May 25, 2018

Microbes and climate change, molecules from the microbiota and the gut-brain axis, C. albicans respiration changes lead to differences in macrophage recognition.

Animal experiments

The Gut Microbiota Mediates the Anti-Seizure Effects of the Ketogenic Diet – Christine A Olson – Cell

Microbial signals drive pre-leukaemic myeloproliferation in a Tet2-deficient host – Marlies Meisel – Nature

Pre-print: Temporal changes in gut microbiota and signaling molecules of the gut-brain axis in mice fed meat protein diets – Yunting Jie – bioRxiv

Water and extremophile microbiome

Detection and Genetic Characterization of Bacteria of the Genus Pseudomonas from Microbial Communities of Lake Baikal – N L Bel’kova – Russian Journal of Genetics

More microbes

Review: Microbial Function on Climate Change – A Review – Endeshaw Abatenh – Environment Pollution and Climate Change

Pre-print: Inhibition of classical and alternative modes of respiration in C. albicans leads to cell wall remodelling and increased macrophage recognition – Lucian Duvenage – bioRxiv

Microbes in the news

How gut microbes are joining the fight against cancer – Giorgia Guglielmi – Nature

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May 24, 2018

Pest gut microbiota indirectly effects plant defenses in corn, evolution of microbial social behavior from shearing in flow environments, a model to predict cytokine responses based on multi-comics data integration.

General microbiome

Shearing in flow environment promotes evolution of social behavior in microbial populations – Gurdip Uppal – eLIFE

Pregnancy and early life

Review: The Neonatal Microbiome and Its Partial Role in Mediating the Association between Birth by Cesarean Section and Adverse Pediatric Outcomes – D Montoya-Williams – Neonatology

Human respiratory microbiome

Chronic rhinosinusitis with nasal polyps is characterized by dysbacteriosis of the nasal microbiota – Thanit Chalermwatanachai – Scientific Reports

Human oral microbiome

Metagenomic study of bacterial microbiota in persistent endodontic infections using Next‐generation sequencing – G Sánchez-Sanhueza – International Endodontic Journal

Human gut microbiome

Iron Sequestration in Microbiota Biofilms As A Novel Strategy for Treating Inflammatory Bowel Disease – Jean-Paul Motta – Inflammatory Bowel Diseases

Temporal and long‐term gut microbiota variation in allergic disease: A prospective study from infancy to school age – Kotryna Simonyté Sjödin – European Journal of Allergy and Clinical Immunology

Bangladeshi children with acute diarrhea show fecal microbiomes with increased Streptococcus abundance, irrespective of diarrhea etiology – Silas Kieser – Environmental Microbiology

Animal experiments

Effects of a protease and essential oils on growth performance, blood cell profiles, nutrient retention, ileal microbiota, excreta gas emission, and breast meat quality in broiler chicks – J H Park – Poultry Science

Colonic Inhibition of Phosphatase and Tensin Homolog Increases Colitogenic Bacteria, Causing Development of Colitis in Il10-/- Mice – Jonathon Mitchell – Inflammatory Bowel Diseases

Review: Microbial Signatures as a Predictive Tool in IBD—Pearls and Pitfalls – Nadine Waldschmitt – Inflammatory Bowel Diseases

Oral hydroxysafflor yellow A reduces obesity in mice by modulating the gut microbiota and serum metabolism – Juan Liu – Pharmacological Research

Impact of commensal flora on periodontal immune response to lipopolysaccharide – Daiki Fukuhara – Journal of Periodontology

Animal microbiome

Poor feed efficiency in sheep is associated with several structural abnormalities in the community metabolic network of their ruminal microbes – Rocky D Patil – Journal of Animal Science

Plant, root, and soil microbiome

Cadmium phytoextraction potential of king grass (Pennisetum sinese Roxb.) and responses of rhizosphere bacterial communities to a cadmium pollution gradient – Li Hu – Environmental Science and Pollution Research

Gut-Associated Bacteria of Helicoverpa zea Indirectly Trigger Plant Defenses in Maize – Jie Wang – Journal of Chemical Ecology

Water and extremophile microbiome

Microbial activity during a coastal phytoplankton bloom on the Western Antarctic Peninsula in late summer – María E Alcamán-Arias – FEMS Microbiology Letters

Effects of partially saturated conditions on the metabolically active microbiome and on nitrogen removal in vertical subsurface flow constructed wetlands – Catiane Pelissari – Water Research

Pre-print: Diversity and community structure of marine microbes around the Benham Rise underwater plateau, northeastern Philippines – Andrian P Gajigan – PeerJ

Food microbiology

Porous Silicon-Based Biosensors: Towards Real-Time Optical Detection of Target Bacteria in the Food Industry – Naama Massad-Ivanir – Scientific Reports

