August 2, 2017

Enjoy your new  Microbiome Digest with some hot news on this very hot day. Methane- eating microbes found in lake deep beneath Antarctic ice sheet, while some some unexpected life was also found at the bottom of high Arctic Lakes.

 

Human respiratory microbiome
Distal airway microbiome is associated with immunoregulatory myeloid cell responses in lung transplant recipients – Nirmal S. Sharma – The Journal of Heart and Lung Transplatation
Human oral microbiome

 
The oral microbiota in patients with pancreatic cancer, patients with IPMNs, and controls: a pilot study – Sara H. Olson – Cancer Causes & Control

 
Metabolic Fingerprints from the Human Oral Microbiome Reveal a Vast Knowledge Gap of Secreted Small Peptidic Molecules – Anna Edlund –  mSystems
Prevalence of periodontal pathogens among italian patients with chronic periodontitis: a retrospective study on 2992 patients – L. Tettamanti- Oral & Implantology

 

 

Human gut microbiome

 
Metabolites and microbial composition of stool of women with fecal incontinence: Study design and methods – Lily A. Arya – Neurology Urodynamics

 
Microscopic Colitis After Fecal Microbiota Transplant – Matthew J. Fasullo – ACG Case Reports Journal
Alteration in the gastric microbiota and its restoration by probiotics in patients with functional dyspepsia – Muneki Igarashi  – BMJ Open Gastroenterology

 
Aggravation of collagen-induced arthritis by orally administered Porphyromonas gingivalis through modulation of the gut microbiota and gut immune system – Keisuke Sato – Scientific Reports

 
The gut microbiota, a new cardiovascular risk factor? – Caroline Chong-Nguyen – La Presse Médicale

 
The Association between Cardiorespiratory Fitness and Gut Microbiota Composition in Premenopausal Women – Yifan Yang – Nutrients

 
Gut microbiota metabolites for sweetening type I diabetes – Thamer Aljtaily – Cellular & Molecular Immunology

 
Vasopressin deletion is associated with sex-specific shifts in the gut microbiome – Christopher T. Fields – Gut Microbes

 
Stable engraftment of human microbiota into mice with a single oral gavage following antibiotic conditioning –  Christopher Staley – Microbiome

 
Animal microbiome 

 
Temporal dynamics of in-situ fiber-adherent bacterial community under ruminal acidotic conditions determined by 16S rRNA gene profiling – Renee M. Petri – PLOS One

 
Plant, root, and soil microbiome

 
Activity, biomass and composition of microbial communities and their degradation pathways in exposed propazine soil – C. Jiang  – Ecotoxicology and Environmental Safety

 
Response of microbial community and catabolic genes to simulated petroleum hydrocarbon spills in soils/sediments from different geographic locations– Qinglong Liu – Journal of Applied Microbiology

 
Primary productivity as a control over soil microbial diversity along environmental gradients in a polar desert ecosystem – Kevin M. Geyer – PeerJ

 
Steering Soil Microbiomes to Suppress Aboveground Insect Pests – Ana Pineda –  Trends in Plant Science

 
Importance of exposure dynamics of metal-based nano-ZnO, -Cu and -Pb governing the metabolic potential of soil bacterial communities  – Yujia Zhai – Ecotoxicology and Environmental Safety

 
Water and extremophile microbiome 

 
Production and degradation of fluorescent dissolved organic matter derived from bacteria –  Ken Arai – Journal of Oceanography

 
Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition – Adriana Alberti – Scientific Data
Watershed Urbanization Linked to Differences in Stream Bacterial Community Composition – Jacob D. Hosen – Frontiers in Microbiology

 
Influence of Igneous Basement on Deep Sediment Microbial Diversity on the Eastern Juan de Fuca Ridge Flank – Jessica M. Labonté – Frontiers in Microbiology

 
Coordinated regulation of growth, activity and transcription in natural populations of the unicellular nitrogen-fixing cyanobacterium Crocosphaera – Samuel T. Wilson – Nature Microbiology

 
The global biogeography of amino acid variants within a single SAR11 population is governed by natural selection – Tom O. Delmont – bioRxiv

 

Food microbiology

 
Microorganisms in Fermented Apple Beverages: Current Knowledge and Future Directions – Fabien J. Cousin – Microorganisms

 
Probiotics / prebiotics

 
Next-generation probiotics targeting Clostridium difficile through precursor-directed antimicrobial biosynthesis – Jennifer K. Spinler – Infection and Immunity

 
Biotechnology
Forum: Genetically Engineered Bacteria for Treating Human Disease – Buyun Ma – Trends in Pharmacological Sciences

 

Microbes in news

 

Methane-eating microbes found beneath Antarctica’s melting ice sheets

Unexpected Life Found at the Bottom of High Arctic Lakes

Tracking microbial succession in petroleum wells

July 16, 2017

Events and jobs
Postdoctoral Fellow – Astrobiology – University of Florida

Microbiology Laboratory Manager – Cranleigh Scientific, Northamptonshire, England

Human respiratory microbiome
Review: Microbiome in chronic obstructive pulmonary disease – Eduard Monso – Annals of Translational Medicine

