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

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June 9, 2018

Human respiratory microbiome

Lung Dysbiosis, Inflammation, and Injury in Hematopoietic Cell Transplantation – David N O’Dwyer, American Journal of Respiratory and Critical Care Medicine

Heterogeneity of Microbiota Dysbiosis in Chronic Rhinosinusitis: Potential Clinical Implications and Microbial Community Mechanisms Contributing to Sinonasal Inflammation – Keehoon Lee, Frontiers in Cell and Infection Microbiology

Human skin microbiome

A systematic literature review of the human skin microbiome as biomarker for dermatological drug development – T. van der Kolk, British Journal of Clinical Pharmacology

Human gut microbiome

Inadequate Vitamin C Status in Prediabetes and Type 2 Diabetes Mellitus: Associations with Glycaemic Control, Obesity, and Smoking – Renée Wilson, Nutrients

Altered Stool Microbiota of Infants with Cystic Fibrosis Shows Reduction in Genera Associated with Immune Programming – Katherine Anosca, bioRxiv

Gut Microbiota Diversity across Ethnicities in the United States – Andrew W Brooks, bioRxiv

From the Mediterranean Diet to the Microbiome – Caroline E Childs, The Journal of Nutrition

Letter: improvements in mental health after faecal microbiota transplantation—an underexplored treatment‐related benefit? – B. H. Mullish, Alimentary Pharmacology and Therapeutics

Letter: improvements in mental health after faecal microbiota transplantation—an underexplored treatment‐related benefit? Authors’ reply – J. Jalanka, Alimentary Pharmacology and Therapeutics

Microbiota‐gut‐brain axis: Interaction of gut microbes and their metabolites with host epithelial barriers – Y. Bhattarai, Neurogastroenterology & Motility

Animal experiments

Bisphenol-A alters microbiota metabolites derived from aromatic amino acids and worsens disease activity during colitis – Jennifer AA DeLuca, Experimental Biology and Medicine

Fumonisin-Exposure Impairs Age-Related Ecological Succession of Bacterial Species in Weaned Pig Gut Microbiota – Ivan Mateos, Toxins

Ethanol extract of Ganoderma lucidum ameliorates lipid metabolic disorders and modulates the gut microbiota composition in high-fat diet fed rats – Wei-Ling Guo, Food & Function

Gut microbiota promotes production of aromatic metabolites through degradation of barley leaf fiber – Daotong Li, The Journal of Nutritional Biochemistry

Dietary Supplementation of Potato Peel Powders Prepared from Conventional and Organic Russet and Non-organic Gold and Red Potatoes Reduces Weight Gain in Mice on a High-Fat Diet – Salem Elkahoui, Journal of Agricultural and Food Chemistry

Microbial dysbiosis associated with impaired intestinal Na+/H+ exchange accelerates and exacerbates colitis in ex-germ free mice – Christy A. Harrison, Mucosal Immunology

Animal microbiome

Comparison of Channel Catfish and Blue Catfish Gut Microbiota Assemblages Shows Minimal Effects of Host Genetics on Microbial Structure and Inferred Function – Jacob W. Bledsoe, Frontiers in Microbiology

Inter-individual variability in copepod microbiomes reveals bacterial networks linked to host physiology – Manoshi S. Datta, The ISME Journal

Metagenomics detection and characterisation of viruses in faecal samples from Australian wild birds – Jessy Vibin, Scientific Reports

Microorganism’s adaptation of Crucian carp may closely relate to its living environments – Huanxin Zhang, Microbiology Open

Diversity, specificity, co-occurrence and hub taxa of the bacterial–fungal pollen microbiome – Binoy Ambika Manirajan, FEMS Microbiology Ecology

Differential carbohydrate utilization and organic acid production by honey bee symbionts – Fredrick J Lee, FEMS Microbiology Ecology

Plant, root, and soil microbiome

The effect of periphyton on seed germination and seedling growth of rice (Oryza sativa) in paddy area – Haiying Lu, Science of The Total Environment

Diversity of Bacteria and the Characteristics of Actinobacteria Community Structure in Badain Jaran Desert and Tengger Desert of China – Ye Sun, Frontiers in Microbiology

Vancomycin and/or Multidrug-Resistant Citrobacter Freundii Altered the Metabolic Pattern of Soil Microbial Community – Mariusz Cycoń, Frontiers in Microbiology

Degradation of dibutyl phthalate in two contrasting agricultural soils and its long-term effects on soil microbial community – Jinjin Cheng, Science of The Total Environment

Impact of Bactrocera oleae on the fungal microbiota of ripe olive drupes – Ahmed Abdelfattah, bioRxiv

Potential of Finger Millet Indigenous Rhizobacterium Pseudomonas sp. MSSRFD41 in Blast Disease Management—Growth Promotion and Compatibility With the Resident Rhizomicrobiome – Jegan Sekar, Frontiers in Microbiology

Biochars from olive mill waste have contrasting effects on plants, fungi and phytoparasitic nematodes – Roberta Marra, Plos One