Probiotics/prebiotics

Survival of Planktonic and Sessile Cells of Lactobacillus rhamnosus and Lactobacillus reuteri upon Exposure to Simulated Fasting-State Gastrointestinal Conditions – Kyle B Klopper – Probiotics and Antimicrobial Proteins

Phages and viruses

Pre-print: A novel oceanic uncultured temperate cyanophage lineage – José Flores-Uribe – bioRxiv

Bioinformatics

Integration of multi-omics data and deep phenotyping enables prediction of cytokine responses – Olivier B Bakker – Nature Immunology

More microbes

Pre-print: New sequential touch method for determining bacterial contact transfer rate from finger to surface – Pengcheng Zhao – bioRxiv

Amy’s non-microbiology picks

Restoration of paper artworks with microemulsions confined in hydrogels for safe and efficient removal of adhesive tapes – Nicole Bonelli – PNAS

May 17, 2018

Genome engineering tools for non-model prokaryotes, microgravity and space radiation’s effects on microbes, an analysis of science podcasts.

General microbiome

Taking the technical microbiome into the next decade – Jo De Vrieze – Environmental Microbiology

Pre-print: Links between environment, diet, and the hunter-gatherer microbiome – Gabriela K Fragiadakis – bioRxiv

Human vaginal microbiome

The effect of vaginal microbial communities on colonization by Staphylococcus aureus with the gene for toxic shock syndrome toxin 1 (TSST-1): a case–control study – Jacob D Pierson – FEMS Pathogens and Disease

Human urinary microbiome

Lactobacillus and Urine Microbiome in Association with Urinary Tract Infections and Bacterial Vaginosis – Jun-Mo Kim – Urogenital Tract Infection

Human gut microbiome

Combination Antibiotics Improves Disease Activity and Alters Microbial Communities In Children with Ulcerative Colitis – Kattayoun Kordy – Journal of Pediatric Gastroenterology and Nutrition

Animal experiments

Postnatal colonization with human “infant-type” Bifidobacterium species alters behavior of adult gnotobiotic mice – Berkley Luk – PLOS ONE

A gene catalogue of the Sprague-Dawley rat gut metagenome – Hudan Pan – Gigascience

Animal microbiome

Changes in intestinal microbiota of Bufo gargarizans and its association with body weight during metamorphosis – Lihong Chai – Archives of Microbiology

Metagenomic analysis of Varroa-free Australian honey bees (Apis mellifera) shows a diverse Picornavirales virome – John M K Roberts – Journal of General Virology

Plant, root, and soil microbiome

Strong associations between plant genotypes and bacterial communities in a natural salt marsh – Gregory P Zogg – Ecology and Evolution

What Is the Role of Archaea in Plants? New Insights from the Vegetation of Alpine Bogs – Julian Taffner – mSphere

Rhizosphere hydrophobicity limits root water uptake after drying and subsequent rewetting – Mohsen Zarebanadkouki – Plant and Soil

Crop rotational diversity increases disease suppressive capacity of soil microbiomes – Ariane L Peralta – Ecosphere

Water and extremophile microbiome

A thiotrophic microbial community in an acidic brine lake in Northern Chile – Lorena Escudero – Antonie van Leeuwenhoek

Codon usage bias reveals genomic adaptations to environmental conditions in an acidophilic consortium – Andrew Hart – PLOS ONE

Microbes in space

Review: Effect of microgravity & space radiation on microbes – Giuliana Senatore – Future Microbiology

Food microbiology

Bacterial community analysis in three types of the fermented seafood, jeotgal, produced in South Korea – Eun-Ji Song – Bioscience, Biotechnology, and Biochemistry

Metabolomics

Transcriptomic and metabolomic analyses reveal that bacteria promote plant defense during infection of soybean cyst nematode in soybean – Wenshu Kang – BMC Plant Biology

Techniques

Review: Building a genome engineering toolbox in non‐model prokaryotic microbes – Emily Freed – Biotechnology and Bioengineering

Pre-print: Effective soil extraction method for cultivating previously uncultured soil bacteria – Tuan Manh Nguyen – bioRxiv

More microbes

Disentangling complex parasite interactions: Protection against cerebral malaria by one helminth species is jeopardized by co-infection with another – Jessica L Abbate – PLOS Neglected Tropical Diseases

Pre-print: Nanotube-mediated cross-feeding couples the metabolism of interacting bacterial cells – Shraddha Shitut – bioRxiv

Science, career, and publishing

Pre-print: Science podcasts: analysis of global production and output from 2004 to 2018 – Lewis E MacKenzie – bioRxiv

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