Category Archives: Food Microbiology

January 13, 2018

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100+ alerts, meaning great papers in every category. Enjoy!

General microbiome
Review: Sphingolipids in host-microbial interactions – Stacey L Heaver – Current Opinion In Microbiology

Editorial: The Human Microbiome – Emily P Balskus – ACS Infectious Diseases

Review: Emergent Heterogeneous Micro-environments in Biofilms:Substratum Surface Heterogeneity and Bacterial Adhesion Force-sensing – Yijin Ren – Fems Microbiology Reviews

Pregnancy and early life
Maturation of the gut microbiome and risk of asthma in childhood – Jakob Stokholm – Nature Communications

Haemophilus is overrepresented in the nasopharynx of infants hospitalized with RSV infection and associated with increased viral load and enhanced mucosal CXCL8 responses – Thomas H A Ederveen – Microbiome

Fetal and early life antibiotics exposure and very early onset inflammatory bowel disease: a population-based study – Anne K Örtqvist – Gut

Review: Early Microbes Modify Immune System Development and Metabolic Homeostasis-The “Restaurant” Hypothesis Revisited – Michael J Nash – Frontiers In Endocrinology

Human respiratory microbiome
Genomics of Corynebacterium striatum, an emerging multi-drug resistant pathogen of immunocompromised patients – Kathleen Nudel – Clinical Microbiology And Infection

Human skin microbiome
Transcriptomic profiling of interacting nasal staphylococci species reveals global changes in gene and non-coding RNA expression – Grith M M Hermansen – Fems Microbiology Letters

Human oral microbiome
Association of Oral Microbiome With Risk for Incident Head and Neck Squamous Cell Cancer – Richard B Hayes – JAMA Oncology

Composition of salivary microbiota in elderly subjects – Taiji Ogawa – Scientific Reports

Human gut microbiome
CX3CR1+ mononuclear phagocytes control immunity to intestinal fungi – Irina Leonardi – Science (New York, N.Y.)

Antagonism toward the intestinal microbiota and its effect on Vibrio cholerae virulence. – Wenjing Zhao – Science (New York, N.Y.)

Evaluation of bloodstream infections, Clostridium difficile infections, and gut microbiota in pediatric oncology patients – Bryan T. Nycz – PLoS One

Antibiotic Treatments for Clostridium difficile Infection Are Associated with Distinct Bacterial and Fungal Community Structures – Regina Lamendella – mSphere

Alterations of the gut microbiota in Hashimoto’s thyroiditis patients – Fuya Zhao – Thyroid : Official Journal Of The American Thyroid Association

Structural insights into a family 39 glycoside hydrolase from the gut symbiont Bacteroides cellulosilyticus WH2 – Ahmad Ali-Ahmad – Journal Of Structural Biology

Review: Gut Microbiota Dysbiosis Drives and Implies Novel Therapeutic Strategies for Diabetes Mellitus and Related Metabolic Diseases – Xuan Li – Frontiers In Immunology

Review: Pathogens, microbiome and the host: emergence of the ecological Koch’s postulates – Pascale Vonaesch – FEMS Microbiology Reviews

Review: Biochemistry of Complex Glycan Depolymerisation by the Human Gut Microbiota – Didier Ndeh – FEMS Microbiology Reviews

Review: Segmented filamentous bacteria, Th17 inducers and helpers in a hostile world – Pamela Schnupf – Current Opinion In Microbiology

Microbial Ecology
Simulation of Escherichia coli Dynamics in Biofilms and Submerged Colonies with an Individual-Based Model Including Metabolic Network Information – Ignace L M M Tack – Frontiers In Microbiology

Initial evenness determines diversity and cell density dynamics in synthetic microbial ecosystems – Elham Ehsani – Scientific Reports

Pan-genome analysis of the genus Finegoldia identifies two distinct clades, strain-specific heterogeneity, and putative virulence factors – Holger Brüggemann – Scientific Reports

Specifying the Harsh Conditions of Life: Resource Competition and Predation in the 1970s – Alita R. Burmeister – The American Naturalist

Animal experiments
Maternal metabolic, immune, and microbial systems in late pregnancy vary with malnutrition in mice – Kristin L Connor – Biology of Reproduction

Fecal Microbiota Transplantation, Commensal Escherichia coli and Lactobacillus johnsonii Strains Differentially Restore Intestinal and Systemic Adaptive Immune Cell Populations Following Broad-spectrum Antibiotic Treatment – Ira Ekmekciu – Frontiers In Microbiology

Impacts of feeding preweaned calves milk containing drug residues on the functional profile of the fecal microbiota – Richard Van Vleck Pereira – Scientific Reports

Gama-aminobutyric Acid Enriched Rice Bran Diet Attenuates Insulin Resistance and Balances Energy Expenditure via Modification of Gut Microbiota and SCFAs – Xu Si – Journal Of Agricultural And Food Chemistry

Proton Pump Inhibitors Increase the Susceptibility of Mice to Oral Infection with Enteropathogenic Bacteria – Eiichiro Yasutomi – Digestive Diseases And Sciences

Rhubarb supplementation promotes intestinal mucosal innate immune homeostasis through modulating intestinal epithelial microbiota in goat kids – Jinzhen Jiao – Journal Of Agricultural And Food Chemistry

Impact of dietary induced precocious gut maturation on cecal microbiota and its relation to the blood-brain barrier during the postnatal period in rats – N Marungruang – Neurogastroenterology And Motility : The Official Journal Of The European Gastrointestinal Motility Society

Exercise Prevents Enhanced Postoperative Neuroinflammation and Cognitive Decline and Rectifies the Gut Microbiome in a Rat Model of Metabolic Syndrome – Xiaomei Feng – Frontiers In Immunology

Rifampicin treatment of Blattella germanica evidences a fecal transmission route of their gut microbiota – Tania Rosas – Fems Microbiology Ecology

Gut Flora-Dependent Metabolite Trimethylamine-N-oxide Accelerates Endothelial Cell Senescence and Vascular Aging through Oxidative Stress – Yilang Ke – Free Radical Biology & Medicine

Nanocomposite of Half-Fin Anchovy Hydrolysates/Zinc Oxide Nanoparticles Exhibits Actual Non-Toxicity and Regulates Intestinal Microbiota, Short-Chain Fatty Acids Production and Oxidative Status in Mice – Ru Song – Marine Drugs

Animal microbiome
Is there a link between aging and microbiome diversity in exceptional mammalian longevity? – Graham M. Hughes – PeerJ (Specifically, bats or Myotis myotis)

Gut Microbes Egested during Bites of Infected Sand Flies Augment Severity of Leishmaniasis via Inflammasome-Derived IL-1β – Ranadhir Dey – Cell Host & Microbe

The Sarda Sheep Host Fecal Proteome – Antonio Palomba – Proteomics

Host Specificity for Bacterial, Archaeal and Fungal Communities Determined for High- and Low-Microbial Abundance Sponge Species in Two Genera – Maryam Chaib De Mares – Frontiers In Microbiology (from December 2017)

Comparative Metagenomics of Cellulose- and Poplar Hydrolysate-Degrading Microcosms from Gut Microflora of the Canadian Beaver (Castor canadensis) and North American Moose (Alces americanus) after Long-Term Enrichment. – Mabel T Wong – Frontiers In Microbiology (from December 2017)

Regular Wounding in a Natural System: Bacteria Associated With Reproductive Organs of Bedbugs and Their Quorum Sensing Abilities – Oliver Otti – Frontiers In Immunology

Plant, root, and soil microbiome
Forest conversion induces seasonal variation in microbial β-diversity – Shengen Liu – Environmental Microbiology

Specificity in Arabidopsis thaliana recruitment of root fungal communities from soil and rhizosphere – Hector Urbina – Fungal Biology

Different impacts of manure and chemical fertilizers on bacterial community structure and antibiotic resistance genes in arable soils – Peng Liu – Chemosphere

Intra-species variation in a widely distributed tree species regulates the responses of soil microbiome to different temperature regimes – Cui-Jing Zhang – Environmental Microbiology Reports

Positive diversity-functioning relationships in model communities of methanotrophic bacteria – Elvira Schnyder – Ecology

Plant Phylogeny and Life History Shape Rhizosphere Bacterial Microbiome of Summer Annuals in an Agricultural Field – Bryan D. Emmett – Frontiers in Microbiology (from December 2017)

Soil microbial communities and enzyme activities in sea-buckthorn (Hippophae rhamnoides) plantation at different ages – Miao Yang – Plos One

The genome and microbiome of a dikaryotic fungus (Inocybe terrigena, Inocybaceae) revealed by metagenomics – Mohammad Bahram – Environmental Microbiology Reports

Ecological mechanisms underlying soil bacterial responses to rainfall along a steep natural precipitation gradient – Bonnie Waring – FEMS Microbiology Ecology

Review: Current Insights into the Role of Rhizosphere Bacteria in Disease Suppressive Soils – Ruth Gómez Expósito – Frontiers in Microbiology (from December 2017)

