Category Archives: Food Microbiology

January 8, 2016

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Breast milk microbiota profiles, what did the Romans ever do for us, it was only a matter of thyme, and going down the wrong clay.

Pregnancy and birth

Human milk microbiota profiles in relation to birthing method, gestation and infant gender – Camilla Urbaniak – Microbiome

Early Gut Colonization of Preterm Infants: Effect of Enteral Feeding Tubes – Gómez, Marta – Journal of Pediatric Gastroenterology and Nutrition

Review: Role of the Placenta in Preterm Birth: A Review – Terry K. Morgan – American Journal of Perinatology

Human oral microbiome

Long-term efficacy of microbiology-driven periodontal laser-assisted therapy – F. S. Martelli – European Journal of Clinical Microbiology & Infectious Diseases

Human gut microbiome

Human parasites in the Roman World: health consequences of conquering an empire – Piers D. Mitchell – Parasitology

Animal models

Microbiota-induced obesity requires farnesoid X receptor – Ava Parséus – Gut

The Gut Microbiome Is Altered in a Letrozole-Induced Mouse Model of Polycystic Ovary Syndrome – Scott T. Kelley – PLOS ONE

Animal microbiome

Heterogeneous size datasets of broiler intestinal microbial communities can be analyzed without normalization – I. Aranda-Olmedo – Poultry Science

Plant, root, and soil microbiome

Assessing Bacterial Diversity in the Rhizosphere of Thymus zygis Growing in the Sierra Nevada National Park (Spain) through Culture-Dependent and Independent Approaches
Javier Pascual – PLOS ONE

Image-based modelling of nutrient movement in and around the rhizosphere – Keith R. Daly – Journal of Experimental Botany

Unearthing the Antibacterial Mechanism of Medicinal Clay: A Geochemical Approach to Combating Antibiotic Resistance – Keith D. Morrison – Scientific Reports

Water and waste microbiology

Virome-associated antibiotic-resistance genes in an experimental aquaculture facility – Stefano Colombo – FEMS Microbiology Ecology

Biodiversity patterns of plankton assemblages at the extremes of the Red Sea – J.K. Pearman – FEMS Microbiology Ecology

Food microbiology

Taxonomic analysis of the microbial community in stored sugar beets using high-throughput sequencing of different marker genes – Sebastian Liebe – FEMS Microbiology Ecology

Bioinformatics and metagenomics

Antibiotic resistance genes across a wide variety of metagenomes – David Fitzpatrick – FEMS Microbiology Ecology

Microbes in the news

You’re Probably Not Mostly Microbes – Ed Yong – The Atlantic

Scientists discover how blue and green clays kill bacteria – National Science Foundation

Heartburn pills may help grow infection-causing bacteria in gut – Lisa Rapaport – News Daily

Good Bacteria In, Bad Bacteria Out: Biofilms In Water Pipes Filter Dangerous Pathogens Out Of Drinking Water – Lizette Borreli – Medical Daily

The Next Food Fad Is Coming: Feed Your Microbiome – Andrea Hayley, Epoch Times

Enterome Announces Collaboration with Johnson & Johnson Innovation Focused on the Discovery of Novel Targets and Therapeutics for Crohn’s Disease – PR Newswire

From the gut to the eye: commensal microbes as potential triggers of autoimmune uveitis – Atlas of Science

Changes coming with QIIME 2 – Greg Caporaso – Qiime

Science, publishing, and career

DATA CHECK: For female scientists, mixed funding results at U.S. agencies – Jeffrey Mervis – Science
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January 7, 2016

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A new estimate of the ratio microbial:human cells in our bodies, a 5300-year old Helicobacter genome, antibiotics alter bile metabolism, microbiota from 59 bird species, and fecal contamination of Kathmandu drinking water.

Events

3rd Microbiome R&D and Business Collaboration Forum: Europe, which will take place in London, on the 11th and 12th of April, 2016. Early registration closes Jan 15th.

Mysterious Microbes Webinar Series 1 of 3: Microbes and the miracle of compost tea, with Noah Fierer and Ryan Heiland, on Jan 14. Learn how and why microbes are the natural secret to green lawns, lush flowers, and abundant produce

General human microbiome

Revised estimates for the number of human and bacteria cells in the body – Ron Sender – bioRxiv

Review: The human microbiota: the role of microbial communities in health and disease – Luz Elena Botero – Acta Biologica Columbiana

Pregnancy and birth microbiome

A comparative study of bifidobacteria in human babies and adults – Shadi Khonsari – Bioscience of Microbiota, Food and Health

Human oral microbiome

Salivary Antimicrobial Peptides in Early Detection of Periodontitis – Güliz N. Güncü – Frontiers in Cellular and Infection Microbiology

Human gut microbiome

The 5300-year-old Helicobacter pylori genome of the Iceman – Frank Maixner – Science

Microbiome animal and other models

Antibiotic-Induced Alterations of the Gut Microbiota Alter Secondary Bile Acid Production and Allow for Clostridium difficile Spore Germination and Outgrowth in the Large Intestine – Casey M. Theriot – mSphere

The Gut Microbiota Reduces Colonization of the Mesenteric Lymph Nodes and IL-12-Independent IFN-γ Production During Salmonella Infection – María Fernández-Santoscoy – Frontiers in Cellular and Infection Microbiology

Steering Endogenous Butyrate Production in the Intestinal Tract of Broilers as a Tool to Improve Gut Health – Lonneke Onrust – Frontiers in Veterinary Science

Animal microbiome

Comparative Gut Microbiota of 59 Neotropical Bird Species – Sarah M. Hird – Frontiers in Microbiology