Monitoring clinical and microbiological evolution of a cystic fibrosis patient over 26 years: experience of a Brazilian CF Centre – Cassiana da Costa Ferreira Leite – BMC Pulmonary Medicine

Distal airway microbiome is associated with immunoregulatory myeloid cell responses in lung transplant recipients – Nirmal S. Sharma – The Journal of Heart and Lung Transplantation

Human oral microbiome
Diabetes Enhances IL-17 Expression and Alters the Oral Microbiome to Increase Its Pathogenicity – E. Xiao – Cell Host and Microbe

Microbiome of peri-implantitis affected and healthy dental sites in patients with a history of chronic periodontitis – Danae Apatzidou – Archives of Oral Biology

Human gut microbiome
Review: Gut–CNS-Axis as Possibility to Modulate Inflammatory Disease Activity—Implications for Multiple Sclerosis – Ann-Katrin Fleck – International Journal of Molecular Sciences

Determination of certain bacterial groups in gut microbiota and endotoxin levels in patients with nonalcoholic steatohepatitis – Ceren Özkul – The Turkish Journal of Gastroenterology

Animal experiments
Meat and bone meal as partial replacement of fishmeal in diets for gilthead sea bream (Sparus aurata) juveniles: Diets digestibility, digestive function, and microbiota modulation – Sara Moutinho – Aquaculture

Arachidonic acid sex-dependently affects obesity through linking gut microbiota-driven inflammation to hypothalamus-adipose-liver axis – Pan Zhuang – Biochimica et Biophysica Acta (BBA) – Molecular Basis of Disease

Disparity in the nasopharyngeal microbiota between healthy cattle on feed, at entry processing and with respiratory disease – Mohamed Zeineldin – Veterinary Microbiology

Animal microbiome
Effects of chromium(III) on enzyme activities and bacterial communities during swine manure composting – Yanan Yin – Bioresource Technology

Antimicrobial Activity of Actinobacteria Isolated From the Guts of Subterranean Termites – R. A. Arango – Environmental Entomology

Oral Disease and Microbiota in Free-roaming cats – Ana Whyte – Topics in Companion Animal Medicine

Plant, root, and soil microbiome
Investigating the durable effect of the hot water treatment used in nurseries on pathogenic fungi inhabiting grapevine wood and involved in Grapevine Trunk Diseases – Emilie Bruez – Crop Protection

Understanding the mycobiota of maize from the highlands of Guatemala, and implications for maize quality and safety – José Rodrigo Mendoza – Crop Protection

The uniqueness and biogeochemical cycling of plant root microbial communities in a floating treatment wetland – Hidetoshi Urakawa – Ecological Engineering

Water and extremophile microbiome
The Other Microeukaryotes of the Coral Reef Microbiome – T.D. Ainsworth – Trends in Microbiology

Taxonomic and functional diversity of a coastal planktonic bacterial community in a river-influenced marine area – Stefan Thiele – Marine Genomics

Built environment
Stimulation effect of electric current density (ECD) on microbial community of a three dimensional particle electrode coupled with biological aerated filter reactor (TDE-BAF) – Yan Feng – BioResource Technology

Food microbiology
Review: Bacteriocin-Antimicrobial Synergy: A Medical and Food Perspective – Harsh Mathur – Frontiers in Microbiology

Review: Low FODMAP Diet in the Treatment of Irritable Bowel Syndrome: A Systematic Review and Meta-Analysis – Dania Schumann – Nutrition

Macrophages treated with non-digestible polysaccharides reveal a transcriptionally unique phenotype – Yongfu Tang – Journal of Functional Foods

Microbial Ecology
Interplay between antibiotic efficacy and drug-induced lysis underlie enhanced biofilm formation at subinhibitory drug concentrations – Wen Yu – bioRxiv

A phylogenetic and evolutionary analysis of antimycin biosynthesis – Rebecca Joynt – bioRxiv

Probiotics / prebiotics
Review: Prenatal and postnatal administration of prebiotics and probiotics – Kristin Sohn – Seminars in Fetal and Neonatal Medicine

Techniques
Phototrophic microorganisms in the symbiotic communities of Baikal sponges: Diversity of psbA gene (encoding D1 protein of photosystem II) sequences – OV Kaluzhnaya – Mol Biol (Mosk)
Unfortunately, this article is in Russian and I cannot access the original. The abstract was interesting though, the goal of the study is to determine whether psbA sequences can be used as a marker for phototrophic organisms.

New sequences
Noncontiguous finished genome sequences and description of Bacillus massiliglaciei, Bacillus mediterraneensis, Bacillus massilinigeriensis, Bacillus phocaeensis and Bacillus tuaregi, five new species identified by culturomics – F. Cadoret – New Microbes and New Infections

Whole-Genome Sequences of Influenza A(H1N1)pdm09 Virus Isolates from Kerala, India – Sara Jones – Genome Announcements

Phoenicibacter massiliensis‘ gen. nov., sp. nov., a new bacterium isolated from the human gut of a pygmy woman – M. Bilen – New Microbes and New Infections

Phenotypic and genomic comparison of Mycobacterium aurum and surrogate model species to Mycobacterium tuberculosis: implications for drug discovery – Amine Namouchi – BMC Genomics

Microbes in the news 
** Mini-Metagenomics Leads to Microbial Discovery – Abby Olena – The Scientist
Refers to Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples – Feiqiao Brian Yu – ELife **

APC Microbiome Institute appoints Spinning Clock to Mind Your Microbes brief – Andy Black – The Drum
An app for kids to learn about the microbiome!