Water and extremophile microbiome
Microbially mediated aluminosilicate formation in acidic anaerobic environments: A cell-scale chemical perspective – J. Sánchez-España – GeoBiology

Responses of Periphyton to Fe2O3 Nanoparticles: A Physiological and Ecological Basis for Defending Nanotoxicity – Jun Tang – Environmental Science & Technology

Variations in bacterial and archaeal communities along depth profiles of Alaskan soil cores – Binu Mani Tripathi – Scientific Reports

Microbiological and Geochemical Survey of CO2-Dominated Mofette and Mineral Waters of the Cheb Basin, Czech Republic – Patryk Krauze – Frontiers In Microbiology

In Situ Field Sequencing and Life Detection in Remote (79°26’N) Canadian High Arctic Permafrost Ice Wedge Microbial Communities – J Goordial – Frontiers In Microbiology (from December 2017)

Built environment
Diversity of Microbial Communities and Quantitative Chemodiversity in Layers of Marine Sediment Cores from a Causeway (Kaichu-Doro) in Okinawa Island, Japan – Taha Soliman – Frontiers In Microbiology

Microbial Contamination on Touch Surfaces in Sick- and Well-Child Waiting Rooms in Pediatric Outpatient Facilities – Irina Gudakova – The Pediatric Infectious Disease Journal

Biostimulation and bioaugmentation of native microbial community accelerated bioremediation of oil refinery sludge – Ajoy Roy – Bioresource Technology

Temporal variation in bacterial and methanogenic communities of three full-scale anaerobic digesters treating swine wastewater – Gyuseong Han – Environmental Science And Pollution Research International

Microbial community of a gasworks aquifer and identification of nitrate-reducing Azoarcus and Georgfuchsia as key players in BTEX degradation – Martin Sperfeld – Water Research

Review: Microbiome analysis and -omics studies of microbial denitrification processes in wastewater treatment: recent advances – Lili Miao – Science China. Life Sciences

Food microbiology
Absorption and Metabolism of Phenolics from Digests of Polyphenol-Rich Potato Extracts Using the Caco-2/HepG2 Co-Culture System – Shima Sadeghi Ekbatan – Foods (Basel, Switzerland)

Effects of polysaccharides from purple sweet potatoes on immune response and gut microbiota composition in normal and cyclophosphamide treated mice – Chao Tang – Food & Function

A Combined LC-MS Metabolomics- and 16S rRNA Sequencing Platform to Assess Interactions between Herbal Medicinal Products and Human Gut Bacteria in Vitro: a Pilot Study on Willow Bark Extract – Eva-Maria Pferschy-Wenzig – Frontiers In Pharmacology

Review: Inflammatory Bowel Diseases and Fermentable Oligosaccharides, Disaccharides, Monosaccharides, and Polyols: An Overview – Sandra Maria Barbalho – Journal Of Medicinal Food

Probiotics / prebiotics / antibiotics
The antimicrobial peptide SAAP-148 combats drug-resistant bacteria and biofilms – Anna de Breij – Science Translational Medicine

Low amounts of dietary fibre increase in vitro production of short-chain fatty acids without changing human colonic microbiota structure – Daisuke Sasaki – Scientific Reports

Single Cell Observations Show Persister Cells Wake Based on Ribosome Content – Jun-Seob Kim – bioRxiv

Evidence for PMAT- and OCT-like biogenic amine transporters in a probiotic strain of Lactobacillus: Implications for interkingdom communication within the microbiota-gut-brain axis. – Mark Lyte – Plos One

Phages and viruses
Metagenomic Virome Analysis of Culex Mosquitoes from Kenya and China. – Evans Atoni – Viruses

Virus Dynamics Are Influenced by Season, Tides and Advective Transport in Intertidal, Permeable Sediments – Verona Vandieken – Frontiers In Microbiology

Influenza A virus infection impacts systemic microbiota dynamics and causes quantitative enteric dysbiosis – Soner Yildiz – Microbiome

Genome Announcements
Draft Genome Sequence of Megamonas funiformis Strain Marseille-P3344, Isolated from a Human Fecal Microbiota. – Mossaab Maaloum – Genome Announcements

Draft Genome Sequences of Bifidobacterium Strains N4G05 and N5G01, Isolated from the Human Vaginal Microbiome. – Aline C Freitas – Genome Announcements

‘Lactomassilus timonensis,’ a new anaerobic bacterial species isolated from the milk of a healthy African mother – A H Togo – New Microbes And New Infections

Microbes in the news
AGA enrolls 1st patient into largest planned fecal microbiota transplantation study – Eric Oliver – GI & Endoscopy

Will This Swallowable Sensor Replace Colonoscopies? – Bob Curley – HealthLine

**A Patient’s Journey: Taming the Glucose Monster – Howard Wolinsky – MedPage Today**

Microbes on the market
CoreBiome Bolsters Its Board of Directors with the Addition of Daniel Pomp, Ph.D. – BusinessWire

Curetis and MGI Advance Strategic Partnership in NGS-Based Molecular Microbiology – BioSpace

Science, publishing, and career
“Available upon request”: not good enough for microbiome data! – Morgan G I Langille – Microbiome

Tiffany’s non-microbiology picks
Chemists go green to make better blue jeans – Nature
I did not know demin was so dirty until I heard about Everlane’ new jeans – and now there are new method to make them!

January 11, 2018

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Today’s Microbiome Digest is quite long, since it contains alerts from two days. There are many interesting articles in Gut, Plant and Water Microbiome Sections. Interesting review to highlight is from L. Tipton about lung mycobiome  and the one from D. Rose Ewald about human microbiota. Today we also have quite few articles about viruses, among which P.C. Hsu revails gene targets of Ebola virus microRNAs involved in the human skin microbiome,  S. S. Jagdale reports on  mutualistic interactions of viruses with lower eukaryotes and C. Winter explains how mixing alters the lytic activity of viruses in the dark ocean.

General microbiome

Complete genomic characterisation of two Escherichia coli lineages responsible for a cluster of carbapenem resistant infections in a Chinese hospital – Zhiyong Zong – bioRxiv

Geometrical Distribution of Cryptococcus neoformans Mediates Flower-Like Biofilm Development – William Lopes – Frontiers in Microbiology

Pregnancy and early life

Editorial: The Neonatal Immune System: A Unique Host-Microbial Interface – Joseph M. Bliss – Frontiers in Pediatrics

Modeling Metabolic Interactions in a Consortium of the Infant Gut Microbiome – Francisco Pinto – Frontiers in Microbiology

Gene-trait matching across the Bifidobacterium longum pan-genome reveals considerable diversity in carbohydrate catabolism among human infant strains – Silvia Arboleya – Genomics

Early-life gut microbiome and egg allergy – Mina Fazlollahi – Allergy

Human respiratory microbiome

Perspective: Fungal Microbiota in Chronic Airway Inflammatory Disease and Emerging Relationships with the Host Immune Response – Irene Zhang – Frontiers in Microbiology

Microbiome and asthma – Milena Sokolowska – Asthma Research and Practice

Review: The lung mycobiome in the next-generation sequencing era – Laura Tipton – Virulence

The lung tissue microbiota of mild and moderate chronic obstructive pulmonary disease – Alexa A. Pragman – Microbiome

 Oral microbiome

Profiling of subgingival plaque biofilm microbiota in female adult patients with clear aligners: a three-month prospective study – Runzhi Guo – PeerJ

Ecological Approaches to Dental Caries Prevention: Paradigm Shift or Shibboleth? – Nebu Philip  – Caries Research

Human skin microbiome

On revealing the gene targets of Ebola virus microRNAs involved in the human skin microbiome – Pei-Chun Hsu – PeerJ

Temporal Variation of the Skin Bacterial Community and Batrachochytrium dendrobatidis Infection in the Terrestrial Cryptic Frog Philoria loveridgei – Mariel Familiar López – Frontiers in Microbiology

Human vaginal microbiome

Microbiota-based analysis reveals specific bacterial traits and a novel strategy for the diagnosis of infectious infertility – Simon Graspeuntner – PLOS One

Human nearly-sterile sites 

Culture-independent analysis of liver abscess using nanopore sequencing – Liang Gong – PLOS One

Human gut microbiome

The Gut Microbiome and Control of Weight Gain – Anita L. Kozyrskyj – Pediatric Obesity

Immunosuppressive effect of the gut microbiome altered by high-dose tacrolimus in mice – Z. Zhang – American Journal of Transplatation

Review: Human microbiota, blood group antigens, and disease – D. Rose Ewald – WIREs

Microbiome, Immunomodulation, and the Neuronal System – Eric Marietta – Neurotherapeutics

Editorial: Improve gut microbiome: a new horizon of cancer therapy – Hiroshi Fukui – Hepatobiliary Surgery and Nutrition

The Gut Microbiome and Multiple Sclerosis – Javier Ochoa-Repáraz – Cold Spring Harbor Perspectives in Medicine

Genomic diversity and distribution of Bifidobacterium longum subsp. longum across the human lifespan – Toshitaka Odamaki – Scientific Reports

Dynamics of metatranscription in the inflammatory bowel disease gut microbiome – Melanie Schirmer – Nature Microbiology