Plant, root, and soil microbiome

Potential Activity, Size, and Structure of Sulfate-Reducing Microbial Communities in an Exposed, Grazed and a Sheltered, Non-Grazed Mangrove Stand at the Red Sea Coast –
Melike Balk – Frontiers in Microbiology

Bacterial endophytes from wild and ancient maize are able to suppress the fungal pathogen Sclerotinia homoeocarpa – Hanan R. Shehata – Journal of Applied Microbiology

High throughput multiplex real time PCR assay for the simultaneous quantification of DNA and RNA viruses infecting cassava plants – Gerald Otti – Journal of Applied Microbiology

Methods for Baiting and Enriching Fungus-Feeding (Mycophagous) Rhizosphere Bacteria  – Max-Bernhard Ballhausen – Frontiers in Microbiology

Cucumber Rhizosphere Microbial Community Response to Biocontrol Agent Bacillus subtilis B068150 – Lihua Li – MDPI Agriculture

Water and waste microbiome

Bacterial diversity in water samples from uranium wastes as demonstrated by 16S rDNA and ribosomal intergenic spacer amplification retrievals – Galina Radeva – Canadian Journal of Microbiology

Master thesis: Evaluation of Two Culture-Independent Methods for Quantification of the Fraction of K-and r-Strategists within Water Microbial Communities – Brandsegg, Hege – Norges teknisk-naturvitenskapelige universitet

Built environment microbiome

The Ecological Dynamics of Fecal Contamination and Salmonella Typhi and Salmonella Paratyphi A in Municipal Kathmandu Drinking Water – Abhilasha Karkey – PLOS Neglected Tropical Diseases

Application of the Environmental Relative Moldiness Index in Finland – Martin Täubel – Applied and Environmental Microbiology

Food microbiology

Review: Phage-Host Interactions of Cheese-Making Lactic Acid Bacteria – Jennifer Mahony – Annual Review of Food Science and Technology

Metagenomics and bioinformatics

The Road to Metagenomics: From Microbiology to DNA Sequencing Technologies and Bioinformatics – Alejandra Escobar-Zepeda – Frontiers in Genetics

Science, publishing, and career

Peer review: tips from field experts for junior reviewers – Sabina Alam – BMC Medicine

Microbes in the news

Gut bacteria from Otzi the Iceman reveals our intimate ties to one microbe – Rachel Feltman – Washington Post

Scientists unearth bacteria from stomach of 5,300-year-old iceman – Carl Zimmer – StatNews

The Famous Ancient “Iceman” Had Ulcer Bacteria In His Gut – Dan Vergano – BuzzFeed

High Stress Environments May Lead To Unhealthy Gut Microbiomes: How To Protect Yourself From The Consequences – Lecia Bushak – Medical Daily

Antibiotics Pave Way for C. Diff Infections – North Carolina State University

Jackson Laboratory Hosted Microbiome Symposium Related to Cancer and Immunology – Lexology

The Bacteria That May Be Causing Your Nasty Cold. “The most common one of them in Mycoplasma Pneumoniae Infection,” Martin explained. – Fox29

Bik’s Picks

A “Pedi” Cures All: Toenail Trimming and the Treatment of Ulcerative Dermatitis in Mice – Sean C. Adams – PLOS ONE
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January 5, 2016

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Bacteria in breastmilk, nose/skin bacteria preventing pneumococcal infection, biofilms on pig carcasses in flowing water, Jurassic microbial mats, and Comammox Nitrospira-like bacteria in drinking water.

Pregnancy and birth

Characterization of bacterial isolates from the microbiota of mothers’ breast milk and their infants – Kimberly Kozak – Gut Microbes

Review: Association Between the Gut Microbiota and Diet: Fetal Life, Early Childhood, and Further Life – D.A. Kashtanova – Nutrition

Human nose/skin microbiome

Corynebacterium accolens Releases Antipneumococcal Free Fatty Acids from Human Nostril and Skin Surface Triacylglycerols – Lindsey Bomar – mBio

Human gut microbiome

A dysbiotic subpopulation of alcohol-dependent subjects – Philippe de Timary – Gut Microbes

Colorectal cancer: role of commensal bacteria and bystander effects – Xingmin Wang – Gut Microbes

Review: Gut inflammation and microbiome in spondyloarthritis – Jayakanthan Kabeerdoss – Rheumatology International

Review: Gut Microbiota and Celiac Disease – Giovanni Marasco – Digestive Diseases and Sciences

Animal models

Pglyrp-Regulated Gut Microflora Prevotella falsenii, Parabacteroides distasonis and Bacteroides eggerthii Enhance and Alistipes finegoldii Attenuates Colitis in Mice – Roman Dziarski – PLOS ONE

Plant, root, and soil microbiome

Dynamics of viral abundance and diversity in a Sphagnum-dominated peatland: temporal fluctuations prevail over habitat – Flore C. Ballaud – Frontiers in Microbiology

Distribution of Root-Associated Bacterial Communities Along a Salt-Marsh Primary Succession – Miao Wang – Frontiers in Plant Science

Early Jurassic microbial mats – a potential response to reduced biotic activity in the aftermath of the end-Triassic mass extinction event – Olof Peterffy – Palaeogeography, Palaeoclimatology, Palaeoecology

Water and extremophile microbiome

Microbial Biofilm Community Variation in Flowing Habitats: Potential Utility as Bioindicators of Postmortem Submersion Intervals – Jennifer M. Lang – Microorganisms