Microbial diversity: ‘key benchmark in the coming Third Wave cosmetic revolution’ – Lucy Whitehouse – Cosmetics Design

Novel bacterial physiology identified in the creation of biofilms – Science Daily

Physicists Just Found a Way to Spin Teeny Tiny Robot Motors With Bacteria – Gemma Conroy – Science Alert

New bacteria being developed for cheese may save industry $10m a year, researchers say – Melanie Vujkovic – ABC

Bacteria-infected mosquitoes are coming to Fresno – but it’s a good thing! – Bryant-Jon Anteola – Fresno Bee

BYU student overcomes flesh-eating bacteria to compete on ‘American Ninja Warrior’ – Braley Dodson – Daily Herald

Bacteria Actively Drive Development of Colorectal Cancer – Newswise
Looking at Streptococcus gallolyticus and its ability to promote colorectal cancer in cell culture, animal models, and human tissue.

Bacteria Hysteria
How surgeons can stop the spread of germs by operating NAKED instead of wearing surgical gowns – Colin Fernandez – Daily Mail

July 3, 2017

 

Pregnancy and early life
Maternal inheritance of bifidobacterial communities and bifidophages in infants through vertical transmission – Sabrina Duranti –  Microbiome

 
Mini Review: The microbiome and disorders of the central nervous system – Valeria D. Felice – Pharmacology Biochemistry and Behavior

 
Human respiratory microbiome

 
Short Report: The metabolic footprint of the airway bacterial community in cystic fibrosis – Vaishnavi Narayanamurthy – Microbiome

 
Human gut microbiome

 
Gut microbial transformation of the dietary imidazoquinoxaline mutagen MeIQx reduces its cytotoxic and mutagenic potency – Jianbo Zhang –  Toxicological Science

 
Review: Practical considerations for large-scale gut microbiome studies – Doris Vandeputte – FEMS Microbiology Reviews

 
Association of altered gut microbiota composition with chronic urticaria – Edris Nabizadeh – Annals of Allergy, Asthma & Immunology

 
Animal microbiome 

 
A genomic investigation of ecological differentiation between free-living and Drosophila-associated bacteria – Nathan J. Winans –  Molecular Ecology

 
The Gut Bacterial Community Composition of Wild Cervus albirostris (White-Lipped Deer) Detected by the 16S Ribosomal RNA Gene Sequencing – Jun-gang Li –  Current Microbiology

 
Microbial influence on Drosophila biology – ME Martino – Current Opinion in Microbiology

 
Plant, root, and soil microbiome

 
Organic carbon and nitrogen availability determine bacterial community composition in paddy fields of the Indo-Gangetic plain – Arvind Kumar –  Biotech

 

Water and extremophile microbiome

 
Spatiotemporal Dynamics of the Bacterial Microbiota on Lacustrine Cladophora glomerata (Chlorophyta) – Michael J. Braus –  bioRxiv

 
Quantity and quality of particulate organic matter controls bacterial production in the Columbia River estuary – Byron C. Crump – Limnology and Oceanography

 
Relating genomic characteristics to environmental preferences and ubiquity in different microbial taxa – Marta Cobo-Simón –  BMC Genomics

 
Comparison of four DNA extraction methods for comprehensive assessment of 16S rRNA bacterial diversity in marine biofilms using high-throughput sequencing – Natàlia Corcoll – FEMS Microbiology Letters

 
Food microbiology

 

Cleaning and disinfection of biofilms composed of Listeria monocytogenes and background microbiota from meat processing surfaces – Annette Fagerlund – Applied and Environmental Microbiology

 

Probiotics / prebiotics

 
A human gut commensal ferments cranberry carbohydrates to produce formate – Ezgi Özcan – Applied and Environmental Microbiology

 
Review: Lifestyles in transition: evolution and natural history of the genus Lactobacillus – Rebbeca M. Duar – FEMS Microbiology Reviews

 
Phages and viruses

 
Synergistic elimination of bacteria by phage and the innate immune system – Chung Yin (Joey) Leung – Journal of Theoretical Biology

 
Biotechnology

 
Effect of zinc oxide nanoparticles on nitrogen removal, microbial activity and microbial community of CANON process in a membrane bioreactor – Xiaojing Zhang – Bioresource Technology

 
Microbes in the news

 
A new approach to tackling drug-resistant bacteria

New technology to cool the body: make the clothes made of microorganisms

 
Microbes on the market (news about biotech companies)

 
New Belgian Biotech will use Microorganisms to Replace Pesticides and Fertilizers

May 9, 2017

Today’s digest is full of exciting papers that look at how climate change is influencing the gut microbiome of lizards, biogeography of bacteria along the Amazon river, lastly how going to the gym might be bad for you.