Water and extremophile microbiome 

Effects of Ice-Algal Aggregate Export on the Connectivity of Bacterial Communities in the Central Arctic Ocean – Josephine Z. Rapp, Frontiers in Microbiology

Built environment

The Airplane Cabin Microbiome – Howard Weiss, Microbial Ecology

Food microbiology

Sequencing of the Cheese Microbiome and Its Relevance to Industry – Bhagya. R. Yeluri Jonnala, Frontiers in Microbiology

Comparison of Bacterial Diversity Between Two Traditional Starters and the Round-Koji-Maker Starter for Traditional Cantonese Chi-Flavor Liquor Brewing – Jie Wang, Frontiers in Microbiology

Microbial ecology

Syntrophic growth with direct interspecies electron transfer between pili-free Geobacter species – Xing Liu, The ISME Journal

Uneven distribution of cobamide biosynthesis and dependence in bacteria predicted by comparative genomics – Amanda N Shelton, bioRxiv

Microbial Diversity and Nitrogen‐metabolizing Gene Abundance in Backyard Food Waste Composting Systems – T. C. Weglarz, Journal of Applied Microbiology

Enhancement of methanogenesis by electric syntrophy with biogenic iron‐sulfide minerals – Souichiro Kato, Microbiology Open

Probiotics/Prebiotics

Probiotics Ameliorate Stool Consistency in Patients with Chronic Constipation: A Randomized, Double-Blind, Placebo-Controlled Study – Jin Young Yoon, Digestive Diseases and Sciences

Supplementation of p40, a Lactobacillus rhamnosus GG-derived protein, in early life promotes epidermal growth factor receptor-dependent intestinal development and long-term health outcomes – Xi Shen, Mucosal Immunology

Bioinformatics

Detection of Multidimensional Co-Exclusion Patterns in Microbial Communities – Levent Albayrak, Bioinformatics

 

May 26, 2018

We have a big variety of topics covered in today’s posts, from built environment to bat microbiome to biolfilms!

Biofilms

Genomic identification of microbial species adhering to maxillofacial prostheses and susceptibility to different hygiene protocols – Juliana Barchelli, The Journal of Bioadhesion and Biofilm Research

Anti-biofilm effect of a butenolide/polymer coating and metatranscriptomic analyses – Wei Ding, The Journal of Bioadhesion and Biofilm Research

Microbial ecology

Keystone taxa as drivers of microbiome structure and functioning – Samiran Banerjee, Nature Reviews Microbiology

Diversity, Stability, and Reproducibility in Stochastically Assembled Microbial Ecosystems – Akshit Goya, Physical Review Letters

Pregnancy and early life

Iron supplementation has minor effects on gut microbiota composition in overweight and obese women in early pregnancy – Marloes Dekker Nitert, British Journal of Nutrition

Human respiratory microbiome

The concordance between upper and lower respiratory microbiota in children with Mycoplasma pneumoniae pneumonia – Wenkui Dai, Emerging Microbes & Infections

The lung microbiome in children with HIV-bronchiectasis: a cross-sectional pilot study – Refiloe Masekela, BMC Pulmonary Medicine

Human skin microbiome

Does Lindioil (Indirubin) treatment affect the composition of Malassezia species on psoriatic skin? – Y. K. Lin, British Journal of Dermatology

Shift in skin microbiota of Western European women across aging – Romain Jugé, Journal of Applied Microbiology

Human vaginal microbiome

Understanding mucosal and microbial functionality of the female reproductive tract by metaproteomics: Implications for HIV transmission – Alicia R. Berard, American Journal of Reproductive Immunology

Vaginal microbiome studies in pregnancy must also analyse host factors – S.S. Witkin, BJOG: An International Journal of Obstetrics & Gynaecology

Vaginal microbiome in early pregnancy and subsequent risk of spontaneous preterm birth: a case‐control study – Negar Tabatabaei, BJOG: An International Journal of Obstetrics & Gynaecology

Human gut microbiome

Structural Alteration of Gut Microbiota during the Amelioration of Human Type 2 Diabetes with Hyperlipidemia by Metformin and a Traditional Chinese Herbal Formula: a Multicenter, Randomized, Open Label Clinical Trial – Xiaolin Tong, mBio

The role of diet in the aetiopathogenesis of inflammatory bowel disease – Hamed Khalili, Nature Reviews Gastroenterology & Hepatology

Animal experiments

Ethanolamine enhances intestinal functions by altering gut microbiome and mucosal anti-stress capacity in weaned rats – Jian Zhou, British Journal of Nutrition

Helicobacter pylori-infected C57BL/6 mice with different gastrointestinal microbiota have contrasting gastric pathology, microbial and host immune responses – Zhongming Ge, Scientific Reports

Evaluation of the impact of glyphosate and its residues in feed on animal health – European Food Safety Authority (EFSA), EFSA Journal

Risks for animal health related to the presence of fumonisins, their modified forms and hidden forms in feed – EFSA Panel on Contaminants in the Food Chain (CONTAM), EFSA Journal