Links between Dietary Protein Sources, the Gut Microbiota, and Obesity – Lise Madsen – Frontiers in Physiology

Ceftriaxone promotes the emergence of AmpC-overproducing Enterobacteriaceae in gut microbiota from hospitalized patients – Victoire de Lastours – European Journal of Clinical Microbiology & Infectious Diseases

Functional analysis of arginine decarboxylase gene speA of Bacteroides dorei by markerless gene deletion – Mikiyasu Sakanaka – FEMS Microbiology Letters

SadA-Expressing Staphylococci in the Human Gut Show Increased Cell Adherence and Internalization – Arif Luqman – Cell Reports

Gut microbiome populations are associated with structure-specific changes in white matter architecture – Irene M. Ong – Translational Psychiatry

Spatiotemporally Heterogeneous Population Dynamics of Gut Bacteria Inferred from Fecal Time Series Data – Hidetoshi Inaminea – mBio

Animal experiments 

Identification of a protective B-cell epitope of the Staphylococcus aureus GapC protein by screening a phage-displayed random peptide library – Mengyao Wang – PLOS One

Lactobacillus plantarum CCFM10 alleviating oxidative stress and restoring the gut microbiota in D-galactose-induced aging mice – Jichun Zhao – Food and Function

Effect of dark sweet cherry powder consumption on the gut microbiota, short-chain fatty acids, and biomarkers of gut health in obese db/db mice – Jose F. Garcia-Mazcorro – PeerJ

Dietary Corn Bran Fermented by Bacillus subtilis MA139 Decreased Gut Cellulolytic Bacteria and Microbiota Diversity in Finishing Pigs – Ping Liu – Frontiers in Cellular and Infection Microbiology

Intestinal and Systemic Immune Responses upon Multi-drug Resistant Pseudomonas aeruginosa Colonization of Mice Harboring a Human Gut Microbiota – Eliane von Klitzing – Frontiers in Microbiology

Modulation of Intestinal Microbiome Prevents Intestinal Ischemic Injury – Alessandra Bertacco – Frontiers in Physiology

Animal microbiome 

Influence of fruit and invertebrate consumption on the gut microbiota of wild white-faced capuchins (Cebus capucinus) – Elizabeth K. Mallott – American Journal of Physical Anthropology

Differential Ecological Specificity of Protist and Bacterial Microbiomes across a Set of Termite Species – Lena Waidele – Frontiers in Microbiology

Molecular identification and phylogenetic analysis of Bothrops insularis bacterial and fungal microbiota – Lidiane Nunes Barbosa – Journal of Toxicology and Environmental Health

Plant, root, and soil microbiome

Diazotroph abundance and community composition in an acidic soil in response to aluminum-tolerant and aluminum-sensitive maize (Zea mays L.) cultivars under two nitrogen fertilizer forms – Chao Wang – Plant and Soil

The influence of microbial communities for triadimefon enantiomerization in soils with different pH values – Khaled Mohamed Ahmed Talab – Chirality

Antimony Redox Biotransformation in the Subsurface: Effect of Indigenous Sb(V) Respiring Microbiota – Liying Wang – Encironmental Science and Technology

Biostimulant Action of Protein Hydrolysates: Unraveling Their Effects on Plant Physiology and Microbiome – Giuseppe Colla – Frontiers in Plant Science

Inner Plant Values: Diversity, Colonization and Benefits from Endophytic Bacteria – Hongwei Liu – Frontiers in Microbiology

Bacillus amyloliquefaciens L-S60 Reforms the Rhizosphere Bacterial Community and Improves Growth Conditions in Cucumber Plug Seedling – Yuxuan Qin – Frontiers in Microbiology

Exploring the Microbiota of Faba Bean: Functional Characterization of Lactic Acid Bacteria – Michela Verni –  Frontiers in Microbiology

Contribution of Zinc Solubilizing Bacteria in Growth Promotion and Zinc Content of Wheat – Sana Kamran – Frontiers in Microbiology

Application of Endophytic Pseudomonas fluorescens and a Bacterial Consortium to Brassica napus Can Increase Plant Height and Biomass under Greenhouse and Field Conditions –  Richard D. Lally – Frontiers in Microbiology

Exploiting rhizosphere microbial cooperation for developing sustainable agriculture strategies – Yoann Besset-Manzoni – Environmental Science and Pollution Research

Dynamics of oxygen and carbon dioxide in rhizospheres of Lobelia dortmanna – a planar optode study of belowground gas exchange between plants and sediment – Nikola Lenzewski – New Phytologist

Characterization of Microbial Communities in Acidified, Sulfur Containing Soils – Grzegorz Czerwonka – Polish Journal of Microbiology

Comparison of Microbial Communities Associated with Halophyte (Salsola stocksii) and Non-Halophyte (Triticum aestivum) Using Culture-Independent Approaches – Salma Mukhtar – Polish Journal of Microbiology

Water and extremophile microbiome 

Data-mining of Antibiotic Resistance Genes Provides Insight into the Community Structure of Ocean Microbiome – Shiguang Hao – bioRxiv

Mixing alters the lytic activity of viruses in the dark ocean – Christian Winter – Ecology

Biological Characterization of Microenvironments in a Hypersaline Cold Spring Mars Analog – Haley M. Sapers – Frontiers in Microbiology

Patterns and Drivers of Vertical Distribution of the Ciliate Community from the Surface to the Abyssopelagic Zone in the Western Pacific Ocean – Feng Zhao – Frontiers in Microbiology

Aerobic and Anaerobic Methanotrophic Communities Associated with Methane Hydrates Exposed on the Seafloor: A High-Pressure Sampling and Stable Isotope-Incubation Experiment – David H. Case – Frontiers in Microbiology

A Multi-season Investigation of Microbial Extracellular Enzyme Activities in Two Temperate Coastal North Carolina Rivers: Evidence of Spatial but Not Seasonal Patterns – Avery Bullock – Frontiers in Microbiology

Functional Stability and Community Dynamics during Spring and Autumn Seasons Over 3 Years in Camargue Microbial Mats – Mercedes Berlanga – Frontiers in Microbiology

Oxygenation of Hypoxic Coastal Baltic Sea Sediments Impacts on Chemistry, Microbial Community Composition, and Metabolism – Elias Broman – Frontiers in Microbiology

Exploring the Cultivable Ectocarpus Microbiome – Hetty KleinJan – Frontiers in Microbiology

Phylogenetic Structure and Metabolic Properties of Microbial Communities in Arsenic-Rich Waters of Geothermal Origin – Simona Crognale – Frontiers in Microbiology

Prokaryotic Community Composition in Arctic Kongsfjorden and Sub-Arctic Northern Bering Sea Sediments As Revealed by 454 Pyrosequencing – Yin-Xin Zeng – Frontiers in Microbiology

Comparative Metagenomics Reveals the Distinctive Adaptive Features of the Spongia officinalis Endosymbiotic Consortium – Elham Karimi – Frontiers in Microbiology

Comparative genomics highlights symbiotic capacities and high metabolic flexibility of the marine genus Pseudovibrio  – Dennis Versluis – GBE Genome BIology and Evolution

Geobacteraceae are important members of mercury-methylating microbial communities of sediments impacted by waste water releases – Andrea G. Bravo – ISME

Dynamics of phytoplankton and heterotrophic bacterioplankton in the western tropical South Pacific Ocean along a gradient of diversity and activity of diazotrophs – France Van Wambeke – Biogeosciences

Microbial methanogenesis in the sulfate-reducing zone of sediments in the Eckernförde Bay, SW Baltic Sea – Johanna Maltby – Biogeosciences

Built environment

Control of corrosive bacterial community by bronopol in industrial water system – Jayaraman Narenkumar – 3 Biotech

A metaproteomics method to determine carbon sources and assimilation pathways of species in microbial communities –  Manuel Kleiner – bioRxiv

Uncovering the Potential of Termite Gut Microbiome for Lignocellulose Bioconversion in Anaerobic Batch Bioreactors – Lucas Auer – Frontiers in Microbiology

Microbial Communities Shaped by Treatment Processes in a Drinking Water Treatment Plant and Their Contribution and Threat to Drinking Water Safety – Qi Li – Frontiers in Microbiology

Food microbiology

Development of novel quinoa-based yoghurt fermented with dextran producer Weissella cibaria MG1 – Emanuele Zannini – International Journal of Food Microbiology

Bacterial Community and Spoilage Profiles Shift in Response to Packaging in Yellow-Feather Broiler, a Highly Popular Meat in Asia – Huhu Wang – Frontiers in Microbiology

Metagenomic Profiling of the Bacterial Community Changes from Koji to Mash Stage in the Brewing of Soy Sauce – Hongbin Wang – Polish Journal of Microbiology

Probiotics / prebiotics

Probiotics or Pro-healers the Role of Beneficial Bacteria in Tissue Repair – Jovanka Lukic – Wound Reparation and Regeneration

Probiotic Lactobacillus sp. inhibit growth, biofilm formation and gene expression of caries-inducing Streptococcus mutans – Reham Wasfi – Journal of Cellular and Molecular Medicine