Human gut microbiome

Preprint : The Landscape Of Type VI Secretion Across Human Gut Microbiomes Reveals Its Role In Community Composition. Verster A. bioRxiv

Ocean, river, and stream microbiome

Disentangling multi‐scale environmental effects on stream microbial communities. Jyrkänkallio‐Mikkola J. Journal of Biogeography

Bacterial biogeography across the Amazon river-ocean continuum  Doherty M. Frontiers in Microbiology

Spatial variation of microbial communities in sediments along the environmental gradients from Xiaoqing River to Laizhou Bay.   Yu SX.  Marine Pollution Bulletin

The impact of long-term water level draw-down on microbial biomass: A comparative study from two peatland sites with different nutrient status Mpamah PA. European Journal of Soil Biology

The metabolic potential of the single cell genomes obtained from the Challenger Deep, Mariana Trench within the Candidate Superphylum Parcubacteria (OD1). León‐Zayas. Environmental Microbiology

Plant, soil, and air microbiome

Postmortem microbial communities in burial soil layers of skeletonized humans. Thomas TB. Journal of Forensic and Legal Medicine

Metagenomic Analysis of Bacterial Communities in the Rhizosphere of Leguminous Crops and Trees. Ahrenhoerster C. The FASEB Journal

Animal gut microbiome

Can fecal samples be used to inform about microbial communities of the equine hindgut? Reed KJ. Journal of Equine Veterinary Science

Normal variation and changes over time in the equine intestinal microbiome Martin EJ. Journal of Equine Veterinary Science

Climate warming reduces gut microbiota diversity in a vertebrate ectotherm. Bestion E. Nature:Ecology and Evolution

Effect of dietary supplementation with Lactobacillus acidophilus D2/CSL (CECT 4529) on caecum microbioma and productive performance in broiler chickens De Cesare A. PLoS One

Biotechnology 

Editorial Petroleum Microbial Biotechnology: Challenges and Prospects Ismail WA.Frontiers in Microbiology

Antibiotic 

Networks of exchanging antibiotic resistance between environmental, commensal, and pathogenic microbes Dantas G- The FASEB Journal

Extreme environment 

Decoupling of microbial carbon, nitrogen, and phosphorus cycling in response to extreme temperature events Mooshammer M. Science Advances

Faecal microbiome 

pH-Mediated Microbial and Metabolic Interactions in Fecal Enrichment Cultures Ilhan ZE. mSpehere

Anemia During Infancy Affects the Fecal Microbiome and Fecal and Serum Metabolomes McClorry S. The FASEB Journal

Microbes in the news

Southern California beaches get bacteria warnings after rain

Monterey County Herald

The Amount Of Bacteria On Gym Equipment Will Make Sure You Never Forget To Wipe Down The Elliptical Again

Bustle


 

April 28, 2017

Quite a few interesting articles and news about microbes: are we colonised with bacteria in utero? What is the relevance of cooperative interactions in microbial biotechnological processes? Microbe colonies  in space? Read more in today’s Microbiome Digest..

General microbiome

Variable habitat conditions drive species covariation in the human microbiota – Charles K. Fisher – PLOS

Pregnancy and early life

*Review: The prenatal gut microbiome: are we colonized with bacteria in utero? – R. W. Walker – Pediatric Obesity

Development of the cutaneous microbiome in the preterm infant: A prospective longitudinal study – Mohan Pammi – PLOS
 Human respiratory microbiome

A commensal streptococcus hijacks a Pseudomonas aeruginosa exopolysaccharide to promote biofilm formation – Jessica A. Scoffield – PLOS
Human oral microbiome

A genome-wide association study identifies nucleotide variants at SIGLEC5 and DEFA1A3 as risk loci for periodontitis – Matthias Munz – Human Molecular Genetics

Human nearly-sterile sites 

A case of polymicrobial anaerobic spondylodiscitis due to Parvimonas micra and Fusobacterium nucleatum – Leanne M Cleaver – JMM Case Reports

Human gut microbiome

Small Molecules from Deep within the Gut – Michael Ehrmann – ChemBioChem

Single Delivery of High-Diversity Fecal Microbiota Preparation by Colonoscopy Is Safe and Effective in Increasing Microbial Diversity in Active Ulcerative Colitis – Jacob Vinita – Inflammatory Bowel Diseases

Fecal Microbiota Transplantation for Refractory Clostridium difficile Colitis in Solid Organ Transplant Recipients – R. J. Friedman-Moraco – American Journal of Transplantation

Abundance profiling of specific gene groups using precomputed gut metagenomes yields novel biological hypotheses – Konstantin Yarygin – PLOS
Animal experiments

Neonatal mono-colonization of germ-free mice with Lactobacillus casei enhances casein immunogenicity after oral sensitization to cow’s milk – Matieny Aicha Maiga – Molecular Nutrition & Food Research

Shifts in the Gut Microbiota Composition Due to Depleted Bone Marrow Beta Adrenergic Signaling Are Associated with Suppressed Inflammatory Transcriptional Networks in the Mouse Colon – Tao Yang – Frontiers in Physiology