Effect of water chemistry on zooplanktonic and microbial communities across freshwater ecotones in different macrophyte-dominated shallow lakes – Tomasz Mieczan – Journal of Limnology

Influences of microbial communities on groundwater component concentrations during managed artificial recharge – Wenjing Zhang – Environmental Earth Sciences

Complete metagenome sequencing based microbial diversity insights from Deccan basaltic hot spring of Unkeshwar, Maharashtra, India – Gajanan T. Mehetre – Genomics Data

Perspective: Unraveling the Functions of the Macroalgal Microbiome – Ravindra Pal Singh – Frontiers in Microbiology

Built environment and waste microbiome

Metagenomic Evidence for the Presence of Comammox Nitrospira-Like Bacteria in a Drinking Water System – Ameet J. Pinto – mSphere

Proteolytic bacterial dominance in a full-scale municipal solid waste anaerobic reactor assessed by 454 pyrosequencing technology – Juliana Cardinali-Rezende – Chemosphere

Food microbiology

Microbial dynamics during shelf-life of industrial Ricotta cheese and identification of a Bacillus strain as a cause of a pink discolouration – E. Sattin – Food Microbiology

Microbes in the news

Outbreaks of Salmonellosis from Small Turtles – Maroya Spalding Walters – Pediatrics

Many of these are amazing because of microbes: 17 of the world’s weirdest water features – Marnie Hunter – CNN

Study details how good bacteria might help prevent middle ear infections and pneumonia – EurekAlert

Study: Bacteria, electrons spin in similar patterns. Bacteria streaming through a lattice behave like electrons in a magnetic material – EurekAlert
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December 17, 2015

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Effects of intranasal flu vaccine on nose microbiota, intestinal microbiota of Dutch children, fungi in dung, optical sensors, and diurnal time scales in drinking water.

General microbiome

Review: Intestinal Microbiota and Metabolic Diseases: Pharmacological Implications – Liang Shen – Trends in Pharmacological Sciences

Editorial: Immunotherapy Not Working? Check Your Microbiota – Nathan R. West – Cancer Cell

Review: Human Microbiome and Its Association With Health and Diseases – Asmaa Althani – Journal of Cellular Physiology

Infection and immunity

The microbiome of diabetic foot osteomyelitis – S. A. V. van Asten – European Journal of Clinical Microbiology & Infectious Diseases

A baleful weed and the king of fruits: tolerance, immunity, and the microbiome – Kairav Sinha – International Journal of Dermatology

Human oral microbiome

Salivary changes in oral mucosal diseases – Yazan Hassona – Periodontology 2000

Human respiratory microbiome

The administration of intranasal live attenuated influenza vaccine induces changes in the nasal microbiota and nasal epithelium gene expression profiles – Y. Tarabichi – Microbiome

Editorial: Precision respiratory medicine and the microbiome – Geraint B Rogers – The Lancet Respiratory Medicine

Review: The microbiome and critical illness – Robert P Dickson – The Lancet Respiratory Medicine

Human urinary tract microbiome

Intracellular Bacterial Communities: A Potential Etiology for Chronic Lower Urinary Tract Symptoms – Victoria C.S. Scott – Urology

Review: The interplay of extracellular matrix and microbiome in urothelial bladder cancer – Massimo Alfano – Nature Reviews Urology

Human gut microbiome

Composition and stability of intestinal microbiota of healthy children within a Dutch population – Tim G. J. de Meij – The FASEB Journal

Long-term risk of cardiovascular and cerebrovascular disease after removal of the colonic microbiota by colectomy: a cohort study based on the Danish National Patient Register from 1996 to 2014 – Anders Boeck Jensen – BMJ Open

Adverse events in faecal microbiota transplant: a review of the literature –
M. Baxter – Journal of Hospital Infection

Editorial: Antidiabetic drug treatment confounds gut dysbiosis associated with type 2 diabetes mellitus – David Holmes – Nature Reviews Endocrinology

Improved taxonomic assignment of human intestinal 16S rRNA sequences by a dedicated reference database – Jarmo Ritari – BMC Genomics

Microbiome models

Response of gut microbiota to salinity change in two euryhaline aquatic animals with reverse salinity preference – Meiling Zhang – Aquaculture

Destabilization of the gut microbiome marks the end-stage of simian immunodeficiency virus infection in wild chimpanzees – Hannah J. Barbian – American Journal of Primatology

Non-lethal Inhibition of Gut Microbial Trimethylamine Production for the Treatment of Atherosclerosis – Zeneng Wang – Cell

Editorial: Immunotherapy Meets Microbiota – Jiaying Tan – Cell

Editorial: Drug the Bug! – Annika Lindskog Jonsson – Cell

Functional anatomy of the colonic bioreactor: Impact of antibiotics and Saccharomyces boulardii on bacterial composition in human fecal cylinders – Alexander Swidsinski – Systematic and Applied Microbiology

The Murine Lung Microbiome Changes During Lung Inflammation and Intranasal Vancomycin Treatment – Kenneth Klingenberg Barfod – The Open Microbiology Journal

Animal microbiome

Biogeographic variation in the microbiome of the ecologically important sponge, Carteriospongia foliascens – Heidi M. Luter – PeerJ

Review: Dung-inhabiting fungi: a potential reservoir of novel secondary metabolites for the control of plant pathogens – Sabrina Sarrocco – Pest Management Science

Book Chapter: Age-Related Variation in the Scent Pouch Bacterial Communities of Striped Hyenas (Hyaena hyaena) – Kevin R. Theis – Chemical Signals in Vertebrates 13