A mixture of Lactobacillus species isolated from traditional fermented foods promote recovery from antibiotic-induced intestinal disruption in mice – Ying Shi – Journal of Applied Microbiology

Beneficial changes in rumen bacterial community profile in sheep and dairy calves as a result of feeding the probiotic Bacillus amyloliquefaciens H57 – Benjamin J Schofield – Journal of Applied Microbiology

Phages and viruses

Enemies with benefits: mutualistic interactions of viruses with lower eukaryotes – Shounak S. Jagdale – Archives of Virology

Biogeography & environmental conditions shape bacteriophage-bacteria networks across the human microbiome – Geoffrey D. Hannigan – bioRxiv

Investigation of prevalence of free Shiga toxin-producing Escherichia coli (STEC)-specific bacteriophages and its correlation with STEC bacterial hosts in a produce-growing area in Salinas, California – Yen-Te Liao – PLOS One

Component tree analysis of cystovirus φ6 nucleocapsid Cryo-EM single particle reconstructions – Lucas M. Oliveira – PLOS One

Bioinformatics

HTSSIP: An R package for analysis of high throughput sequencing data from nucleic acid stable isotope probing (SIP) experiments – Nicholas D. Youngblut – PLOS One

Biotechnology

Cyanobacterial diversity held in microbial biological resource centers as a biotechnological asset: the case study of the newly established LEGE culture collection – Vitor Ramos – Journal of Applied Phycology

Rapidly moving new bacteria to model-organism status – Hualan Liu – Current Opinion in Biotechnology

Techniques

Development of a biosensor protein bullet as a fluorescent method for fast detection of Escherichia coli in drinking water – Ignacio Gutiérrez-del-Río – PLOS One

Research Note: Methods for detecting Gemmata spp. bacteremia in the microbiology laboratory – Jacques-Robert Christen – BMS Genomics

A metaproteomics method to determine carbon sources and assimilation pathways of species in microbial communities – Manuel Kleiner – bioRxiv

Microbes in the news 

Gene/cell connection provides new insight into how our gut microbiome stays healthy

A powerful new weapon against drug-resistant bacteria was inspired by the human body

ASU developing biodegradable plastics made from bacteria

Pharmaceutical Pollution Drives Microbial Resistance in Urban Streams

Microbes and Art

This scientist creates ephemeral works of art with bioluminescent bacteria

January 9, 2018

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Today, a brief digest with several reviews: microbiota in multiple sclerosis, food allergy, microbiome and diabetes, modulation of cardiovascular diseases and more. Additionally: GI tract gas analysis, SCFA effects on human, and the effect of inulin-type fructans on human microbiota.  

Human Microbiome

Review: The Local Defender and Functional Mediator: Gut Microbiome – Yang H. – Digestion

Review: Update of treatment algorithms for Clostridium difficile infection – R.E. Ooijevaar – Clinical Microbiology and Infection

Review: Gut microbiome and pediatric multiple sclerosis – Helen Tremlett – Multiple Sclerosis Journal

Review: “Evaluating Causality of Gut Microbiota in Obesity and Diabetes in Humans” – A.S. Meijnikman – Endocrine Reviews

Review: Mechanisms of food allergy – Hugh A. Sampson – Journal of Allergy and Clinical Immunology

Review: Microbial modulation of cardiovascular disease – J. Mark Brown  – Nature Reviews Microbiology

A human pilot trial of ingestible electronic capsules capable of sensing different gases in the gut – Kourosh Kalantar-Zadeh – Nature Electronics

An introduction to the microbiome and MS – Sebastien Trott – Multiple Sclerosis Journal

Anatomic Site of Sampling and the Rectal Mucosal Microbiota in HIV negative MSM engaging in CRAI – Nicole Pescatore – AIDS Research and Human Retroviruses

Clinical sources and antimicrobial susceptibility of Prevotella timonensis at the university hospital of Montpellier, France – Salim Aberkane – Anaerobe

A human pilot trial of ingestible electronic capsules capable of sensing different gases in the gut – Kourosh Kalantar-Zadeh – Nature Electronics

Microbiota derived short chain fatty acids promote histone crotonylation in the colon through histone deacetylases – Rachel Fellows – Scientific Reports

Increased Abundance of Clostridium and Fusobacterium in Gastric Microbiota of Patients with Gastric Cancer in Taiwan – Yung-Yu Hsieh – Scientific Reports

SCFAs strongly stimulate PYY production in human enteroendocrine cells – P. Larraufie – Scientific Reports

Profiling the lymphoid-resident T cell pool reveals modulation by age and microbiota – Aurélie Durand – Nature Communications

 

Animal Microbiome

Evaluation of the effects of different diets on microbiome diversity and fatty acid composition of rumen liquor in dairy goat – P. Cremonesi – Animal

Ecological plasticity in the gastrointestinal microbiomes of Ethiopian Chlorocebus monkeys – Pål Trosvik – Scientific Reports

Dietary soybean meal affects intestinal homoeostasis by altering the microbiota, morphology and inflammatory cytokine gene expression in northern snakehead – Shuyan Miao – Scientific Reports

 

Food Microbiome

Bacterial community assembly from cow teat skin to ripened cheeses is influenced by grazing systems – Marie Frétin – Scientific Reports

 

Beneficial Microbes and Beneficial Compounds

Tetraglochin cristatum (Britton) Roth: a medicinal plant from the Argentinean highlands with potential use in vaginal candidiasis – María Alejandra Moreno – Journal of Ethnopharmacology

Habitual dietary fibre intake influences gut microbiota response to an inulin-type fructan prebiotic: a randomised, double-blind, placebo-controlled, cross-over, human intervention study – Genelle Healey – British Journal of Nutrition

Genomic diversity and distribution of Bifidobacterium longum subsp. longum across the human lifespan – Toshitaka Odamaki – Scientific Reports

 

Extremophiles

Deepest and hottest hydrothermal activity in the Okinawa Trough: the Yokosuka site at Yaeyama Knoll – Junichi Miyazaki – Royal Society Open Science

January 8, 2018

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Today’s Microbiome Digest has many interesting articles. Read how microscope-based artificial intelligence could alleviate shortage of clinical microbiologists, the article by K. P. Smith. N. A. Kamennaya reports on “Pomacytosis”, a semi-extracellular phagocytosis of cyanobacteria, while M. F. Dias investigated the effect of different drinking waters on mouse gut microbiota.

Events

One-day Symposium (12 Jan 2018): Microbial symbiosis in the marine environment – live streamming

Jobs

Postdoctoral positions in evolutionary genomics, UT Austin

General microbiome

Dietary trehalose enhances virulence of epidemic Clostridium difficile – J. Collins – Nature

Transmission in the Origins of Bacterial Diversity, From Ecotypes to Phyla – Frederick M. Cohan – Microbiology Spectrum

How much do rRNA gene surveys underestimate extant bacterial diversity? – Luis M. Rodriguez-R – Applied and Environmental Microbiology

Vibrio cholerae genomic diversity within and between patients –  Inès Levade – Microbial Genomics

Automated Interpretation of Blood Culture Gram Stains using a Deep Convolutional Neural Network – Kenneth P. Smith – Applied and Environmental Microbiology

Regulated ploidy of Bacillus subtilis and three new isolates of Bacillus and Paenibacillus – Benjamin Böttinger – FEMS Microbiology Letters

Human respiratory microbiome

Heavy metal exposure and nasal Staphylococcus aureus colonization: analysis of the National Health and Nutrition Examination Survey (NHANES) – Shoshannah Eggers – Environmental Health

Oral microbiome

Microbial Analysis of Endodontic Infections in Root-filled Teeth with Apical Periodontitis before and after Irrigation Using Pyrosequencing – Homan Zandi – Journal of Endodontics

Human vaginal microbiome

Long-term Lactobacillus rhamnosus BMX 54 application to restore a balanced vaginal ecosystem: a promising solution against HPV-infection – Ettore Palma – BMC Infectious Diseases

Lactobacillus-deficient vaginal microbiota dominate post-partum women in rural Malawi – Ronan Doyle – Applied and Environmental Microbiology

Human nearly-sterile sites

Microbiota and the liver – Ting-Chin David Shen – Liver Transplatation

Human gut microbiome

Comparison of DNA extraction methods for human gut microbial community profiling – Mi Young Lim – Systematic and Applied Microbiology

Changes in Gut Microbiota–Related Metabolites and Long-term Successful Weight Loss in Response to Weight-Loss Diets: The POUNDS Lost Trial – Yoriko Heianza – Diabetes Care

Adaptation of human gut microbiota to bariatric surgeries in morbidly obese patients: A systematic review – Hanieh-Sadat Ejtahed – Microbial Pathogenesis

The germ-organ theory of non-communicable diseases – Mariana X. Byndloss – Nature Reviews Microbiology

Evolution of a dominant natural isolate of Escherichia coli in the human gut over a year suggests a neutral evolution with reduced effective population size – Mohamed Ghalayini – Applied and Environmental Microbiology