Animal microbiome

Viral gut metagenomics of sympatric wild and domestic canids, and monitoring of viruses: Insights from an endangered wolf population – Nádia Conceição-Neto – Ecology and Evolution

The environmental and host-associated bacterial microbiota of Arctic seawater-farmed Atlantic salmon with ulcerative disorders – C Karlsen – Journal of Fish Diseases

Plant, root, and soil microbiome

Soil aggregation and associated microbial communities modify the impact of agricultural management on carbon content – Pankaj Trivedi – Environmental Microbiology

In-depth characterization of bacterial and archaeal communities present in the abandoned Kettara pyrrhotite mine tailings (Morocco) – Odile Bruneel –  Extremophiles

Water and extremophile microbiome 

Geochemistry and microbial diversity of cave waters in the gypsum karst aquifers of Emilia Romagna region, Italy – Ilenia M. D’Angeli – Science of The Total Environment
Probiotics / prebiotics

Characterization, identification and application of lactic acid bacteria isolated from Leymus chinensis silage – Qing Zhang – Grassland Science
Biotechnology

*Review: Cooperation in microbial communities and their biotechnological applications – Matteo Cavaliere – Environmental Microbiology

Techniques

MicrobiomeAnalyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data – Achal Dhariwal – Nucleic Acid Research

Microbes in the news

Adaptive Phage Therapeutics – Terminally Ill Patient Successfully Treated With Bacteriophage – BioSpace

Research Links Microbiome Makeup To Remission in Pediatric Crohn’s – Gastroenterology & Endoscopy News

NASA Astronauts Are Close to Identifying Unknown Microbe Colonies That Grow in Space – Sciencealert.com

 

April 19, 2017

Exciting papers with locoregional effects of microbiota in a mouse model of colon carcinogenesis, maternal high fat diet detrimentally alterring epigenetic and gut microbiome pathways leading to fatty liver disease in mice.

Events and jobs

ASM Microbe 2017 : New Orleans

QC Microbiology Product Testing Associate – Experis : Irvine, CA
General microbiome

Review: Applying the design-build-test paradigm in microbiome engineering – Hoang Long Pham – Current Opinion in Biotechnology

Cohort Profile: African Collaborative Center for Microbiome and Genomics Research’s (ACCME) Human Papillomavirus (HPV) and Cervical Cancer Study – Sally N. Adebamowo – International Journal of Epidemiology

Review: Cultured microbes represent a substantial fraction of the human and mouse gut microbiota – Ilias Lagkouvardos – Gut Microbes

Human skin microbiome

A distinct cutaneous microbiota pofile in autoimmune bullous disease patients – Mor Miodovnika – Experimental Dermatology

Human gut microbiome

Review : A psychology of the human brain–gut–microbiome axis – Andrew P. Allen – Social and Personality Psychology Compass

Multivariate modelling of faecal bacterial profiles of patients with IBS predicts responsiveness to a diet low in FODMAPs – Sean M P Bennet – Gut

Animal microbiome

Temporal changes in cutaneous bacterial communities of terrestrial- and aquatic- phase newts (Amphibia) – Joana Sabino-Pinto – Environmental Microbiology

The low diverse gastric microbiome of the jellyfish Cotylorhiza tuberculata is dominated by four novel taxa – Tomeu Viver – Environmental Microbiology

Studying the effect of administration route and treatment dose on the selection of enrofloxacin resistance in commensal Escherichia coli in broilers – Ilias Chantziaras -Journal of Antimicrobial Chemotherapy

The skin microbiome of the Common thresher shark (Alopias vulpinus) has low taxonomic and potential metabolic β-diversity – Michael P. Doane – Environmental Microbiology Reports

Animal experiments

Intestinal, extra-intestinal and systemic sequelae of Toxoplasma gondii induced acute ileitis in mice harboring a human gut microbiota – Eliane von Klitzing – PLOS ONE

Effects of the inclusion of a Bacillus direct-fed microbial on performance parameters, bone quality, recovered gut microflora, and intestinal morphology in broilers consuming a grower diet containing corn distillers dried grains with solubles – J. D. Latorre – Poultry Science

Effect of high-fat diet and growth stage on the diversity and composition of intestinal microbiota in healthy bovine livestock – Shengyin Jiao – Journal of the Science of Food and Agriculture

*Locoregional effects of microbiota in a preclinical model of colon carcinogenesis – Sarah Tomkovich – Cancer Research

Selection of Cholesterol-Lowering Lactic Acid Bacteria and its Effects on Rats Fed with High-Cholesterol Diet – Yufang Liu – Current Microbiology

*Enhanced offspring predisposition to steatohepatitis with maternal high-fat diet is associated with epigenetic and microbiome alterations – Umesh D. Wankhade – PLOS ONE

Plant, root, and soil microbiome

Archaea and bacteria mediate the effects of native species root loss on fungi during plant invasion – Steven D Mamet- The ISME Journal

An acid-tolerant ammonia-oxidizing γ-proteobacterium from soil – Masahito Hayatsu – The ISME Journal

Investigation of Arsenotrophic Microbiome in Arsenic-Affected Bangladesh Groundwater – Munawar Sultana – Groundwater