Plateau hypoxia attenuates the metabolic activity of intestinal flora to enhance the bioavailability of nifedipine – Juanhong Zhang, Drug Delivery

Animal microbiome

Fecal Microbiota Composition Changes after a Body Weight Loss Diet in Beagle Dogs – A Salas, Journal of Animal Sciences

The fecal bacterial microbiota of bats; Slovenia – Modest Vengust, PLOS One

Plant, root, and soil microbiome

Fertilization shapes a well-organized community of bacterial decomposers for accelerated paddy straw degradation – Yushan Zhan, Scientific Reports

Paddy-upland rotation for sustainable agriculture with regards to diverse soil microbial community – Ping-Fu Hou, Scientific Reports

Annual post‐market environmental monitoring report on the cultivation of genetically modified maize MON 810 in 2016 – European Food Safety Authority (EFSA), EFSA Journal

Conserved Responses in a War of Small Molecules between a Plant-Pathogenic Bacterium and Fungi – Joseph E. Spraker, mBio

Pseudomonads contribute to regulation of Pratylenchus penetrans (Nematoda) populations on apple – Tristan T. Watson, Canadian Journal of Microbiology

Water and extremophile microbiome

Taxon-specific aerosolization of bacteria and viruses in an experimental ocean-atmosphere mesocosm – Jennifer M. Michaud, Nature Communications

Combined genotyping, microbial diversity and metabolite profiling studies on farmed Mytilus spp. from Kiel Fjord – Caroline Utermann, Scientific Reports

Bathyarchaeota: globally distributed metabolic generalists in anoxic environments – Zhichao Zhou, FEMS Microbiology Reviews

Probiotics / prebiotics

Dietary fibers, prebiotics, and exopolysaccharides produced by lactic acid bacteria: potential health benefits with special regard to cholesterol-lowering effects – E. Korcz, Food and Function

Pharmacomicrobiomics: exploiting the drug-microbiota interactions in anticancer therapies – Concetta Panebianco, Microbiome

Built environment

City-scale distribution and dispersal routes of mycobiome in residences – Xinzhao Tong, Microbiome

Unraveling bacterial fingerprints of city subways from microbiome 16S gene profiles – Alejandro R. Walker, Biology Direct

Bioinformatics

ASaiM: a Galaxy-based framework to analyze microbiota data – Bérénice Batut, GigaScience

Comprehensive benchmarking and ensemble approaches for metagenomic classifiers – Alexa B. R. McIntyre, Genome Biology

Techniques

The Present and Future of Whole Genome Sequencing (WGS) and Whole Metagenome Sequencing (WMS) for Surveillance of Antimicrobial Resistant Microorganisms and Antimicrobial Resistance Genes across the Food Chain – Elena A. Oniciuc, Genes

A microbial endocrinology-based simulated small intestinal medium for the evaluation of neurochemical production by gut microbiota – Daniel N Villageliú, FEMS Microbiology Ecology

May 21, 2018

A long update to make up for the past few days, with extra emphasis on Plant/root/soil studies and water studies!

General microbiome

Why do microbes exhibit weak biogeographic patterns? – Kyle M. Meyer, ISME

Understanding and designing the strategies for the microbe-mediated remediation of environmental contaminants using omics approaches – Muneer A. Malla, Frontiers in Microbiology

Two-year microbial adaptation during hydrogen-mediated biogas upgrading process in a serial reactor configuration – L. Treu, Bioresource Technology

Microbial ecology

Grazer-induced transcriptomic and metabolomic response of the chain-forming diatom Skeletonema marinoi – Alberto Amato, ISME

Cooperation, competition and antibiotic resistance in bacterial colonies – Isabel Frost, ISME

Genome-resolved metagenomics identifies genetic mobility, metabolic interactions, and unexpected diversity in perchlorate-reducing communities – Tyler P. Barnum, ISME

Diversity and Hidden Host Specificity of Chytrids infecting Colonial Volvocacean Algae – Silke Van den Wyngaert, Journal of Eukaryotic Microbiology

Human bone microbiome

Understanding the microbiome of diabetic foot osteomyelitis: insights from molecular and microscopic approaches – Khalid Johani, Clinical Microbiology and Infection

Human oral microbiome

Bacterial-derived exopolysaccharides enhance antifungal drug tolerance in a cross-kingdom oral biofilm – Dongyeop Kim, ISME

Human vaginal microbiome

Metabolomics as a clinical testing method for the diagnosis of vaginal dysbiosis – Emiley Watson, American Journal of Reproductive Immunology

Human gut microbiome

Design and rationale of the INSYTE study: A randomised, placebo controlled study to test the efficacy of a synbiotic on liver fat, disease biomarkers and intestinal microbiota in non-alcoholic fatty liver disease – Eleonora Scorletti, Contemporary Clinical Trials

Gastrointestinal Disorders Associated with Primary Immunodeficiency Diseases – Stella Hartono, Clinical Reviews in Allergy & Immunology