Plant, root, and soil microbiome

Effects of chemical and biological pesticides on plant growth parameters and rhizospheric bacterial community structure in Vigna radiata – Sunil Singh – Journal of Hazardous Materials

Experimental Evidence that Fungi are Dominant Microbes in Carbon Content and Growth Response to Added Soluble Organic Carbon in Moss-rich Tundra Soil – O. Roger Anderson

Fertilizing with Animal Manure Disseminates Antibiotic Resistance Genes to the Farm Environment – Matti Ruuskanen – Journal of Environmental Quality

Water microbiome

Microbiology: lessons from a first attempt at Lake Ellsworth – D. A. Pearce – Philosophical Transactions A

Comprehensive genomic analyses of the OM43 clade including a novel species from Red Sea indicate ecotype differentiation among marine methylotrophs – Francy Jimenez-Infante – Applied and Environmental Microbiology

Built environment microbiome

Exposure to culturable and total microbiota in cultural heritage conservation laboratories – Rafał L. Górny – Int J Occup Med Environ Health

The impact of sampling, PCR, and sequencing replication on discerning changes in drinking water bacterial community over diurnal time-scales – Quyen Melina Bautista-de los Santos – Water Research

Food microbiology

The impact of yeast starter cultures on the microbial communities and volatile compounds in cocoa fermentation and the resulting sensory attributes of chocolate – Nádia Nara Batista – Journal of Food Science and Technology

Techniques

Optical sensors for sensing microbial life on a surface – M. Fischer – Applied and Environmental Microbiology

Metagenomes, viruses, and bioinformatics

Rise of Microbial Culturomics: Noncontiguous Finished Genome Sequence and Description of Beduini massiliensis gen. nov., sp. nov. – Gaël Mourembou – OMICS: A Journal of Integrative Biology

A metagenomic approach from aphid’s hemolymph sheds light on the potential roles of co-existing endosymbionts – Caroline De Clerck – Microbiome

MeFiT: Merging and Filtering Tool for Illumina Paired-End Reads for 16S rRNA Amplicon Sequencing – Hardik I. Parikh – ArXiv

Putative bacterial interactions from metagenomic knowledge with an integrative systems ecology approach – Philippe Bordron – MicrobiologyOpen

What Can We Learn from a Metagenomic Analysis of a Georgian Bacteriophage Cocktail?
Henrike Zschach – Viruses

MEEPTOOLS: A maximum expected error based FASTQ read filtering and trimming toolkit – Vishal N. Koparde – Arxiv

Microbes in the news

Book review: I, superorganism – learning to love your inner ecosystem – Jon Turney

Science, publishing, and career

South Korean professors charged over alleged plagiarism scheme: Prosecutors accuse academics of colluding with publishers to boost their standing and sell more books – David Matthews – Times Higher Education
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December 15, 2015

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Self-tracking the microbiome (quantified self), a human gut-on-a-chip model, indoor air bacteria in residences in the San Francisco Bay Area, and using probiotics on corals during oil spills.

General microbiome

Biometrics’ new identity—measuring more physical and biological traits: Research into the characteristics that are unique to an individual is addressing the need to correctly identify people in a variety of medical, social and security contexts – Andrea Rinaldi – EMBO Reports

Commentary: Self-tracking the microbiome: where do we go from here? – Carine Gimbert – Microbiome

Conference abstracts: 3th ISM World Congress on Targeting Microbiota – Journal of International Society of Microbiota Volume 1 No. 1

Pregnancy and birth

Buccal administration of human colostrum: impact on the oral microbiota of premature infants – K Sohn – Journal of Perinatology

Human mouth/ear microbiome

Pathophysiology of sinusitis of odontogenic origin – Silvio Taschieri – Journal of Investigative and Clinical Dentistry

Human gut microbiome

Different sub-type strains of Akkermansia muciniphila abundantly colonize in southern China – Xianfeng Guo – Journal of Applied Microbiology

Simultaneous fecal microbial and metabolite profiling enables accurate classification of pediatric irritable bowel syndrome – Vijay Shankar – Microbiome

Mucosal Barrier Depletion And Loss Of Bacterial Diversity Are Primary Abnormalities In Paediatric Ulcerative Colitis – Misagh Alipour – Journal of Crohn’s and Colitis

Systematic review with meta-analysis: long-term outcomes of faecal microbiota transplantation for Clostridium difficile infection – Y.-T. Li – Alimentary Pharmacology & Therapeutics

Microbiome models

Contributions of microbiome and mechanical deformation to intestinal bacterial overgrowth and inflammation in a human gut-on-a-chip – Hyun Jung Kim – PNAS

Effects of antibiotics (oxytetracycline, florfenicol or tulathromycin) on neonatal calves’ faecal microbial diversity – J. Oultram – Veterinary Record

Animal microbiome

Metagenomic Assembly Reveals Hosts of Antibiotic Resistance Genes and the Shared Resistome in Pig, Chicken and Human Feces – Liping Ma – Environmental Science & Technology

The impact of rearing environment on the development of gut microbiota in tilapia larvae – Christos Giatsis – Scientific Reports

The characterization and manipulation of the bacterial microbiome of the Rocky Mountain wood tick, Dermacentor andersoni – Katie A. Clayton – Parasites & Vectors

Impact of oil spills on coral reefs can be reduced by bioremediation using probiotic microbiota – Henrique Fragoso ados Santos – Scientific Reports

Plant, root, and soil microbiome

Stronger warming effects on microbial abundances in colder regions – Ji Chen – Scientific Reports

Seasonal dynamics of the microbiome of chernozems of the long-term agrochemical experiment in Kamennaya Steppe – T. I. Chernov – Eurasian Soil Science