Unexpected associated microalgal diversity in the lichen Ramalina farinacea is uncovered by pyrosequencing analyses – Patricia Moya – Plos ONE

Tuber indicum shapes the microbial communities of ectomycorhizosphere soil and ectomycorrhizae of an indigenous tree (Pinus armandii) – Qiang Li – Plos ONE

The ‘known’ genetic potential for microbial communities to degrade organic phosphorus is reduced in low-pH soils – Ian D. E. A. Lidbury – Microbiology Open

Shifting microbial communities sustain multiyear iron reduction and methanogenesis in ferruginous sediment incubations – M. S. Bray – Gebiology

Water and extremophile microbiome

Discovery of anaerobic lithoheterotrophic haloarchaea, ubiquitous in hypersaline habitats – Dimitry Y Sorokin – The ISME Journal

Cultivation and characterization of Candidatus Nitrosocosmicus exaquare, an ammonia-oxidizing archaeon from a municipal wastewater treatment system – Laura A Sauder – The ISME Journal

Minireview: Microbial ecology of mountain glacier ecosystems: Biodiversity, ecological connections, and implications of a warming climate – Scott Hotaling – Environmental Microbiology

Probiotics / prebiotics
Colonic gas homeostasis: Mechanisms of adaptation following HOST-G904 galactooligosaccharide use in humans – M. Mego – Neurogastroenterology and Motility

Techniques

Stochastically reduced communities—Microfluidic compartments as model and investigation tool for soil microorganism growth in structured spaces – Jialan Cao – Engineering in Life Sciences

Protocol : Metagenomics and CAZyme Discovery – Benoit J. Kunath – Protein-Carbohydrate Interactions : Methods in Molecular Biology

The resident microflora of voided midstream urine of healthy controls: standard versus expanded urine culture protocols – L. Coorevits – European Journal of Clinical Microbiology & Infectious Diseases

Microbes in the news

Study finds amoeba ‘grazing,’ killing bacteria usually protected by film

How Bacteria-Laden Beetle Poop Is Killing American Squash and Melons

Glowing bacteria detect buried landmines

Science, publishing, and career

Saturday, Science Advocates Prepare for a Long March

Anitha’s non-microbiology picks

Research unlocks molecular key to animal evolution and disease

Cumulative culture can emerge from collective intelligence in animal groups – Takao Sasaki – Nature Communications

March 18, 2017

Events and jobs

Research Fellow in Omics analysis – King’s College London – Apply by April 12, 2017

Postdoctoral Research Position in Marine Microbial Ecology – University of Southern Mississippi

General microbiome

Microbial Influences in Cardio–Metabolic Diseases – Rachel Petersen – New York Academy of Sciences

*Review: Microbiota: a key orchestrator of cancer therapy – Soumen Roy – Nature Reviews Cancer

*Review: Caenorhabditis elegans as a model for microbiome research – Fan Zhang – Frontiers in Microbiology

Human respiratory microbiome

The relationship between nasopharyngeal CCL5 and microbiota on disease severity among infants with bronchiolitis – Kohei Hasegawa – Allergy

Human gut microbiome

The Food Contaminant Deoxynivalenol Exacerbates the Genotoxicity of Gut Microbiota – Delphine Payros – mBio

Delayed utilization of some fast-fermenting soluble dietary fibers by human gut microbiota when presented in a mixture – Yunus E. Tuncil – Journal of Functional Foods

Animal experiments

Deciphering the combinatorial influence of diet and the microbiota on experimental colitis – Sean R. Llewellyn – bioRxiv

The role of adaptive immunity as an ecological filter on the gut microbiota in zebrafish – Keaton Stagaman – ISME J

Animal microbiome

Comparison of bacterial populations in bedding material, on teat ends, and in milk of cows housed in compost bedded pack barns – R. L. Albino – Animal Production Science

Community analysis of microbial sharing and specialization in a Costa Rican ant–plant–hemipteran symbiosis – Elizabeth G. Pringle – Proceedings of the Royal Society Biological Sciences

Microbial community composition of deep-sea corals from the Red Sea provides insight into functional adaption to a unique environment – Till Röthig – Scientific Reports

Plant, root, and soil microbiome

Root microbiota drive direct integration of phosphate stress and immunity – Gabriel Castrillo – Nature

Striking alterations in the soil bacterial community structure and functioning of the biological N cycle induced by Pennisetum setaceum invasion in a semiarid environment – G. Rodríguez-Caballero – Soil Biology and Biochemistry

Plant growth promoting rhizobacteria are more effective under drought: a meta-analysis – Rachel L. Rubin – Plant and Soil

Effect of biodynamic soil amendments on microbial communities in comparison with inorganic fertilization – Sibylle Faust – Applied Soil Ecology

Water and extremophile microbiome

Bacterial diversity in fumarole environments of the Paricutín volcano, Michoacán (Mexico) – Miguel Medrano-Santillana – Extremophiles

Prokaryotic Abundance and Activity in Permafrost of the Northern Victoria Land and Upper Victoria Valley (Antarctica) – Rosabruna La Ferla – Microbial Ecology

Microbial communities of aquatic environments on Heard Island characterized by pyrotag sequencing and environmental data – Michelle A. Allen – Scientific Reports