Animal experiments

Changes in mouse gut bacterial community in response to different types of drinking water – Marcela F. Dias – Water Research

Plant, root, and soil microbiome

Microbial Communities of High-Elevation Fumaroles, Penitentes, and Dry Tephra “Soils” of the Puna de Atacama Volcanic Zone – Adam J. Solon – Microbial Ecology

Shifts in soil bacterial and archaeal communities during freeze-thaw cycles in a seasonal frozen marsh, Northeast China – Jiusheng Ren – Science of The Total Environment

The ‘Neglected’ Soil Virome – Potential Role and Impact – Akbar Adjie Pratama – Trends in Microbiology

Water and extremophile microbiome 

Study of marine bacteria inactivation by photochemical processes: disinfection kinetics and growth modeling after treatment – Javier Moreno-Andrés – Environmental Science and Pollution Research

Metabolic capability and in situ activity of microorganisms in an oil reservoir – Yi-Fan Liu – Microbiome

Phylogenetic distribution of roseobacticides in the Roseobacter group and their effect on microalgae – Eva C Sonnenschein – BioRxiv

“Pomacytosis”—Semi-extracellular phagocytosis of cyanobacteria by the smallest marine algae – Nina A. Kamennaya – PLOS Biology

The Green Berry Consortia of the Sippewissett Salt Marsh: Millimeter-Sized Aggregates of Diazotrophic Unicellular Cyanobacteria – Elizabeth G. Wilbanks – Frontiers in Microbiology

Dynamic changes in carbonate chemistry in the microenvironment around single marine phytoplankton cells – Abdul Chrachri – Nature Communications

Homogenization of lake cyanobacterial communities over a century of climate change and eutrophication – Marie-Eve Monchamp – Nature Ecology & Evolution

Bacterial Recycling of Archaeal Biomass as a New Strategy for Extreme Life in the Dead Sea Deep Sediment – Camille Thomas – EarthArXiv Preprints

Food microbiology

Seasonal variances in bacterial microbiota and volatile organic compounds in raw milk – Beata Nalepa – International Journal of Food Microbiology

Phages and viruses

Is weak CD4+ gain in the course of suppressive combination antiretroviral therapy for HIV infection a current clinical challenge? A case report and brief review of the literature – Camilla Tincati – BMC Infectious Diseases

Techniques

NanoAmpli-Seq: A workflow for amplicon sequencing from mixed microbial communities on the nanopore sequencing platform – Szymon T Calus – bioRxiv

Microbes in the news

Scientists engineer sound-reflecting bacteria

Experts: ‘Raw Water’ Offers Unfiltered Risk

 

January 7, 2018

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Today’s digest is brief but full of fun and exciting news about microbes, including self-portraits of microbes on your skin and how AI (artificial intellegence) is used to identify bacteria.

Gut Microbiome

REVIEW: Gut as a target for cadmium toxicity. Tinkov, AA. Environmental Pollution

Plant, Soil, and Water Microbiome

Effects of short-term fallow managements on soil microbial properties: A case study in China. Li, G. Applied Soil Ecology

Animal Experiments and Microbiome

Environmental concentrations of antibiotics impair zebrafish gut health. Zhou, L. Environmental Pollution

Polystyrene microplastics induce microbiota dysbiosis and inflammation in the gut of adult zebrafish. Jin, Y. Environmental Pollution

Food Microbiome

REVIEW: Seafood spoilage microbiota and associated volatile organic compounds at different storage temperatures and packaging. Odeyemi, OA. International Journal of Food Microbiology.

Microbes in the NEWS

The Swab Test: Amount Of Bacteria On Touchscreens May Surprise You

-CBS Philly

Artificial intelligence used to identify bacteria

-Digital Journal

Physicists Solve the Biodiversity Arms-Race Paradox: “Kill the Winner”

-Inverse

A Self-Portrait of the Microbes that Live on our Skin

-Labiotech.eu (blog)

Microbiology Jobs

Part-Time Lab Technician II, Biology/Microbiology

-Inside Higher Ed Careers

January 5, 2018

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Today’s digest has an interesting commentary on the oral-gut connection and a brilliant piece on microbial diversity. Lastly, a look at how grapevines influence belowground diversity and networks

General Microbiome

A role for the endometrial microbiome in dysfunctional menstrual bleeding. Pelzer ES. Antonie Van Leeuwenhoek.

Performance and microbial community variations of anaerobic digesters under increasing tetracycline concentrations. Xiong Y. Applied Microbiology and Biotechnology

In Nature, There Is Only Diversity. McLaren MR. MBio.

Gut Microbiome

Commentary: Oral-gut connection: one step closer to an integrated view of the gastrointestinal tract? Lira-Junior R. Mucosal Immunology

Bile acids at the cross-roads of gut microbiome-host cardiometabolic interactions. Ryan PM. Diabeticology and Metabolic Syndrome

REVIEW: Diet, Microbiota, and Metabolic Health: Trade-Off Between Saccharolytic and Proteolytic Fermentation. Korpela K. Annual of Food Science and Technology

Nasal and Lung Microbiome

REVIEW: Fungi in Bronchiectasis: A Concise Review. Máiz L. Internatioanal Journal of Molecular Sciences

Alterations in the mucosa-associated fungal microbiota in patients with ulcerative colitis. Qiu X. Oncotarget

The association between anterior nares and nasopharyngeal microbiota in infants hospitalized for bronchiolitis. Luna PN. Microbiome

Fecal Microbiome

Editorial Comment: Fecal microbiota transplantation as a possible treatment of irritable bowel syndrome. Juncadella AC. Annals of Translational Medicine

Plant, Soil, and Water Microbiome

Co-variation between Distribution of Microbial Communities and Biological Metabolization of Organics in Urban Sewer Systems. Jin P. Environmental Science and Technology.

Do invasive plants structure microbial communities to accelerate decomposition in intermountain grasslands? McTee MR. Ecology and Evolution

Grapevine rootstocks shape underground bacterial microbiome and networking but not potential functionality. Marasco R. Microbiome

Biodiversity of the microbial mat of the Garga hot spring. Rozanov AS. BMC Evolutionary Biology

Animal Experiments and Microbiome

Microbiota Reconstitution Does Not Cause Bone Loss in Germ-Free Mice. Quach D. mSphere

Physiological Translocation of Lactic Acid Bacteria during Pregnancy Contributes to the Composition of the Milk Microbiota in Mice. de Andrés J. Nutrients

Extreme sensitivity to ultraviolet light in the fungal pathogen causing white-nose syndrome of bats. Palmer JM. Nature Communication

OCCURRENCE OF PASTEURELLACEAE BACTERIA IN THE ORAL CAVITY OF SELECTED MARSUPIAL SPECIES. Hansen MJ. Journal of Zoo and Wildlife Medicine

Marine Microbiome

Agelas Wasting Syndrome Alters Prokaryotic Symbiont Communities of the Caribbean Brown Tube Sponge, Agelas tubulata.Deignan LK. Microbial Ecology

Environmental drivers of heterogeneity in the trophic-functional structure of protozoan communities during an annual cycle in a coastal ecosystem. Xu G. Marine Pollution Bulletin

Antibiotic Resitance

Editorial: Empiric antibiotic use in allogeneic hematopoietic cell transplantation: should we avoid anaerobe coverage? Shono Y. Blood Advances

Characterization of genetic determinants involved in antibiotic resistance in Aeromonas spp. and fecal coliforms isolated from different aquatic environments. Carnelli A. Research in Microbiology

 

 

January 2, 2018

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Happy New Year from the Microbiome Digest team!

General microbiome

Pre-print: Understanding How Microbiomes Influence The Systems They Inhabit: moving from a correlative to a causal research framework – E K Hall – bioRxiv

Human vaginal microbiome

A retrospective pilot study to determine whether the reproductive tract microbiota differs between women with a history of infertility and fertile women – Bryan A Wee – Australian and New Zealand Journal of Obstetrics and Gynaecology

Human gut microbiome

Rates of Gut Microbiome Divergence in Mammals – Alex H Nishida – Molecular Ecology

Animal microbiome

Processes shaping gut microbiota diversity in allopatric populations of the endemic lizard Podarcis lilfordi from Menorcan islets (Balearic Islands) – Laura Baldo – FEMS Microbiology Ecology

Individual- and Species-Specific Skin Microbiomes in Three Different Estrildid Finch Species Revealed by 16S Amplicon Sequencing – Kathrin Engel – Microbial Ecology

Plant, root, and soil microbiome

Vertical variation of a black soil’s properties in response to freeze-thaw cycles and its links to shift of microbial community structure – Ziming Han – Science of the Total Environment

Biomass, activity and structure of rhizosphere soil microbial community under different metallophytes in a mining site – Wenhao Yang – Plant and Soil

Symbiotic nitrogen fixation by rhizobia — the roots of a success story – Catherine Masson-Boivin – Current Opinion in Plant Biology

Water and extremophile microbiome

Microbial community structure and function in sediments from e-waste contaminated rivers at Guiyu area of China – Jun Liu – Environmental Pollution