Water and extremophile microbiome

Metagenome-assembled genomes uncover a global brackish microbiome – Luisa W. Hugerth – Genome Biology

Similar microbial communities found on two distant seafloor basalts – Esther Singer – Frontiers in Microbiology

Microbial communities on seafloor basalts at Dorado Outcrop reflect level of alteration and highlight global lithic clades – Michael D. Lee – Frontiers in Microbiology

Bacterioplankton dynamics within a large anthropogenically impacted urban estuary – Thomas C. Jeffries – Frontiers in Microbiology

Marine microbial community structure assessed from combined metagenomic analysis and ribosomal amplicon deep-sequencing – Savvas Genitsaris – Marine Biology Research

Groundwater isolation governs chemistry and microbial community structure along hydrologic flowpaths – Sarah Ben Maamar – Frontiers in Microbiology

Review: Forged Under the Sun: Life and Art of Extremophiles from Andean Lakes – Virginia Helena Albarracín – Photochemistry and Photobiology

Food microbiology

Comparative genomics Lactobacillus reuteri from sourdough reveals adaptation of an intestinal symbiont to food fermentations – Jinshui Zheng – Scientific Reports

Built environment microbiology

Relative and contextual contribution of different sources to the composition and abundance of indoor air bacteria in residences – Marzia Miletto – Microbiome

Review: Antibiotic resistance in urban aquatic environments: can it be controlled? – Célia M. Manaia – Applied Microbiology and Biotechnology

Metagenomics, phages, and bioinformatics

Computational approaches to predict bacteriophage–host relationships – Robert A. Edwards – FEMS Microbiology Reviews

Partial least squares regression can aid in detecting differential abundance of multiple features in sets of metagenomic samples – Ondrej Libiger – Frontiers in Genetics

Techniques

A new fungal large subunit ribosomal RNA primer for high throughput sequencing surveys – Rebecca C Mueller – FEMS Microbiology Ecology

Biofilms

Classic Spotlight: Before They Were Biofilms – George A. O’Toole – Journal of Bacteriology

Microbes in the news

How Bacteria and Brown Fat Can Spur Weight Loss – Mandy Oaklander – Time

A cultural revolution in the study of the gut microbiome – Medical Xpress

Why Your Body Is Like A Rainforest… Micro-Macro Exhibition at Eden features artwork from students at local secondary schools – PirateFM

Italian olive trees are withering from this deadly bacteria – PBS Newshour

Behind the scenes: Microbial biogeography of a university campus – Ashley Ross – MicroBEnet

Irish company makes biggest breakthrough for microbiology testing in dairy industry in 100 years – Independent Ireland

Bacteria, Archaea – Some Methane In Hydraulic Fracturing Is Even More Natural Than Assumed – Science 2.0

Sweet and sticky: Bacteria use sugars to bind to human cells – Phys.org

Science, publishing, and career

The Unwritten Code of Conduct: Each day this week, my supervisor has walked into my office and made verbal demands that I remove content from my beloved blog – The Research Whisperer

A lesson on misleading graphs from the National Review – Lenny Teytelman – The Spectroscope

Women in STEM research: Better Data and Information Sharing Could Improve Oversight of Federal Grant-making and Title IX Compliance – US Government Accountability Office

Why do scientists like anonymity? Lenny Teytelman – Protocols

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December 12, 2015

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Events

3rd Microbiome R&D and Business Collaboration Forum: Europe, 11-12 April, 2016, London

Pregnancy and birth

Study protocol (no data yet): Intestinal microbiota composition after antibiotic treatment in early life: the INCA study – N. B. M. M. Rutten – BMC Pediatrics

Review: The very low birth weight infant microbiome and childhood health – Maureen W. Groer – Birth Defects Research Part C: Embryo Today: Reviews

Review: Development of the infant intestinal microbiome: A bird’s eye view of a complex process – Sharon B. Meropol – – Birth Defects Research Part C: Embryo Today: Reviews

Review: Microbial programming of health and disease starts during fetal life – Petya T. Koleva – Birth Defects Research Part C: Embryo Today: Reviews

Human gut microbiome

Review: Gut microbiota in health and disease: an overview focused on metabolic inflammation – R. Nagpal – Beneficial Microbes

Animal models

Effects of antibiotics (oxytetracycline, florfenicol or tulathromycin) on neonatal calves’ faecal microbial diversity – J. Oultram – Veterinary Record

Water microbiome

Wind and sunlight shape microbial diversity in surface waters of the North Pacific Subtropical Gyre – Jessica A Bryant – ISME Journal

Bioprospecting around Arctic islands: Marine bacteria as rich source of biocatalysts
– Concetta De Santi – Journal of Basic Microbiology

Built environment microbiology

Review: Microlayer enrichment in natural treatment systems: linking the surface microlayer to urban water quality – Megan A. Rippy – Wiley Interdisciplinary Reviews: Water

Food microbiology

Dynamics and Diversity of Microbial Community Succession of Surimi During Fermentation with Next-Generation Sequencing – Dandan Zhao – Journal of Food Safety

Infection microbiology

Making the Leap from Research Laboratory to Clinic: Challenges and Opportunities for Next-Generation Sequencing in Infectious Disease Diagnostics – Brittany Goldberg – mBio

Microbes in the news

Scientist who injected himself with 3.5 million year old bacteria ‘feels fine’ – Brittany A. Roston – Slash Gear

Kim Kardashian Has a Cold: Health issues are the new frontier in celebrity PR – Ruth Graham – Slate

Biotech startup will mine the gut for drugs affecting human behavior – Ike Swetlitz – STAT news

Functions of global ocean microbiome key to understanding environmental changes: Mary Ann Moran – University of Georgia / EurekAlert

Foodstuffs: N.H. Sauerkraut Maker Rides the Microbiome Wave Into Tom Brady’s Pantry (Maybe) – Sam Evans-Brown – NHPR

Kickstarter project: Snotbot, custom-built drones that hover in the air above a surfacing whale and collect the blow (or snot) exhaled from its lungs – Kickstarter
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December 11, 2015

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Mammalian corpse decomposition – beautiful work by Jessica Metcalf.