A Pelagic Microbiome (Viruses to Protists) from a Small Cup of Seawater – Flavia Flaviani – Viruses

Built environment

Microbial dynamics in anaerobic digestion reactors for treating organic urban residues during the start-up process – Rocio J. Alcántara-Hernández – Letters in Applied Microbiology

Variability of airborne bacteria in an urban Mediterranean area (Thessaloniki, Greece) – Savvas Genitsaris – Atmospheric Environment

*Review: A review of microscopy and comparative molecular-based methods to characterize “Plastisphere” communities – Caroline De Tender – Analytical Methods

Techniques

*Review: Emerging Trends for Microbiome Analysis: From Single-Cell Functional Imaging to Microbiome Big Data – Jian Xu – Engineering

*Review: Metaproteomic strategies and applications for gut microbial research – Mingming Xiao – Applied Microbiology and Biotechnology

Microbes in the news

Bacteria-Enriched Lotion Battles Skin Infections – Jenna Flannigan – Live Science

Frozen, Freeze-dried Products for Fecal Microbiota Transplantation as Effective as Fresh? – Pharmacy Times

Study by Irish scientists finds porridge to be good for the heart and gut – RTE

Certain Bacteria Within Gut Microbiome May Halt Inflammation Naturally, Study Says – Patricia Inacio – IBD News Today

Antibiotic overuse might be bad for bees – Mary Beth Griggs – Popular Science

Microbiome research Studies aim to help health, environment – David Wahlberg – The Times Record

My cats poop for science – Jonathan M. Giltin – ars Technica

Microbes on the market

Seres doubles down on a microbiome do-over as the FDA clears a make-or-break study – John Carroll – Endpoint News

Bacteria Hysteria

Revealed: Which supermarket’s chicken is most likely to contain food poisoning bacteria? – Tom Belger – Liverpool Echo

March 12, 2017

The first day of daylight saving time in the USA and if your Sunday morning started in a (relative) darkness just read about the viruses in the oceanic basement.  Then find out why yogurt can help your mood.  More interesting papers about the gut-brain connection, a microbiota-centric view of diseases of the upper gastrointestinal tract, microbiome and Type 1 & 2 diabetes, and a new method of detecting bacteria during root canal treatments.

General microbiome

Review: Calling All Hosts: Bacterial Communication In Situ – Jessica L. Cleary – Chem

Gut-Brain connection

The Association Between Temperament and Microbiota in Healthy Individuals: A Pilot Study  – Kim H – Psychosomatic medicine

Gut-brain actions underlying comorbid anxiety and depression associated with inflammatory bowel disease –  Aine Abautret-Daly -Acta Neuropsychiatrica

Human gut microbiome

A microbiota-centric view of diseases of the upper gastrointestinal tract – Gerardo Nardone- Gastroenterology & Hepatology

Review: Systems Biology of Metabolism: A Driver for Developing Personalized and Precision Medicine – Jens Nielsen – Cell Metabolism

Intestinal Microbiota in Type 2 Diabetes and Chronic Kidney Disease – A. Sabatino – Current Diabetes Reports

The intestinal proteome of diabetic and control children is enriched with different microbial and host proteins  – Elsa Pinto – Microbiology

Therapeutic efficacy of oral immunization with a non-genetically modified Lactococcus lactis-based vaccine CUE-GEM induces local immunity against Helicobacter pylori infection – Wei Liu – Applied Microbiology & Biotech

Water and extremophile microbiome

Viruses in the Oceanic Basement – OD Nigro -MBio

Models

A microengineered collagen scaffold for generating a polarized crypt-villus architecture of human small intestinal epithelium -Yuli Wang – Biomaterials

Built environment

Review: Microbiome involved in microbial electrochemical systems (MESs): Rijuta G Saratale- Chemosphere

Microbes in the news

Probiotic found in yogurt can reverse depression symptoms, Researchers at the University of Virginia School of Medicine finds

New method of detecting bacteria during root canal treatments 

March 5, 2017

Here are few interesting articles for your Sunday morning edition. Canadian bacteria-like fossils may be the oldest evidence of life yet.  Black carbon, one of the main components of air pollution,  is reported to drastically change the development of bacterial biofilms and key aspects of bacterial colonization and survival.  A novel organ culture system described for the mouse intestine shows that the nervous system influences the microbiome/immune system crosstalk.  And the power of alternative assays for discovery: Deep sequencing of cell-free DNA from a large patient cohort revealed previously unknown and highly prevalent microbial and viral diversity in humans.