Pre-print: Micro-scale ecology regulates particulate organic matter turnover in model marine microbial communities – Tim N Enke – bioRxiv

Food microbiology

Autochthonous facility-specific microbiota dominates washed-rind Austrian hard cheese surfaces and its production environment – Narciso M Quijada – International Journal of Food Microbiology

Bioinformatics

CoMet: a workflow using contig coverage and composition for binning a metagenomic sample with high precision – Damayanthi Herath – BMC Bioinformatics

Techniques

Serial Dilution-Based Growth Curves and Growth Curve Synchronization for High-Resolution Time Series of Bacterial Biofilm Growth – Fernando Govantes – Host-Pathogen Interactions

Microbes in the news

Fiber Is Good for You. Now Scientists May Know Why. – Carl Zimmer – The New York Times

Fast, Cheap Testing for Tuberculosis? Soon It May Be Possible – Donald G McNeil – The New York Times

How probiotics can help ward off health complications in premature babies – CTV News

Science, career, and publishing

Pre-print: Disequilibrium in Gender Ratios among Authors who Contributed Equally – Nichole A Broderick – bioRxiv

December 26, 2017

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Quite a few articles today especially in the plant/soil and water/extremophile sections. Plus: a new zebrafish model of the human gut microbiome, fiber and bifidos protect against north american diet-induced increased gut permeability in mice, prebiotics from the Morinda plant not only alter the gut microbiome but improve Alzheimers-like symptoms in a rat model, micro-eukaryotes may be an important factor in a deadly skin fungus infection in the Cascades Frog, and a new Leaf-FISH technique to visualize bacterial communities on plants. Happy Holidays!

Human oral microbiome

The oral microbiome—the relevant reservoir for acute pediatric appendicitis? – Carlotta Blod – International Journal of Colorectal Disease

Differences in carbon source usage by dental plaque in children with and without early childhood caries – Yan Zhao – International Journal of Oral Science

Review: Task Force on Design and Analysis in Oral Health Research: Host-Microbiome Interactions in Dysbiosis – T.E. Van Dyke – JDR Clinical & Translational Research

Human gut microbiome

Review: Probiotics and necrotizing enterocolitis – Ravi Mangal Patel – Seminars in Pediatric Surgery

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Animal experiments

Fusimonas intestini gen. nov., sp. nov., a novel intestinal bacterium of the family Lachnospiraceae associated with diabetes in mice – Hiroyuki Kusada – Scientific Reports

*Zebrafish Axenic Larvae Colonization with Human Intestinal Microbiota – Arias-Jayo Nerea – Zebrafish

*Bifidobacteria or Fiber Protects against Diet-Induced Microbiota-Mediated Colonic Mucus Deterioration – Bjoern O. Schroeder – Cell Host & Microbe

In Silico Analysis of the Small Molecule Content of Outer Membrane Vesicles Produced by Bacteroides thetaiotaomicron Indicates an Extensive Metabolic Link between Microbe and Host – William A. Bryant – Frontiers in Microbiology

*Prebiotic Effect of Fructooligosaccharides from Morinda officinalis on Alzheimer’s Disease in Rodent Models by Targeting the Microbiota-Gut-Brain Axis – Diling Chen – Frontiers in Aging Neuroscience

Animal microbiome

Effect of Environmental Factors and an Emerging Parasitic Disease on Gut Microbiome of Wild Salmonid Fish – Anti Vasemägi – mSphere

*Composition of Micro-eukaryotes on the Skin of the Cascades Frog (Rana cascadae) and Patterns of Correlation between Skin Microbes and Batrachochytrium dendrobatidis – Jordan G. Kueneman – Frontiers in Microbiology

Plant, root, and soil microbiome

Chemical investigation of metabolites produced by an endophytic fungi Phialemonium curvatum from the leaves of Passiflora edulis –  G. R. Nalin Rathnayake – Natural Product Research

Novel hydrocarbonoclastic metal-tolerant Acinetobacter and Pseudomonas strains from Aconcagua river oil-polluted soil – Valentina Méndez – Journal of soil science and plant nutrition

Spatial patterns of enzyme activities in the rhizosphere: Effects of root hairs and root radius – Xiaomin Ma – Soil Biology and Biochemistry

The rhizosphere microbial community response to a bio-organic fertilizer: finding the mechanisms behind the suppression of watermelon Fusarium wilt disease – Jia Zhao – Acta Physiologiae Plantarum

Efficiency of two inoculation methods of Pseudomonas putida on growth and yield of tomato plants – Luis G. Hernández-Montiel – Journal of soil science and plant nutrition

Rhizospere yeasts improve P uptake of a maize arbuscular mycorrhizal association – Marcela Sarabia – Applied Soil Ecology

Ammonia-oxidizing microorganisms: key players in the promotion of plant growth – Adenike Eunice Amoo – Journal of soil science and plant nutrition

Review: Potassium solubilizing bacteria (KSB): Mechanisms, promotion of plant growth, and future prospects ­ A review – H. Etesami – Journal of soil science and plant nutrition

Long-term phosphorus fertilization effects on arbuscular mycorrhizal fungal diversity in Uruguayan grasses – Silvina García – Journal of soil science and plant nutrition

Alcaligenes faecalisassociated with Mimosa calodendron rizhosphere assist plant survival in arsenic rich soils – Érica Barbosa Felestrino – Journal of soil science and plant nutrition

Functional land-use change effects on soil fungal communities in Chilean temperate rainforests – César Marín – Journal of soil science and plant nutrition

Probiotic strain Stenotrophomonas acidaminiphila BJ1 degrades and reduces chlorothalonil toxicity to soil enzymes, microbial communities and plant roots – Qingming Zhang – AMB Express

Low light availability alters root exudation and reduces putative beneficial microorganisms in seagrass roots –  Belinda C. Martin – Frontiers in Microbiology

Effects of biochar on nutrients and the microbial community structure of tobacco-planting soils – Gao Lin – Journal of soil science and plant nutrition

Root-associated bacterial and fungal community profiles of Arabidopsis thaliana are robust across contrasting soil P levels – Chanz Robbins – Phytobiomes

Water and extremophile microbiome

Biogeographical patterns of bacterial and archaeal communities from distant hypersaline environments – M.R. Mora-Ruiz del – Systematic and Applied Microbiology

Cloning, Over-Expression, and Purification of Carbonic Anhydrase from an Extremophilic Bacterium: An Introduction to Advanced Molecular Biology – Vijayakumar Somalinga – The American Biology Teacher

Salinivibrio kushneri sp. nov., a moderately halophilic bacterium isolated from salterns – Clara López-Hermoso – Systematic and Applied Microbiology

Genome sequencing and heterologous expression of antiporters reveal alkaline response mechanisms of Halomonas alkalicola – Lei Zhai – Extremophiles

Benthic phototrophic community from Kiran soda lake, south-eastern Siberia – Ekaterina I. Burganskaya – Extremophiles

Enhancing the adaptability of the deep-sea bacterium Shewanella piezotolerans WP3 to high pressure and low temperature by experimental evolution under H2O2 stress – Zhe Xie – Applied and Environmental Microbiology

Fungal community structure at pelagic and littoral sites in Lake Biwa determined with high-throughput sequencing – Peixue Song – Limnology

Spatiotemporal dynamics of marine bacterial and archaeal communities in surface waters off the northern Antarctic Peninsula – Camila N. Signori – Deep Sea Research Part II: Topical Studies in Oceanography

Microbial Ecology

Dissertation: The Macroecology of Microorganisms: From Pattern to Process – David Clark – University of Essex

Review: Using metabolic networks to resolve ecological properties of microbiomes – Emilie E.L. Muller – Current Opinion in Systems Biology

Microbial stress mediated intercellular nanotubes in an anaerobic microbial consortium digesting cellulose – Martina John – Scientific Reports

Built environment

Distribution of Legionella and bacterial community composition among regionally diverse US cooling towers – Anna C. Llewellyn – PLOS one

Food microbiology

Identification of natural antimicrobial peptides from bacteria through metagenomic and metatranscriptomic analysis of high-throughput transcriptome data of Taiwanese oolong teas – Kai-Yao Huang – BMC Systems Biology

Strain-Level Metagenomic Analysis of the Fermented Dairy Beverage Nunu Highlights Potential Food Safety Risks – Aaron M. Walsh – Applied and Environmental Microbiology

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Probiotics / prebiotics

Review: Recent Development of Prebiotic Research—Statement from an Expert Workshop – Giorgio La Fata – Nutrients

Effects of fermented soymilk with Lactobacillus casei Shirota on skin condition and the gut microbiota: a randomised clinical pilot trial – T. Nagino – Beneficial Microbes

Phages and viruses

Novel ssDNA viruses detected in the virome of bleached, habitat-forming kelp Ecklonia radiata –  Douglas Beattie – Frontiers in Marine Science

Bioinformatics

Vipie: web pipeline for parallel characterization of viral populations from multiple NGS samples – Jake Lin – BMC Genomics

Techniques

*Leaf-FISH: Microscale imaging of bacterial taxa on phyllosphere –  Elena L. Peredo – Frontiers in Microbiology

A new suite of plasmid vectors for fluorescence-based imaging of root colonizing pseudomonads –  Rosemarie Wilton – Frontiers in Plant Science

Synthetic microbial consortia enable rapid assembly of pure translation machinery – Fernando Villarreal – Nature Chemical Biology

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Microbes in the news

Essential science: Link between gut microbes and despair – Tim Sandle – Digital Science

Enjoy the holidays, but don’t forget your fiber – Tim Sandle – Digital Science

 

December 23, 2017

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Events and jobs
Assistant Professor of Environmental Microbiology (Tenure-Track) – George Mason University – Fairfax, Virginia, USA
The George Mason University, Department of Environmental Science and Policy (ESP) is seeking an enthusiastic and energetic individual for a Tenure-Track Assistant Professor position in Molecular Environmental Microbiology to supplement existing departmental strengths in applied ecology, aquatic ecology, one health and conservation. This is a full-time, tenure-track position to begin August 2018.