Impact on the quality of life of an episode of Clostridium difficileinfection in a hospital setting – A. Duburcq, Journal of Epidemiology and Public Health

Animal experiments

Inhalational exposure to particulate matter air pollution alters the composition of the gut microbiome – Ece A. Mutlu, Environmental Pollution

Effects of long-term intake of a yogurt fermented with Lactobacillus delbrueckii subsp.bulgaricus 2038 and Streptococcus thermophilus1131 on mice – Yuki Usui, International Immunology

Dietary mung bean protein reduces high-fat diet-induced weight gain by modulating host bile acid metabolism in a gut microbiota-dependent manner – Akiho Nakatani, Biochemical and Biophysical Research Communications

Dietary nitrate modulates gut microbiota profile and prevents the activation of mucosal inflammatory pathways induced by broad-spectrum antibiotics – Bárbara S. Rocha, Free Radical Biology and Medicine

Animal microbiome

Coral bleaching from a single cell perspective – Daniel Aagren Nielsen, ISME

Plant, root, and soil microbiome

Lack of thinning effects over inter-annual changes in soil fungal community and diversity in a Mediterranean pine forest – Carles Castaño, Forest Ecology and Management

Response of soil microbial communities to agroecological versus conventional systems of extensive agriculture – Diego N. Chavarria, Agriculture, Ecosystems & Environment

Intraspecific variation in indirect plant–soil feedbacks influences a wetland plant invasion – Warwick J. Allen, Ecology

Native bacteria promote plant growth under drought stress condition without impacting the rhizomicrobiome – Elisabeth Armada, FEMS Microbiology Ecology

Plant roots redesign the rhizosphere to alter the three‐dimensional physical architecture and water dynamics – Sheikh M. F. Rabbi, New Phytologist

The Invasive Brazilian Pepper Tree (Schinus terebinthifolius) Is Colonized by a Root Microbiome Enriched With Alphaproteobacteria and Unclassified Spartobacteria – Karim Dawkins, Frontiers in Microbiology

Dynamics of Aspen Roots Colonization by Pseudomonads Reveals Strain-Specific and Mycorrhizal-Specific Patterns of Biofilm Formation – Marie-Francoise Noirot-Gros, Frontiers in Microbiology

The Emergence of Endophytic Microbes and Their Biological Promise – Gary Strobel, Journal of Fungi

Changes in soil nitrogen dynamics caused by prescribed fires in dense gorse lands in SW Pyrenees – Leire Múgica, Science of The Total Environment

Response of soil microbial communities to agroecological versus conventional systems of extensive agriculture – Diego N. Chavarria, Agriculture, Ecosystems & Environment

Application of biosolids drives the diversity of antibiotic resistance genes in soil and lettuce at harvest – Lu Yang, Soil Biology and Biochemistry

Mycorrhizal Status In Endemic Pipewort: Eriocaulon eurypeplon Körn (Fam: Eriocaulaceae) – Vishal R. Kamble, IOSR Journal of Pharmacy and Biological Sciences

Model formulation of microbial CO2production and efficiency can significantly influence short and long term soil C projections – Ford Ballantyne IV & Sharon A. Billings, ISME

Effect of endophytic fungus Piriformospora indica on yield and some physiological traits of millet (Panicum miliaceum) under water stress – Goudarz Ahmadvand, Crop and Pasture Science

Composition and functional genes analysis of bacterial communities from urban parks of Shanghai, China and their role in ecosystem functionality – Xin Wang, Landscape and Urban Planning

Plant, fungal, bacterial, and nitrogen interactions in the litter layer of a native Patagonian forest – Lucía Vivanco​, PeerJ

Root-exuded coumarin shapes the root microbiome – Derek S. Lundberg, PNAS

Deforestation decreases spatial turnover and alters the network interactions in soil bacterial communities – Jing Tian, Soil Biology and Biochemistry

Distinct nitrogen provisioning from organic amendments in soil as influenced by farming system and water regime – Martina Lori, Frontiers in Microbiology

Biodiversity of urban soils for sustainable cities – C. Guilland, Environmental Chemistry Letters

Predator–prey mass ratio drives microbial activity under dry conditions in Sphagnum peatlands – Monika K. Reczuga, Ecology and Evolution

Organic and Biofertilization on Crop Production in Semiarid Regions – Ayman M. Helmy, The Handbook of Environmental Chemistry

Prevalence of Botrytis cinerea at different phenological stages of table grapes grown in the northern region of South Africa – Patricia C. Carmichael, Scientia Horticulturae

Water and extremophile microbiome

Genomic evidence for intraspecific hybridization in a clonal and extremely halotolerant yeast – Cene Gostinčar, BMC Genomics

Interactive effects of multiple stressors revealed by sequencing total (DNA) and active (RNA) components of experimental sediment microbial communities – Simone C. Birrer, Science of The Total Environment