Microbiome of death

Microbial community assembly and metabolic function during mammalian corpse decomposition – Jessica L. Metcalf – Science

Human oral microbiome

Review: Oral microbiome, periodontitis and risk of head and neck cancer – Leonardo Victor Galvão-Moreira – Oral Oncology

Review: The emerging landscape of salivary diagnostics – Yong Zhang – Periodontology 2000

Review: Influence of saliva on the oral microbiota – Philip D. Marsh – Periodontology 2000

Human skin microbiome

OK, not microbial, but entertaining: A comparative clinical study of different hair removal procedures and their impact on axillary odor reduction in men – Anthony Lanzalaco – Journal of Cosmetic Dermatology

Human respiratory microbiome

Correspondence: Potential roles of disordered airway microbiota in patients with severe asthma – Zongxin Ling – Journal of Allergy and Clinical Immunology

Human gut microbiome

Stress and the Microbiota–Gut–Brain Axis in Visceral Pain: Relevance to Irritable Bowel Syndrome – Rachel D. Moloney – CNS Neuroscience & Therapeutics

Review: SLE: Another Autoimmune Disorder Influenced by Microbes and Diet? – Qinghui Mu – Frontiers in Immunology

Review: The Intestinal Microbiome and the Liver Transplant Recipient: What We Know
and What We Need to Know – Iliana Doycheva

Microbiome models

Vancomycin treatment and butyrate supplementation modulate gut microbe composition and severity of neointimal hyperplasia after arterial injury – Karen J. Ho – Physiological Reports

Can closed artificial ecosystem have an impact on insect microbial community? A case study of yellow mealworm (Tenebrio molitor L.) – Leyuan Li – Ecological Engineering

Plant, root, and soil microbiome

Increasing aridity reduces soil microbial diversity and abundance in global drylands – Fernando T. Maestre – PNAS

The interaction between iron nutrition, plant species and soil type shapes the rhizosphere microbiome – Youry Pii – Plant Physiology and Biochemistry

Nitrification and Nitrifying Bacteria in a Coastal Microbial Mat – Haoxin Fan – Frontiers in Microbiology

Diversity of Phytophthora Species from Declining Mediterranean Maquis Vegetation, including Two New Species, Phytophthora crassamura and P. ornamentata sp. nov. – Bruno Scanu – PLOS ONE

Algae–bacteria interactions: Evolution, ecology and emerging applications – Rishiram Ramanan – Biotechnology Advances

Water microbiome

Particle-Associated Differ from Free-Living Bacteria in Surface Waters of the Baltic Sea – Angelika Rieck – Frontiers in Microbiology

The global ocean microbiome – Mary Ann Moran – Science

Hypothesis: Fractal Hypothesis of the Pelagic Microbial Ecosystem—Can Simple Ecological Principles Lead to Self-Similar Complexity in the Pelagic Microbial Food Web? – Selina Våge – Frontiers in Microbiology

Food microbiology

Microbiome profiling in fresh-cut products – Chiara Gorni – Trends in Food Science & Technology

FoodMicrobionet: A database for the visualisation and exploration of food bacterial communities based on network analysis – Eugenio Parente – International Journal of Food Microbiology

Bioinformatics and metagenomics

The MG-RAST metagenomics database and portal in 2015 – Andreas Wilke – Nucleic Acids Research

Infection and transplantation

The Interplay of Host Microbiota and Parasitic Protozoans at Mucosal Interfaces: Implications for the Outcomes of Infections and Diseases – Ann-Katrein Bär – PLOS Neglected Tropical Diseases

Viruses and phages

The role of viruses in the evolution of cyanobacteria – S. V. Shestakov – Biology Bulletin Reviews

Microbes in the news

Thousands of unexpected microbes break down our bodies after death – Elizabeth Pennisi – Science
Meet the Necrobiome: The Waves of Microbes That Will Eat Your Corpse – Ed Yong – The Atlantic
Tiny Witnesses: Microbes Can Tell When A Murder Victim Died – Rob Stein – NPR

New Superbug Resistant To All Antibiotics Linked To Imported Meat – Judy Stone – Forbes

Chipotle, E. coli, and more: The surprising truths about food-borne illnesses – Sheila Kaplan – STAT news

What Your Microbiome Wants for Dinner – David R Montgomery and Anne Bikle

Bacteria engineered with synthetic circadian clocks – EurekAlert

Melanoma Meets Microbiome – Kenneth Y. Tsai – NEJM Journal Watch

Can the health of a pregnant woman’s gut influence her baby? – Massey University

Science, publishing, and career

Making the most of the postdoc experience – Lorena Escudero – Frontiers Blog

Should post-publication peer review be anonymous? The PubPeer organisers and two other scholars debate the merits and pitfalls of anonymity in peer review – Times Higher Education

No evidence that gender contributes to personal research funding success in The Netherlands: A reaction to van der Lee and Ellemers – PNAS

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December 8, 2015

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The CF microbiome, microbes attaching to glycoproteins in sweat, gut bacteria make cockroach poop smell attractive for other cockroaches, mycobiome of South African Cabernet vines, and seasonality of Japanese cherry orchard soil fungi.