Manager, QC Microbiology – Catalent Pharma Solutions, Inc. – Madison, Wisconsin, USA

Post-Doc – Microbiology & Immunology – Cornell University – Ithaca, NY, USA

Biological Sciences Full-Time Instructor (Microbiology Emphasis) – West Valley-Mission Community College District – Saratoga, CA, USA

General microbiome
Review: Building conventions for unconventional lymphocytes. – Lesley Pasman – Immunological Reviews (from September, but not posted before)

Pregnancy and early life
Gut microbiome in gestational diabetes: a cross-sectional study of mothers and offspring 5 years postpartum – Sayyid Hasan – AOGS

Multi-site human microbiome
Review: The role of microbial amyloid in neurodegeneration. – Robert P Friedland – Plos Pathogens

Human respiratory microbiome
Review: Airway microbiome research: a modern perspective on surveillance cultures? – Damien Roux – Annals Of Translational Medicine

Human skin microbiome
Review: Over a Decade of recA and tly Gene Sequence Typing of the Skin Bacterium Propionibacterium acnes: What Have We Learnt? – Andrew McDowell – Microorganisms

Human oral microbiome
Ecological Balance of Oral Microbiota is Required to Maintain Oral Mesenchymal Stem Cell Homeostasis. – Yingying Su – Stem Cells (Dayton, Ohio)

Shift in the Subgingival Microbiome following Scaling and Root Planing in Generalized Aggressive Periodontitis. – Guojing Liu – Journal Of Clinical Periodontology

Human gut microbiome
Quinones are growth factors for the human gut microbiota. – Kathrin Fenn – Microbiome

Opinion: Microbiome-Germline Interactions and Their Transgenerational Implications. – Michael Elgart – Bioessays : News And Reviews In Molecular, Cellular And Developmental Biology

Review: Modeling metabolism of the human gut microbiome – Stefanía Magnúsdóttir – Current Opinion in Biotechnology

Microbial ecology
Opinion: Engineering microbial communities using thermodynamic principles and electrical interfaces. – Christian Zerfaß – Current Opinion In Biotechnology

Animal experiments
Age-dependent alterations of glucose clearance and homeostasis are temporally separated and modulated by dietary fat. – Mads T F Damgaard – The Journal Of Nutritional Biochemistry

Shift of hindgut microbiota and microbial short chain fatty acids profiles in dairy calves from birth to pre-weaning. – Yang Song – FEMS Microbiology Ecology

Impact of genistein on the gut microbiome of humanized mice and its role in breast tumor inhibition. – Bidisha Paul – Plos One

Tomato Powder Inhibits Hepatic Steatosis and Inflammation Potentially Through Restoring SIRT1 Activity and Adiponectin Function Independent of Carotenoid Cleavage Enzymes in Mice. – Cheng-Chung Li – Molecular Nutrition & Food Research

Faecal microRNAs: indicators of imbalance at the host-microbe interface? – G M Moloney – Beneficial Microbes

Modulation of the fecal microbiota in Sprague-Dawley rats using genetically modified and isogenic corn lines. – Penggao Li – Journal Of Agricultural And Food Chemistry

Sex-dependent impact of Roundup on the rat gut microbiome – Veronica L. Lozano – Toxicology Reports

Effects of garlic-supplemented diet on growth performance and intestinal microbiota of rainbow trout (Oncorhynchus mykiss) – Miray Etyemez Büyükdeveci – Aquaculture

Animal microbiome
Identification and chemical characterization of N acyl-homoserine lactone quorum sensing signals across sponge species and time. – Maya Britstein – FEMS Microbiology Ecology

Reptile-associated Borrelia species in the goanna tick (Bothriocroton undatum) from Sydney, Australia. – Jessica L Panetta – Parasites & Vectors

Multi-Omic Biogeography of the Gastrointestinal Microbiota of a Pre-Weaned Lamb – Antonio Palomba – Proteomes

Identification, comparison and validation of robust rumen microbial biomarkers for methane emissions using diverse Bos Taurus breeds and basal diets – Marc D. Auffret – Frontiers in Microbiology

Plant, root, and soil microbiome
Structure and function of the microbial consortia of activated sludge in typical municipal wastewater treatment plants in winter. – Bo Zhang – Scientific Reports

Key microbial taxa in the rhizosphere of sorghum and sunflower grown in crop rotation. – Tanzelle Oberholster – The Science Of The Total Environment

Metagenomic analysis of soil and freshwater from zoo agricultural area with organic fertilization. – Aylan K Meneghine – Plos One

Field study reveals core plant microbiota and relative importance of their drivers. – Kelly Hamonts – Environmental Microbiology

Enhanced arsenic uptake and polycyclic aromatic hydrocarbon (PAH)-dissipation using Pteris vittata L. and a PAH-degrading bacterium. – Lu Sun – The Science Of The Total Environment

Division of labor during biofilm matrix production – Anna Dragos – bioRxiv

Succession of Fungal and Oomycete Communities in Glyphosate-Killed Wheat Roots – Daniel Schlatter – Phytopathology

Long-term and legacy effects of manure application on soil microbial community composition – Yuting Zhang – Biology and Fertility of Soils

Ammonium nitrogen content is a dominant predictor of bacterial community composition in an acidic forest soil with exogenous nitrogen enrichment – Yanxia Nie – Science of the Total Environment

Water and extremophile microbiome
Consequences of contamination on the interactions between phytoplankton and bacterioplankton. – Goni-Urriza Marisol – Chemosphere

Identification of active denitrifiers by DNA-Stable Isotope Probing and amplicon sequencing reveals Betaproteobacteria as responsible for attenuation of nitrate contamination in a low impacted aquifer. – M Inés Bellini – FEMS Microbiology Ecology

The importance of filamentous cyanobacteria in the development of oxygenic photogranules. – Kim Milferstedt – Scientific Reports

Temperate phages as self-replicating weapons in bacterial competition. – Xiang-Yi Li – Journal Of The Royal Society, Interface (In freshwater metazoan Hydra vulgaris)

The Biogeographical Distribution of Benthic Roseobacter Group Members along a Pacific Transect Is Structured by Nutrient Availability within the Sediments and Primary Production in Different Oceanic Provinces – Marion Pohlner – Frontiers in Microbiology

Organic matter processing by microbial communities throughout the Atlantic water column as revealed by metaproteomics – Kristin Bergauer – PNAS (From November 2017, not posted before)

Homoacetogenesis in Deep-Sea Chloroflexi, as Inferred by Single-Cell Genomics, Provides a Link to Reductive Dehalogenation in Terrestrial Dehalococcoidetes – Holly L. Sewell – mBio

Seasonal and depth-wise variations in bacterial and archaeal groups in the Arabian Sea oxygen minimum zone – Mandar Bandekar – Deep Sea Research Part II: Topical Studies in Oceanography

Review: Microalgae–bacteria biofilms: a sustainable synergistic approach in remediation of acid mine drainage – Sudharsanam Abinandan – Applied Microbiology and Biotechnology

Built environment
Changes in bacterial and archaeal communities during the concentration of brine at the graduation towers in Ciechocinek spa (Poland) – Agnieszka Kalwasińska – Extremophiles

The Coal Seam Microbiome (CSMB) Reference Set, a lingua franca for the microbial coal-to-methane community – Silas H.W. Vick – International Journal of Coal Geology

Food microbiology
Review: Impact of nanosilver on gut microbiota: a vulnerable link. – Dinesh Kumar Dahiya – Future Microbiology

Probiotics / prebiotics
Effects of fermented soymilk with Lactobacillus casei Shirota on skin condition and the gut microbiota: a randomised clinical pilot trial. – T Nagino – Beneficial Microbes

Effect of tablets containing probiotic candidate strains on gingival inflammation and composition of the salivary microbiome: a randomised controlled trial. – M K Keller – Beneficial Microbes

Phages and viruses
Review: Inflammatory Bowel Disease’s Specific Changes of Enteric Mycobiota and Virome. – Yi Chu – Journal Of Digestive Diseases

Review: Phages of life – the path to pharma. – Amanda Forde – British Journal Of Pharmacology

