Ying Zheng – Journal of Microbiology

A global atlas of the dominant bacteria found in soil – Manuel Delgado-Baquerizo – Science

Variations of Bacterial Community Diversity Within the Rhizosphere of Three Phylogenetically Related Perennial Shrub Plant Species Across Environmental Gradients – Xiaofan Na –  Frontiers in Microbiology

Combined effects of phosphate-solubilizing bacterium XMT-5 (Rhizobium sp.) and submerged macrophyte Ceratophyllum demersum on phosphorus release in eutrophic lake sediments – Haifeng Li – Environmental Science and Pollution Research

Successful phytoremediation of crude-oil contaminated soil at an oil exploration and production company by plants-bacterial synergism – Kaneez Fatima – International Journal of Phytoremediation

Alginate-perlite encapsulated Pseudomonas putida A (ATCC 12633) cells: preparation, characterization and potential use as plant inoculants – Andrés S. Liffourrena – Journal of Biotechnology

Variations of Bacterial Community Diversity Within the Rhizosphere of Three Phylogenetically Related Perennial Shrub Plant Species Across Environmental Gradients – Xiaofan Na – Frontiers in Microbiology / Terrestrial Microbiology

Water and extremophile microbiome 

Conductive Particles Enable Syntrophic Acetate Oxidation between Geobacter and Methanosarcina from Coastal Sediments – Amelia-Elena Rotaru – mBio

Mind the gut: genomic insights to population divergence and gut microbial composition of two marine keystone species – Katharina Fietz – BMC Microbiome

Enhanced degradation of phenol in floating treatment wetlands by plant-bacterial synergism – Hamna Saleem – International Journal of Phytoremediation

Bacterial community diversity in a full scale biofilter treating wastewater odor – M. J. Allievi – Water Science & Technology

Food microbiology

Sausage fermentation and starter cultures in the era of molecular biology methods – Irene Franciosa – International Journal of Food Microbiology

Contribution of the novel sulfur-producing adjunct Lactobacillus nodensis to flavor development in Gouda cheese – Elaine O’Brien – Journal of Dairy Science

Probiotics / prebiotics

Probiotics drive gut microbiome triggering emotional brain signatures – Deepika Bagga – Gut Microbiome

Phages and viruses

Reactivation of latent HIV-1 in vitro using an alcoholic extract from Euphorbia umbellata (Euphorbiaceae) latex – Ana L Valadao – bioRxiv

Mycobacteria recycle their peptidoglycan via a novel pathway which influences antimicrobial resistance and limits proliferation in macrophages – Patrick J. Moynihan – bioRxiv

Biotechnology

Microbiological aspects of thermophile pretreatment of activated sludge inhibiting electricity generation of microbial fuel cell – Yang-Guo Zhao – Water Science & Technology

Methane-yielding microbial communities processing lactate-rich substrates: a piece of the anaerobic digestion puzzle – Anna Detman – BMC Biotechnology for Biofuels

Microbes in the news 

Researchers find a gene that lets bacteria kill all male flies

Targeting Gut Bacteria to Reduce Disease

Applying live bacteria to skin improves eczema

Walnuts impact gut microbiome and improve health

By wrapping itself in antibodies, this bacterium may become a stable, beneficial part of the gut

A healthy digestive system is all you need in life

 

 

April 28, 2018

Genomic analysis of tick endosymbionts, re-evaluation of the phylogenetic placement of mitochondria outside alphaproteobacteria, gravity sensing in fungi acquired by horizontal gene transfer from bacteria.

General microbiome

Review: Malaria and the microbiome: a systematic review – Matthew M Ippolito – Clinical Infectious Diseases

Pregnancy and early life

The fallopian tube microbiome: implications for reproductive health – Elise S Pelzer – Oncotarget

Animal microbiome

The influence of diet and environment on the gut microbial community of field crickets – Soon Hwee Ng – Ecology and Evolution

Comparison of closely related, uncultivated Coxiella tick endosymbiont population genomes reveals clues about the mechanisms of symbiosis – Despina Tsementzi – Environmental Microbiology

Insights into the bacterial symbiont diversity in spiders – Lihua Zhang – Ecology and Evolution

Plant, root, and soil microbiome

Legume endosymbionts: Drought stress tolerance in second‐generation chickpea (Cicer arietinum) seeds – V Kumari – Journal of Agronomy and Crop Science