Physicochemical drivers of microbial community structure in sediments of Lake Hazen, Nunavut, Canada – Matti O. Ruuskanen, Frontiers in Microbiology

Strains of the toxic and bloom-forming Nodularia spumigena (cyanobacteria) can degrade methylphosphonate and release methane – Jonna E. Teikari, ISME

Seasonal resource conditions favor a summertime increase in North Pacific diatom–diazotroph associations – Christopher L. Follett, ISME

Predator and prey biodiversity relationship and its consequences on marine ecosystem functioning—interplay between nanoflagellates and bacterioplankton – Jinny Wu Yang, ISME

Light and temperature control the seasonal distribution of thaumarchaeota in the South Atlantic bight – Qian Liu, ISME

Distributions of phytoplankton carbohydrate, protein and lipid in the world oceans from satellite ocean colour – Shovonlal Roy, ISME

Relationship between dissolved organic matter quality and microbial community composition across polar glacial environments – H J Smith, FEMS Microbiology Ecology

Sediment depth-dependent spatial variations of bacterial communities in mud deposits of the eastern China marginal seas – Yanlu Qiao, Frontiers in Microbiology

Food microbiology

Origin and varietal based proteomic and peptidomic fingerprinting of Theobroma cacao in non-fermented and fermented cocoa beans – Neha Kumari, Food Research International

Metagenomic and metatranscriptomic analysis of the microbial community in Swiss-type Maasdam cheese during ripening – Ilhan Cem Duru, International Journal of Food Microbiology

Combined effect of cold atmospheric plasma, intrinsic and extrinsic factors on the microbial behavior in/on (food) model systems during storage – C. Smet, Innovative Food Science & Emerging Technologies

Polyphenols from selected dietary spices and medicinal herbs differentially affect common food-borne pathogenic bacteria and lactic acid bacteria – Chak-Lun Chan, Food Control

Probiotics

Enhanced viability of probiotics (Pediococcus pentosaceusLi05) by encapsulation in microgels doped with inorganic nanoparticles – Mingfei Yao, Food Hydrocolloids

Dysbiosis of microbiome and probiotic treatment in a genetic model of autism spectrum disorders – Tabouy Laure, Brain, Behavior, and Immunity

Bioinformatics

dbCAN2: a meta server for automated carbohydrate-active enzyme annotation – Han Zhang, Nucleic Acids Research

A Multi-Omics Database for Parasitic Nematodes and Trematodes – John Martin, Eukaryotic Genomic Databases

MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis – Jasmine Chong, Nucleic Acids Research

AAI-profiler: fast proteome-wide exploratory analysis reveals taxonomic identity, misclassification and contamination – Alan J Medlar, Nucleic Acids Research

Techniques

Mutant phenotypes for thousands of bacterial genes of unknown function – Morgan N. Price, Nature

Methods for Generating Microbial Cocultures that Grow in the Absence of Fixed Carbon or Nitrogen – Matthew J. Smith, Synthetic Biology

Development of a 16S rRNA-targeted fluorescence in situ hybridization probe for quantification of the ammonia-oxidizer Nitrosotalea devanaterra and its relatives – C.X. Restrepo-Ortiz, Systematic and Applied Microbiology

Creation of a fibre categories database to quantify different dietary fibres – Stacey Fuller, Journal of Food Composition and Analysis

May 13, 2018

 

Today’s post is short but interesting: a study on Green tea consumption’s affect on the microbiome, a review on skin allergies, and another review on the saliva and its affects on the oral microbiome.

Multi-site human microbiome

Invasive candidiasis – Peter G. Pappas, Nature Reviews

Green tea liquid consumption alters the human intestinal and oral microbiome – Xiaojie Yuan, Molecular Nutrition and Food Research

Human skin microbiome

The ins and outs of an ‘outside-in’ view of allergies: atopic dermatitis and allergy prevention – Marcus Shaker, Current Opinion in Pediatrics

Human gut microbiome

Effects of synbiotics on ileal microbiota – Shunichiro Komatsu, Indian Journal of Medical Research

Microbial and metabolic multi‐omic correlations in systemic sclerosis patients – Chiara Bellocchi, Annals of the New York Academy of Sciences

Fecal Clostridiales distribution and short‐chain fatty acids reflect bowel habits in irritable bowel syndrome – Giorgio Gargari, Environmental Microbiology

Gut microbial diversity is associated with lower arterial stiffness in women – Cristina Menni, European Heart Journal

Human oral microbiome

Saliva in the “Omics” era: a promising tool in Paediatrics – Eftychia Pappa, Oral Diseases

Animal experiments

High turnover of faecal microbiome from algal feedstock experimental manipulations in the Pacific oyster (Crassostrea gigas) – Ariel Levi Simons, Microbial Biotechnology

Effects of moderate, voluntary ethanol consumption on the rat and human gut microbiome – Kassi L. Kosnicki, Addiction Biology

Fecal microbiome of periparturient dairy cattle and associations with the onset of Salmonella shedding – Lohendy Muñoz-Vargas, Plos One