Bioinformatics
Hybrid-denovo: A de novo OTU-picking pipeline integrating single-end and paired-end 16S sequence tags. – Xianfeng Chen – Gigascience

** 3D molecular cartography using LC-MS facilitated by Optimus and ‘ili software. – Ivan Protsyuk – Nature Protocols **

Non-biological synthetic spike-in controls and the AMPtk software pipeline improve fungal high throughput amplicon sequencing data – Jonathan M Palmer – bioRxiv

Multi-omics integration—a comparison of unsupervised clustering methodologies – Giulia Tini – Briefings in Bioinformatics

Review: Genome-scale metabolic networks in time and space – Ove Øyås – Current Opinion in Systems Biology

Techniques
Flow cytometric fingerprinting for microbial strain discrimination and physiological characterization. – Benjamin Buysschaert – Cytometry. Part A : The Journal Of The International Society For Analytical Cytology

Off-axis electron holography of bacterial cells and magnetic nanoparticles in liquid – Tanya Prozorov – Journal of the Royal Society

Microbes in the news
Higher Numbers of 2 Bacteria Species Found in Sarcoidosis Patients, Study Finds – Janet Stewart – Sarcoidosis News

The Surprising Way Your Brain and Gut Are Connected – Julia Malacoff – Shape

Gut Bacteria May Influence Infant Intelligence – Batya Swift Yasgur – MedScape

What Humans Can Learn About Gut Health From Monkey ‘Huddling’ – Francesca Friday – Observer

How to keep your gut healthy over the holidays – Yella Hewings-Martin – Medical News Today

Studies Link Oral Microbiome to Cancers – Pam Harrison – MedPage

Bacteria Found Alive in Earth’s Most Extreme Environments for the First Time Hold Clues to Life on Other Planet – Sydney Pereira – Newsweek

Antibiotic resistance: ‘Sleeping’ bacteria that can survive drug treatment identified – Phys.Org

Bacteria-Basted Supertrees Are Sucking Pollution From Our Waste Sites – James Poulos – Good

Everything you know about toxic shock syndrome is probably wrong – Sara Chodosh – Popular Science

Microbes on the market
Direct-to-consumer DNA and microbiome test launched in Europe – PharmaPhorum

BiomX acquires RondinX to expand microbiome targets for IBD, liver disease – Jonathan Solomon – HealIO

DSM Acquires BioCare Copenhagen to Expand Gut Health Ingredients Portfolio with Probiotics – CISION

Sarcoidosis Industry Overview with Total Market Share and Distribution of Sarcoidosis for 7 MM for 2025 – Miltech

Global Human Microbiome Market Analysis, Share, Production, Growth, Trends and Forecast 2017 to 2022 – Arun P. – GeoPolMonitor

Global Microbiome Therapeutic Market Outlook – Johnson and Johnson, AB-Biotics, Vedanta Biosciences, AbbVie Inc – Kevin Harper – The News Columnist

Bacteria Hysteria
‘This is how the X-Men started’: Internet shocked by astronaut discovery of ‘alien bacteria’ on International Space Station – Sarah K. Burris – RawStory

Science, publishing, and career
Graduate Biomedical Science Education Needs a New Philosophy – Gundula Bosch – mBio

December 22, 2017

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As the end of this year approaches, we have a post filled with plant/soil microbiome papers, as well as a few interesting food microbiology papers — enjoy!

General microbiome

A population genomics approach shows widespread geographical distribution of cryptic genomic forms of the symbiotic fungus Rhizophagus irregularis – Romain Savary, ISME

Pregnancy and early life

Gut microbiome in gestational diabetes: a cross-sectional study of mothers and offspring 5 years postpartum – Sayyid Hasan, Acta Obstetricia et Gynecologica Scandinavica

Liver microbiome

Environmental peer pressure: CD4+ T cell help in tolerance and transplantation – Dana Tedesco, Liver Transplantation

Skin microbiome

Food allergy and atopic dermatitis: Prediction, progression, and prevention – Carla Mastrorilli, Pediatric Allergy and Immunology

Respiratory microbiome

The Lung Microbiome in Idiopathic Pulmonary Fibrosis: A Promising Approach for Targeted Therapies – Fastrès Aline, International Journal of Molecular Sciences

Allergy – European Journal of Allergy and Clinical Immunology

Plant, root, and soil microbiome

Microbial and organic matter patterns in a prescribed burned and thinned managed forest ecosystem – Dessy A. Owiti, Ecosphere

Microbial Interactions and Perspectives for Bioremediation of Pesticides in the Soils – Ratna Prabha, Plant-Microbe Interactions in Agro-Ecological Perspectives

Fungi: An Effective Tool for Bioremediation – Sachin Gupta, Plant-Microbe Interactions in Agro-Ecological Perspectives

Arbuscular Mycorrhizal Fungi Improve Tolerance of Agricultural Plants to Cope Abiotic Stress Conditions – Pablo Cornejo, Plant-Microbe Interactions in Agro-Ecological Perspectives

Assessment of bacterial communities of black soybean grown in fields – Akifumi Sugiyama, Communicative & Integrative Biology

Plant-plant competition outcomes are modulated by plant effects on the soil bacterial community – S. Hortal, Scientific Reports

Trichoderma and Its Potential Applications – Monika Jangir, Plant-Microbe Interactions in Agro-Ecological Perspectives

Bacterial Rhizoremediation of Petroleum Hydrocarbons (PHC) – Jai Godheja, Plant-Microbe Interactions in Agro-Ecological Perspectives

Potential of Beneficial Bacteria as Eco-friendly Options for Chemical-Free Alternative Agriculture – Ch. Srinivasarao, Plant-Microbe Interactions in Agro-Ecological Perspectives

Potential Microbiological Approaches for the Remediation of Heavy Metal-Contaminated Soils – R. Krishnamoorthy, Plant-Microbe Interactions in Agro-Ecological Perspectives

Commercial Microbial Products: Exploiting Beneficial Plant-Microbe Interaction – Pallavi, Plant-Microbe Interactions in Agro-Ecological Perspectives

Interaction Between Beneficial Bacteria and Sugarcane – Guilherme Grodzki Oliveira Figueiredo, Plant-Microbe Interactions in Agro-Ecological Perspectives

Potential for Developing Low-Input Sustainable Agriculture in the Tropical Andes by Making Use of Native Microbial Resources – Luis Andrés Yarzábal, Plant-Microbe Interactions in Agro-Ecological Perspectives

Plant-Microbe Interactions in the Rhizosphere: Mechanisms and Their Ecological Benefits – Kulandaivelu Velmourougane, Plant-Microbe Interactions in Agro-Ecological Perspectives

Plant Interaction with Methylotrophic Communities – Manish Kumar, Plant-Microbe Interactions in Agro-Ecological Perspectives

Toward an Integrated Resource Management: Harnessing Trichoderma for Sustainable Intensification in Agriculture – Sumita Pal, Plant-Microbe Interactions in Agro-Ecological Perspectives,

Harnessing the Plant Microbiome: A Key Towards Sustainable Agriculture – Sanjana Kaul, Plant-Microbe Interactions in Agro-Ecological Perspectives

Rhizoremediation of Environmental Contaminants Using Microbial Communities – Ashish A. Prabhu, Plant-Microbe Interactions in Agro-Ecological Perspectives

Role of Plant Growth-Promoting Rhizobacteria for Improving Crop Productivity in Sustainable Agriculture – Abhijeet S. Kashyap, Plant-Microbe Interactions in Agro-Ecological Perspectives

Molecular evidence strongly supports deadwood-inhabiting fungi exhibiting unexpected tree species preferences in temperate forests – Witoon Purahong, ISME

Animal microbiome

Rare symbionts may contribute to the resilience of coral–algal assemblages – Maren Ziegler, ISME

Excess labile carbon promotes the expression of virulence factors in coral reef bacterioplankton – Anny Cárdenas, ISME

Evidence for a primate origin of zoonotic Helicobacter suis colonizing domesticated pigs – Bram Flahou, ISME

Water and extremophile microbiome

Single cell genomics of uncultured marine alveolates shows paraphyly of basal dinoflagellates – Jürgen F H Strassert, ISME

Aquatic urban ecology at the scale of a capital: community structure and interactions in street gutters – Vincent Hervé, ISME

Ecological and genomic profiling of anaerobic methane-oxidizing archaea in a deep granitic environment – Kohei Ino, ISME

Food microbiome

Evaluation of the use of malic acid decarboxylase-deficient starter culture in NaCl-free cucumber fermentations to reduce bloater incidence – Y. Zhai, Journal of Applied Microbiology

Effect of phenolic compounds on the growth of selected probiotic and pathogenic bacteria – R. Pacheco-Ordaz, Letters in Applied Microbiology

Recent advances in the microencapsulation of omega-3 oil and probiotic bacteria through complex coacervation: A review – Divya Eratte, Trends in Food Science & Technology

Q fever and prevalence of Coxiella burnetii in milk – Andreana Pexara, Trends in Food Science & Technology

Microbes and art

Bioessays Cover Art