Pregnancy and early life

Prediction of complicated disease course for children newly diagnosed with Crohn’s disease: a multicenter inception cohort study – Subra Kugathasan – The Lancet

Multi-site human microbiome

Humans are colonized by many uncharacterized and highly divergent microbes -Mark A. Kowarsky -bioRxiv

Human respiratory microbiome

Air pollution alters Staphylococcus aureus and Streptococcus pneumonia biofilms, antibiotic tolerance and colonization – Shane J. K. Hussey – Journal of Environmental Microbiology

Human vaginal microbiome

The global health impact of vaginal dysbiosis – Janneke H.H.M. van de Wijgert – Research in Microbiology

Human gut microbiome

An Intestinal Organ Culture System Uncovers a Role for the Nervous System in Microbe-Immune Crosstalk – Nissan Yissachar – Cell

Animal microbiome

Genetic and functional analysis of the bovine uterine microbiota. Part I: Metritis versus healthy cows, Part II: Purulent vaginal discharge versus healthy cows – M.L.S. Bicalho – The journal of Dairy Science

Plant, root, and soil microbiome

Review: Soil-Plant-Microbe Interactions in Stressed Agriculture Management– Shobhit Raj Vimal – Pedosphere

Water and extremophile microbiome

Evidence for early life in Earth’s oldest hydrothermal vent precipitates – Matthew S. Dodd – Nature

Microbes in the news

Study Shows Link Between Microbiome in the Gut and Parkinson’s – University of Alabama at Birmingham

A Japanese study performed by sequencing the gut microbiota of 367 healthy individuals ranging from newborn to 104 years old shows microbiome changes with age

UN issues list of 12 most worrying bacteria

Microbes on the market

Rebiotix Inc. has its lead product for C. diff. treatment granted Fast Track, Orphan Drug, and Breakthrough Therapy status by the FDA.  

December 28, 2016

Human gut microbiome

Tissue-Associated Bacterial Alterations in Rectal Carcinoma Patients Revealed by 16S rRNA Community Profiling – Andrew M. Thomas – Frontiers in Cellular and Infection Microbiology

Gastrointestinal neuromuscular apparatus: An underestimated target of gut microbiota – Michele Pier Luca Guarino – World Journal of Gastroenterology

Immune Response of Healthy Adults to the Ingested Probiotic Lactobacillus casei Shirota
– L. S. Harbige – Scandinavian Journal of Immunology

Review: Host-Microbiome Interaction and Cancer: Potential Application in Precision Medicine – Alejandra V. Contreras – Frontiers in Physiology

Review: IL-17: overview and role in oral immunity and microbiome – L Abusleme – Oral Diseases

Animal experiments

Bacillus sp. QSI-1 Modulate Quorum Sensing Signals Reduce Aeromonas hydrophila Level and Alter Gut Microbial Community Structure in Fish – Shuxin Zhou – Frontiers in Cellular and Infection Microbiology

Use of Asian selected agricultural byproducts to modulate rumen microbes and fermentation – Yasuo Kobayashi – Journal of Animal Science and Biotechnology

Correlation of Gut Microbiota Composition with Resistance to Experimental Autoimmune Encephalomyelitis in Rats – Suzana Stanisavljević – Frontiers in Microbiology

Comparative Analysis of the Rats’ Gut Microbiota Composition in Animals with Different Ginsenosides Metabolizing Activity – Wei-Wei Dong – Journal of Agricultural Food Chemistry

Animal microbiome

Potential for Nitrogen Fixation in the Fungus-Growing Termite Symbiosis – Panagiotis Sapountzis – Frontiers in Microbiology

Impact and Influence of the Natural Vibrio-Squid Symbiosis in Understanding Bacterial–Animal Interactions – Mark J. Mandel and Anne K. Dunn – Frontiers in Microbiology

Plant, root, and soil microbiome

The Relationship between pH and Bacterial Communities in a Single Karst Ecosystem and Its Implication for Soil Acidification – Yuan Yun – Frontiers in Microbiology

Parasites and competitors suppress bacterial pathogen synergistically due to evolutionary trade-offs – Xiaofang Wang – Evolution

Review: The Plant as Metaorganism and Research on Next-Generation Systemic Pesticides – Prospects and Challenges – Zisis Vryzas – Frontiers in Microbiology

Extremophile microbiome

Cryo-protective effect of an ice-binding protein derived from Antarctic bacteria – Marco Mangiagalli – The FEBS Journal

Outdoor and indoor microbiome

Bacterial characterization in ambient submicron particles during severe haze episodes at Ji’nan, China – Caihong Xu – Science of The Total Environment

An emerging paradox: Toward a better understanding of the potential benefits and adversity of microbe exposures in the indoor environment – J. Mensah-Attipoe – Indoor Air

Waste and pollution microbiome

Effect of the chemical composition of filter media on the microbial community in wastewater biofilms at different temperatures – Iffat Naz – RSC Advances

Phages and viruses

Inferring phage–bacteria infection networks from time-series data – Luis F. Jover – Royal Society Open Science

Microbes in the news

How hospitals, nursing homes keep lethal ‘superbug’ outbreaks secret – Deborah J. Nelson, David Rohde, Benjamin Lesser and Ryan McNeill – Reuters

Causes Of Rheumatoid Arthritis: Gum Disease Bacteria Triggers Joint Inflammation, Latest Research Suggests – Lizette Borreli – Medical Daily

Genome Sequencing Sheds Light On Shigella Outbreaks In California – Saranya Palanisamy – Tech Times

Now, dental implants that kill bacteria and anchor to bone – The Tribune India

Antibiotic resistance just became more complex – EurekAlert

How Germs, Dirt and Hookworms Can Boost Your Health – Ruben Castaneda – US News