Procyanidin B2 protects against d-galactose-induced mimetic aging in mice: Metabolites and microbiome analysis – Ying Xiao, Food and Chemical Toxicology

Plant, root, and soil microbiome

Remediation of saline soils contaminated with crude oil using the halophyte Salicornia persica in conjunction with hydrocarbon-degrading bacteria – Ali Ebadi, Journal of Environmental Management

Impact of transgenic Cry1Ac + CpTI cotton on diversity and dynamics of rhizosphere bacterial community of different root environments – Peng Li, Science of The Total Environment

Potential use of high-throughput sequencing of soil microbial communities for estimating the adverse effects of continuous cropping on ramie (Boehmeria nivea L. Gaud) – Siyuan Zhu, Plos One

Microbes in space

Furnishing spaceship environment: evaluation of bacterial biofilms on different materials used inside International Space Station – Elena Perrin, Research in Microbiology

Food microbiology

Diversity and fate of spore forming bacteria in cocoa powder, milk powder, starch and sugar during processing: A review – Ana Paula Maciel Pereira, Trends in Food Science & Technology

Techniques

Development of a 16S rRNA-targeted fluorescence in situhybridization probe for quantification of the ammonia-oxidizer Nitrosotalea devanaterra and its relatives – C.X. Restrepo-Ortiz, Systematic and Applied Microbiology

 

March 11, 2018

Events and jobs

EVEN seminar: Weakest link in water quality control: Drinking water biofilm in premise plumbing – INSTAAR, CU Boulder

General microbiome

Multiscale Evolutionary Dynamics of Host-Associated Microbiomes – Aura Ferreiro, Cell

Egalitarianism in Biofilms – Dawen Gao, Microbial Ecology

Acclimation of Culturable Bacterial Communities under the Stresses of Different Organic Compounds – Hui Wang, Frontiers in Microbiology

Human multi-site microbiome

The Mycobiome: A Neglected Component in the Microbiota-Gut-Brain Axis – Raphaël Enaud, Microorganisms

Human gut microbiome

Gut Microbiota Alteration After Long-Term Consumption of Probiotics in the Elderly – Renyuan Gao, Probiotics and Antimicrobial Proteins

Sex differences in gut microbiota in patients with major depressive disorder – Chen JJ, Neuropsychiatric Disease and Treatment

Oral microbiome

Influence of periodontal treatment on subgingival and salivary microbiotas – Daniel Belstrøm, Journal of Periodontology

Microbiome at sites of gingival recession in children with Hutchinson–Gilford progeria syndrome – Seyed Hossein Bassir, Journal of Periodontology

Subgingival microbial profile of obese women with periodontal disease – Carina M. Silva-Boghossian, Journal of Periodontology

Animal experiments

The effect of probiotics and polysaccharides on the gut microbiota composition and function of weaned rats – Mengxia Wang, Food and Function

Cecal Versus Fecal Microbiota in Ossabaw Swine and Implications for Obesity – Matthew R Panasevich, Physiological Genomics

Antibiotics-induced modulation of large intestinal microbiota altered aromatic amino acid profile and expression of neurotransmitters in the hypothalamus of piglets – Kan Gao, Journal of Neurochemistry

Animal microbiome

Nutrient factories: Metabolic function of beneficial microorganisms associated with insects – Nana Y. D. Ankrah, Environmental Microbiology

Community composition, diversity, and metabolism of intestinal microbiota in cultivated European eel (Anguilla anguilla) – Wei Huang, Applied Microbiology and Biotechnology

Environmental and Host Effects on Skin Bacterial Community Composition in Panamanian Frogs – Brandon J. Varela, Frontiers in Microbiology

Influence of Novel Highly Pathogenic Avian Influenza A (H5N1) Virus Infection on Migrating Whooper Swans Fecal Microbiota – Na Zhao, Frontiers in Cellular and Infectious Microbiology

Plant, root, and soil microbiome

The Soil-Borne Legacy – Peter A.H.M. Bakker, Cell

Water and extremophile microbiome

Haloarchaea from the Andean Puna: Biological Role in the Energy Metabolism of Arsenic – Omar Federico Ordoñez, Microbial Ecology

Occurrence of Legionella in Nonpotable Reclaimed Water – William J. Johnson, American Water Works Association

Water Bacterial and Fungal Community Compositions Associated with Urban Lakes, Xi’an, China – Haihan Zhang, International Journal of Environmental Research and Public Health

Food microbiome

Microbial community and physicochemical dynamics during the production of ‘Chicha’, a traditional beverage of Indigenous people of Brazil – Ludmila Vilela Resende, World Journal of Microbiology and Biotechnology

Techniques

Primer selection impacts specific population abundances but not community dynamics in a monthly time-series 16S rRNA gene amplicon analysis of coastal marine bacterioplankton – Emma K. Wear, Environmental Microbiology

Microbes in the news

Pitting Viruses Against Bacteria To Combat The Antibiotic Crisis – SciFri

March 4, 2018

Events and jobs

Phd position in antimicrobial resistance development in biofilm communities – University of Leuven