General microbiome

Perspective: Behavioral Microbiomics: A Multi-Dimensional Approach to Microbial Influence on Behavior – Adam C.-N. Wong – Frontiers in Microbiology

Research highlight: Microbiota-based nutrition plans – Cláudio Nunes-Alves – Nature Reviews Microbiology

Pregnancy and birth

Maternal risk factors for abnormal vaginal flora during pregnancy – Cecilia Tibaldi – International Journal of Gynecology & Obstetrics

Human respiratory microbiome

MiniReview: The cystic fibrosis microbiome in an ecological perspective and its impact in antibiotic therapy – Andreia P. Magalhães – Applied Microbiology and Biotechnology

Human oral microbiome

Oral Microbiota and Risk for Esophageal Squamous Cell Carcinoma in a High-Risk Area of China – Xingdong Chen – PLOS ONE

Human skin microbiome

Sweating the small stuff: Glycoproteins in human sweat and their unexplored potential for microbial adhesion – Robyn A Peterson – Glycobiology

Human gut microbiome

Gut microbiota manipulation with prebiotics in patients with non-alcoholic fatty liver disease: a randomized controlled trial protocol – BMC Gastroenterology

Review: Current roles of specific bacteria in the pathogenesis of inflammatory
bowel disease – Lucy McMullen – Microbiology

Animal and bioreactor models

Intestinal microbiota contributes to individual susceptibility to alcoholic liver disease – M Llopis – Gut

Development of a Laboratory Model of a Phototroph-Heterotroph Mixed-Species Biofilm at the Stone/Air Interface – Federica Villa – Frontiers in Microbiology

Animal microbiome

Gut bacteria mediate aggregation in the German cockroach – Ayako Wada-Katsumata – PNAS

The deep-sea glass sponge Lophophysema eversa harbors potential symbionts responsible for the nutrient conversions of carbon, nitrogen and sulfur – Ren-Mao Tian – Environmental Microbiology

Plant, root, and soil microbiome

The Anti-Phytophthora Effect of Selected Potato-Associated Pseudomonas Strains: From the Laboratory to the Field – Anouk Guyer – Frontiers in Microbiology

Defoliation reduces soil biota – and modifies stimulating effects of elevated CO2 – Marie Dam – Ecology and Evolution

Sequence-based Analysis of the Vitis vinifera L. cv Cabernet Sauvignon Grape Must Mycobiome in Three South African Vineyards Employing Distinct Agronomic Systems – Mathabatha E. Setati – Frontiers in Microbiology

Paradox of plant growth promotion potential of rhizobacteria and their actual promotion effect on growth of barley (Hordeum vulgare L.) under salt stress – Massimiliano Cardinale – Microbiological Research

Survey of Annual and Seasonal Fungal Communities in Japanese Prunus mume Orchard Soil by Next-Generation Sequencing – Yoshinao Aoki – Advances in Microbiology

Actinobacterial Diversity in the Sediments of Five Cold Springs on the Qinghai-Tibet Plateau – Jian Yang – Frontiers in Microbiology

Bacterial diversity assessment of pristine mangrove microbial community from dhulibhashani, sundarban using 16S rRNA gene tag sequencing – Pijush Basak – Genomics Data

Microbialites in the shallow-water marine environments of the Holy Cross Mountains (Poland) in the aftermath of the Frasnian–Famennian biotic crisis – Michał Rakociński – Global and Planetary Change

No tillage combined with crop rotation improves soil microbial community composition and metabolic activity – Bingjie Sun – Environmental Science and Pollution Research

Assessing the contribution of fallen autumn leaves to airborne fungi in an urban environment – Peter J. Irga – Urban Ecosystems

Water and extremophile microbiome

Weak Coherence in Abundance Patterns Between Bacterial Classes and Their Constituent OTUs Along a Regulated River – Clara Ruiz-González – Frontiers in Microbiology

Combined Culture-Based and Culture-Independent Approaches Provide Insights into Diversity of Jakobids, an Extremely Plesiomorphic Eukaryotic Lineage – Tomáš Pánek – Frontiers in Microbiology

Metabolic characteristics of dominant microbes and key rare species from an acidic hot spring in Taiwan revealed by metagenomics – Kuei-Han Lin – BMC Genomics

Waste treatment

Microbial community structure associated with the high loading anaerobic codigestion of olive mill and abattoir wastewaters – Hana Gannoun – Bioresource Technology

Microbial analysis of in situ biofilm formation in drinking water distribution systems: implications for monitoring and control of drinking water quality – Isabel Douterelo – Environmental Biotechnology

Food microbiology

Pyrosequencing reveals bacterial diversity in Korean traditional wheat-based nuruk – Jyotiranjan Bal – Journal of Microbiology

Metagenomics and bioinformatics

Hunting Down Frame Shifts: Ecological Analysis of Diverse Functional Gene Sequences – Michal Strejcek – Frontiers in Microbiology

GenomeTester4: a toolkit for performing basic set operations – union, intersection and complement on k-mer lists – Lauris Kaplinski – GigaScience

Microbes in the news

Cockroaches communicate via bacteria in their feces – Elizabeth Pennisi – Science Magzine

MSU professor trekking to the Amazon to study bacteria of insects that spread disease
– Anne Cantrell, MSU News Service – Bozeman Daily