Quantifying the Spatiotemporal Dynamics of Plant Root Colonization by Beneficial Bacteria in a Microfluidic Habitat – Jayde A Aufrecht – Advanced Biosystems

Response of the wheat rhizosphere soil nematode community in wheat/walnut intercropping system in Xinjiang, Northwest China – Peng-hua Bai – Applied Entomology and Zoology

Pre-print: Host identity and functional traits determine the community composition of the arbuscular mycorrhizal fungi in facultative epiphytic plant species – Maria del Mar Alguacil – bioRxiv

Seagrass rhizosphere microenvironment alters plant‐associated microbial community composition – Kasper Elgetti Brodersen – Environmental Microbiology

Water and extremophile microbiome

Impacts of elevated atmospheric CO2 concentration on terrestrial-aquatic carbon transfer and a downstream aquatic microbial community – Emma Rochelle-Newell – Aquatic Sciences

Community differentiation of bacterioplankton in the epipelagic layer in the South China Sea – Yi Zhang – Ecology and Evolution

Built environment

Review: Ecotoxicological effects of microplastics on biota: a review – Sadasivam Anbumani – Environmental Science and Pollution Research

Bioinformatics

Renewing Felsenstein’s phylogenetic bootstrap in the era of big data – F Lemoine – Nature

Pre-print: Machine learning based prediction of functional capabilities in metagenomically assembled microbial genomes – Fred Farrell – bioRxiv

Techniques

Review: Overview of Next‐Generation Sequencing Technologies – Barton E Slatko – Current Protocols in Molecular Biology

More microbes

Deep mitochondrial origin outside the sampled alphaproteobacteria – Joran Martijn – Nature

Evolutionary novelty in gravity sensing through horizontal gene transfer and high-order protein assembly – Tu Ahn Nguyen – PLOS Biology

Pre-print: Differentiation of vegetative cells into spores: a kinetic model applied to Bacillus subtilis – Emilie Gauvry – bioRxiv

Pre-print: A decay effect of bacterial growth rate associated with genome reduction – Kouhei Tsuchiya – bioRxiv

Microbes in the news

Mass suicide documented in bacteria – Nature

Researchers assassinate disease-causing bacteria with virus cocktail – EurekAlert

Bacteria in the small intestine indispensable for fat absorption – EurekAlert

Why a rinse won’t do: on menstrual cups, bacteria, and toxic shock syndrome – Siouxsie Wiles – The Spinoff

Study reveals how bacteria communicate in groups to avoid antibiotics – EurekAlert

Podcast: Gut Punch – Marketing Microbiome Hype – Michael Joyce – Health News Review

Microbes on the market

Global Microbiome Therapeutics Market to Witness Comprehensive Growth By 2024 – Healthcare Trends

uBiome Sponsors Annual Fundraising Walk, SF Take Steps, to Support the Crohn’s and Colitis Foundation – benzinga

Microbiome Company A-Mansia Secures €16M – Allison Johnson – Biocentury

Science, career, and publishing

A photo celebration of scientists at work – Jack Leeming – Nature

Scientists’ early grant success fuels further funding – Holly Else – Nature

Pre-print: Strength in numbers: collaborative science for new experimental model systems – Ross F Waller – bioRxiv

April 26, 2017

General microbiome

Baseline urine metabolic phenotype in patients with severe alcoholic hepatitis and its association with outcome – Jaswinder Singh Maras – Hepatology communications

Checkpoint Checkmate: Microbiota Modulation of Cancer Immunotherapy – Eric C. Keen – Clinical chemistry

Metagenomics Analysis of Bacterial Population of Tympanosclerotic Plaques and Cholesteatomas – M. Tayyar Kalcioglu – Otolaryngology–Head and Neck Surgery

Drinking alcohol is associated with variation in the human oral microbiome in a large study of American adults – Xiaozhou Fan – Microbiome

Pregnancy and early life

Preterm infants have distinct microbiomes not explained by mode of delivery, breastfeeding duration or antibiotic exposure – Cecilie Dahl – International Journal of Epidemiology

Gut microbial functional maturation and succession during human early life – Tomás Cerdó – Environmental microbiology

Human respiratory microbiome

Modelling upper respiratory tract diseases: getting grips on host-microbe interactions in chronic rhinosinusitis using in vitro technologies – Charlotte De Rudder Microbiome