Professor in Microbiome/Microbiota-Host Interactions – University of Alabama

Microbiology Lab Scientist – Lyneer Staffing

General microbiome

Impact of Brazilian microbiome for boosting agriculture, animal husbandry and human being: a book review – Arthur Prudêncio de Araujo Pereira, Journal of Cleaner Production

Are animals a source of Stenotrophomonas maltophiliain human infections? Contributions of a nationwide molecular study – Aurélie Jayol, European Journal of Clinical Microbiology & Infectious Diseases

The organization of bacterial genomes: Towards understanding the interplay between structure and function – Daan J.W. Brocken, Current Opinion in Systems Biology

Pregnancy and early life

Selective maternal seeding and environment shape the human gut microbiome – Katri Korpela, Genome Research

Ecological Shifts of Supragingival Microbiota in Association with Pregnancy – Wenzhen Lin, Frontiers in Cellular and Infectious Microbiology

Human respiratory microbiome

Impaired diversity of the lung microbiome predicts progression of idiopathic pulmonary fibrosis – Youhei Takahashi, Respiratory Research

Human gut microbiome

Methanogens in humans: potentially beneficial or harmful for health – Prem Prashant Chaudhary, Applied Microbiology and Biotechnology

Gut microbiota alterations and dietary modulation in childhood malnutrition – The role of short chain fatty acids – Ceyda Tugba Pekmez, Clinical Nutrition

Differential human gut microbiome assemblages during soil-transmitted helminth infections in Indonesia and Liberia – Bruce A. Rosa, Microbiome

Market Integration Predicts Human Gut Microbiome Attributes across a Gradient of Economic Development – Keaton Stagaman, mSystems

A Review of Microbiota and Irritable Bowel Syndrome: Future in Therapies – Bruno K. Rodiño-Janeiro, Advances in Therapy

Characterizing the metabolic phenotype of intestinal villus blunting in Zambian children with severe acute malnutrition and persistent diarrhea – Marta Farràs, PLOS one

Animal experiments

Differences in gut microbiota composition in finishing Landrace pigs with low and high feed conversion ratios – Zhen Tan, Antonie van Leeuwenhoek

Human milk oligosaccharides protect against the development of autoimmune diabetes in NOD-mice – Ling Xiao, Scientific Reports

TRIM31 Deficiency Is Associated with Impaired Glucose Metabolism and Disrupted Gut Microbiota in Mice – Jing Cheng, Frontiers in Physiology

Animal microbiome

Quantitative prediction of shrimp disease incidence via the profiles of gut eukaryotic microbiota – Jinbo Xiong, Applied Microbiology and Biotechnology

Bioturbation activity of three macrofaunal species and the presence of meiofauna affect the abundance and composition of benthic bacterial communities – Élise Lacoste, Marine Environmental Research

Spatial Organization of the Gastrointestinal Microbiota in Urban Canada Geese – Sergei V. Drovetski, Scientific Reports

Skin microbiomes of California terrestrial salamanders are influenced by habitat more than host phylogeny – Alicia K. Bird, Frontiers in Microbiology

Plant, root, and soil microbiome

Recent Insights on Biological and Ecological Aspects of Ectomycorrhizal Fungi and Their Interactions – Antonietta Mello, Frontiers in Microbiology

Micro-decomposer communities and decomposition processes in tropical lowlands as affected by land use and litter type – Valentyna Krashevska, Oecologia

One-time phosphate fertilizer application to grassland columns modifies the soil microbiota and limits its role in ecosystem services – Israel Ikoyi, Science of The Total Environment

Size-Controlled Production of Gold Bionanoparticles Using the Extremely Acidophilic Fe(III)-Reducing Bacterium, Acidocella aromatica – Intan Nurul Rizki, Minerals

Nematicidal protease genes screened from a soil metagenomic library to control Radopholus similismediated by Pseudomonas fluorescens pf36 – Deqiang Chen, Applied Microbiology and Biotechnology

The structural and functional contributions of β-glucosidase-producing microbial communities to cellulose degradation in composting – Xiangyun Zang, Biotechnology for Biofuels

Diversity and contributions to nitrogen cycling and carbon fixation of soil salinity shaped microbial communities in Tarim Basin – Min Ren, Frontiers in Microbiology

Decomposer food web in a deciduous forest shows high share of generalist microorganisms and importance of microbial biomass recycling – Ruben López-Mondéjar, The ISME Journal

Soil bacterial community shifts driven by restoration time and steppe types in the degraded steppe of Inner Mongolia – Minjie Yao, CATENA

One-time phosphate fertilizer application to grassland columns modifies the soil microbiota and limits its role in ecosystem services – Israel Ikoyi, Science of The Total Environment

Enumeration of Culturable Endophytic Bacterial Population of Different Lycopersicum esculentum L. Varieties – Monika Singh, International Journal of Current Microbiology and Applied Sciences

Isolation and Characterization of Methanol Utilizing Microorganisms from Leguminous Crops – Umang Ahlawat, International Journal of Current Microbiology and Applied Sciences

Isolation of Mercury-Resistant Fungi from Mercury-Contaminated Agricultural Soil – Reginawanti Hindersah, Agriculture

Root-associated fungi shared between arbuscular mycorrhizal and ectomycorrhizal conifers in a temperate forest – Hirokazu Toju, Frontiers in Microbiology

Antagonistic Potential and Molecular Characterization of Trichoderma spp. against Rhizoctonia solani Infecting Ghost Pepper in Manipur, India – Khedarani Koijam, International Journal of Current Microbiology and Applied Sciences

Isolation of Biocontrol (Bacterial) Agents from Chickpea (Cicer arietinum linnaeus) – S. Vijaya Kumar, International Journal of Current Microbiology and Applied Sciences

Potentiality of Native Pseudomonas spp. in Promoting Sugarcane Seedling Growth and Red Rot (Colletotrichum falcatum went) Management – P. Kishore Varma, International Journal of Current Microbiology and Applied Sciences

Interactions between isolates of the fungus Beauveria bassiana and Zea mays – Aimee McKinnon, Lincoln University (thesis)

Metagenome Sequencing of Prokaryotic Microbiota from Two Hypersaline Soils of the Odiel Salt Marshes in Huelva, Southwestern Spain – Blanca Vera-Gargallo, Genome Anouncements

Degradation shaped bacterial and archaeal communities with predictable taxa and their association patterns in Zoige wetland at Tibet plateau – Yunfu Gu, Scientific Reports

Water and extremophile microbiome

Survival of Listeria monocytogenes and Staphylococcus aureus in Synthetic Brines. Studying the Effects of Salt, Temperature and Sugar through the Approach of the Design of Experiments – Antonio Bevilacqua, Frontiers in Microbiology

Saccharolobus caldissimus gen. nov., sp. nov., a facultatively anaerobic iron-reducing hyperthermophilic archaeon isolated from an acidic terrestrial hot spring, and reclassification of Sulfolobus solfataricus as Saccharolobus solfataricus comb. nov. and Sulfolobus shibatae as Saccharolobus shibatae comb. nov. – Hiroyuki D. Sakai,  International Journal of Systematic and Evolutionary Microbiology

Distinct Osmoadaptation Strategies in the Strict Halophilic and Halotolerant Bacteria Isolated from Lunsu Salt Water Body of North West Himalayas – Shivani Vaidya, Current Microbiology

Archaeal Viruses from High-Temperature Environments – Jacob H. Munson-McGee, Genes

Strategies of adaptation of microorganisms of the three domains of life to high salt concentrations – Nina Gunde-Cimerman, FEMS Microbiology Reviews

Tertiary treatment and dual disinfection to improve microbial quality of reclaimed water for potable and non-potable reuse: A case study of facilities in North Carolina – Emily S. Bailey, Science of The Total Environment

The Early Earth Geochemical and Isotope Record of Serpentinizing Environments from Archean Stichtite (Mg6Cr2(OH)16[CO3] · 4H2O) – Erik B. Melchiorre, Precambrian Research

Process performance and population dynamics of ammonium tolerant microorganisms during co-digestion of fish waste and manure – Linn Solli, Renewable Energy

Toxicity assessment of pharmaceutical compounds on mixed culture from activated sludge using respirometric technique: The role of microbial community structure – I.A. Vasiliadou, Science of The Total Environment

Divergent assemblage patterns of abundant and rare microbial sub-communities in response to inorganic carbon stresses in a simultaneous anammox and denitrification (SAD) system – Duntao Shu, Bioresource Technology

Pretreatment of saline antibiotic wastewater using marine microalga – Xueqing Shi, Bioresource Technology

Bioinformatics

Handling gene and protein names in the age of bioinformatics: the special challenge of secreted multimodular bacterial enzymes such as the cbhA/cbh9Agene of Clostridium thermocellum – Wolfgang H. Schwarz, World Journal of Microbiology and Biotechnology

Techniques

Optimization of fecal sample processing for microbiome study — The journey from bathroom to bench – Wei-Kai Wu, Journal of the Formosan Medical Association

The Application of Omics Data to the Development of AOPs – Mary T. McBride, A Systems Biology Approach to Advancing Adverse Outcome Pathways for Risk Assessment

From correlation to causation: analysis of metabolomics data using systems biology approaches – Antonio Rosato, Metabolomics

Application of ensemble deep neural network to metabolomics studies – Taiga Asakura, Analytica Chimica Acta

Genome-reconstruction for eukaryotes from complex natural microbial communities – Patrick T West, Genome Research

Microbes in the news

Magnetic bacteria cause a stir – Christian Harding, Chemistry World

Federal Panel Passes Antibiotic-Resistant Bacteria Resolutions – Troy Brown, MedScape

Dangerous bacteria found in raw milk from Pennsylvania dairy – Coral Beach, Food Safety Network