Human skin microbiome

Skin microbiota and allergic symptoms associate with exposure to environmental microbes – Jenni Lehtimäki – PNAS

Human gut microbiome

Review :Dysbiosis in Functional Bowel Disorders – Paul Enck – Annals of Nutrition and Metabolism

Review: Inflammatory Bowel Disease and Immunonutrition: Novel Therapeutic Approaches Through Modulation of Diet and the Gut Microbiome – Larissa S Celiberto- Immunology

Comment : Richness and ecosystem development across faecal snapshots of the gut microbiota – Gwen Falony – Nature microbiology
Effects of gut microbiota manipulation on ex vivo lipolysis in human abdominal subcutaneous adipocytes – Johan W. E. Jocken – Adipocyte

Chronic kidney disease, uremic milieu, and its effects on gut bacterial microbiota dysbiosis – Lee D Chaves – American Journal of Physiology-Renal Physiology

Microbiota transplantation: concept, methodology and strategy for its modernization – Faming Zhang – Protein & Cell

The effects of sequencing platforms on phylogenetic resolution in 16 S rRNA gene profiling of human feces – Tae Woong Whon – Scientific Data

Gut Microbiota: From Microorganisms to Metabolic Organ Influencing Obesity – Richard W. Stephens – Obesity

Gut Microbes and Health: A Focus on the Mechanisms Linking Microbes, Obesity, and Related Disorders – Marialetizia Rastelli – Obesity

Review article: Impact of dietary gut microbial metabolites on the epigenome – Clarissa Gerhauser – Philosophical. Transactions of the Royal Society B

Animal experiments 

Gut Microbiota-Derived Tryptophan Metabolites Modulate Inflammatory Response in Hepatocytes and Macrophages – Cell Reports – Smitha Krishnan

Modulation of Active Gut Microbiota by Lactobacillus rhamnosus GG in a Diet Induced Obesity Murine Model – Yosep Ji – Frontiers in Microbiology

Lactobacilli Are Prominent Members of the Microbiota Involved in the Ruminal Digestion of Barley and Corn – Hee E. Yang

Intestinal microbiome of broiler chickens after use of nanoparticles and metal salts – Еlena Yausheva – Environmental Science and Pollution Research

Distinct consequences of amoxicillin and ertapenem exposure in the porcine gut microbiome – Sheila Connelly – Anaerobe

Indole, a Signaling Molecule Produced by the Gut Microbiota, Negatively Impacts Emotional Behaviors in Rats – Mathilde Jaglin – Frontiers in Neuroscience

Animal microbiome 

Microbiome of Total Versus Live Bacteria in the Gut of Rex Rabbits – Xiangchao Fu – Frontiers in Microbiology

Plant, root, and soil microbiome

Inferring Roles in Defense from Metabolic Allocation of Rice Diterpenoids – Xuan Lu – The Plant Cell

Genotypic variation in Pinus radiata responses to nitrogen source are related to changes in the root microbiome – Marta Gallart – FEMS Microbiology Ecology

Competition and habitat filtering jointly explain phylogenetic structure of soil bacterial communities across elevational gradient – Qian Zhang – Environmental Microbiology

Seagrass rhizosphere microenvironment alters plant‐associated microbial community composition – Kasper Elgetti Brodersen – Environmental Microbiology

Water and extremophile microbiome

Comparing Rock-inhabiting Microbial Communities in Different Rock Types from a High Arctic Polar Desert – Yong-Hoe Choe – FEMS Microbiology Ecology

Microbial communities in bakken region produced water – Daniel Lipus – FEMS Microbiology Letters

Aerobic microbial taxa dominate deep subsurface cores from the Alberta oil sands – Christina M Ridley – FEMS Microbiology Ecology

Metal contaminations impact archaeal community composition, abundance and function in remote alpine lakes – Sergi Compte‐Port – Environmental Microbiology

 Probiotics / prebiotics

Clinical and Microbiological Effect of a Multispecies Probiotic Supplementation in Celiac Patients With Persistent IBS-type Symptoms: A Randomized, Double-Blind, Placebo-controlled, Multicenter Trial – Ruggiero Francavilla – Journal of Clinical Gastroenterology

Review: Are Probiotics Effective in Targeting Alcoholic Liver Diseases? – Meegun Hong – Probiotics and Antimicrobial Proteins