Bacterial Biofilms: A Charged Environment – Kathryn Calkins – Biomedical Beat

Maintaining Wellness, Starting From Your Gut – Julie Chen – Huffington Post

Fall into Fungi – Alex Alexiev – MicroBEnet

Caps can play a part in cleaning water, not just bottling it – Jim Johnson – Plastic News

Dirty Yamuna water harbours drug-resistant bacteria – Neetu Chandra Sharma – Daily Mail India

Cooperating bacteria isolate cheaters – Phys.org

What you should know about this ‘new’ STD: interview with Raquel Dardik – Kristine Thomason – CNN

Bacteria Hysteria

Bacteria tests: What’s growing beneath your feet? – Alex Osiadacz – KLTV

Science, publication, and career

Five selfish reasons to work reproducibly – Florian Markowetz – Genome Biology

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December 3, 2015

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Microbiomes of gallstones, soil along a bike trip, nematodes in cattle, kiddie pools, and 100 years of phage research.

Pregnancy and birth

Prophages of the genus Bifidobacterium as modulating agents of the infant gut microbiota – Gabriele Andrea Lugli – Environmental Microbiology

Gut microbiota analysis reveals a marked shift to bifidobacteria by a starter infant formula containing a synbiotic of bovine milk-derived oligosaccharides and Bifidobacterium animalis subsp. lactis CNCM I-3446 – Umberto Simeoni – Environmental Microbiology

Human skin microbiome

Alas no pictures: Microbial colonization of normal skin: direct visualization of 194 skin biopsies – Anika C. Jahns – Anaerobe

Human gut microbiome

Structural robustness of the gut mucosal microbiota is associated with Crohn’s disease remission after surgery – S Mondot – Gut

Metagenomic sequencing of bile from gallstone patients to identify different microbial community patterns and novel biliary bacteria – Hongzhang Shen – Scientific Reports

Improvement in Human Immune Function with Changes in Intestinal Microbiota by Salacia reticulata Extract Ingestion: A Randomized Placebo-Controlled Trial – Yuriko Oda – PLOS ONE

Establishing a Fecal Microbiota Transplant Service for the treatment of Clostridium difficile Infection – Samuel P. Costello – Clinical Infectious Diseases

Review: From Hype to Hope: The Gut Microbiota in Enteric Infectious Disease –
Peter T. McKenney – Cell

Research Highlight: Can Your Microbiome Tell You What to Eat? – Jairam K.P. Vanamala – Cell Metabolism

Review: Nutrition in cancer patients with cachexia: a role for the gut microbiota? – Laure B. Bindels – Clinical Nutrition Experimental

Review: What’s bugging the gut in OCD? A review of the gut microbiome in obsessive-compulsive disorder – Jasmine Turna – Depression and Anxiety

Book Chapter: Bile Acids, the Microbiome and Metabolic Disease-Implications for Surgery – Cyrus Jahansouz – Metabolic Syndrome and Diabetes

Animal and bioreactor models

Gut Microbiota Orchestrates Energy Homeostasis during Cold – Claire Chevalier – Cell

Microbiota-Modulated Metabolites Shape the Intestinal Microenvironment by Regulating NLRP6 Inflammasome Signaling – Maayan Levy – Cell

Levan Enhances Associated Growth of Bacteroides, Escherichia, Streptococcus and Faecalibacterium in Fecal Microbiota – Kaarel Adamberg – PLOS ONE

Animal microbiome

Cattle: Exploring the Gastrointestinal “Nemabiome”: Deep Amplicon Sequencing to Quantify the Species Composition of Parasitic Nematode Communities – Russell W. Avramenko – PLOS ONE

Seals: Brain Meta-Transcriptomics from Harbor Seals to Infer the Role of the Microbiome and Virome in a Stranding Event – Stephanie M. Rosales – PLOS ONE

Shrimp: Bacterial concentration and diversity in fresh tropical shrimps (Penaeus notialis) and the surrounding brackish waters and sediment – D. Sylvain Dabadé – International Journal of Food Microbiology

Plant, root, and soil microbiome

Science and art: Soil microbial communities along the route of a venturous cycling trip – Magdalena Nagler – Applied Soil Ecology

Disease suppression in winter wheat from novel symbiosis with forest fungi – Mary Ridout – Fungal Ecology

Multifunctionality and diversity of culturable bacterial communities strictly associated with spores of the plant beneficial symbiont Rhizophagus intraradices – Fabio Battini – Microbiological Research

Plant Host Species and Geographic Distance Affect the Structure of Aboveground Fungal Symbiont Communities, and Environmental Filtering Affects Belowground Communities in a Coastal Dune Ecosystem – Aaron S. David – Plant Microbe Interactions

The impact of charcoal and soil mixtures on decomposition and soil microbial communities in boreal forest – Nathalie Pluchon – Applied Soil Ecology

Endophytic Actinobacteria and the Interaction of Micromonospora and Nitrogen Fixing Plants – Martha E. Trujillo – Frontiers in Microbiology

The microbiome and functions of black soils are altered by dibutyl phthalate contamination – Zhigang Wang – Applied Soil Ecology

Microbiological and faunal soil attributes of coffee cultivation under different management systems in Brazil – D.R. Lammel – Brazilian Journal of Biology

Spatial Patterns in Biofilm Diversity across Hierarchical Levels of River-Floodplain Landscapes – Marc Peipoch – PLOS ONE

Extremophile microbiome

Bacterial biogeography influenced by shelf–basin exchange in the Arctic surface sediment at the Chukchi Borderland – Dukki Han – Environmental Microbiology

Built environment microbiology

First microbiota assessments of children’s paddling pool waters evaluated using 16S rRNA gene-based metagenome analysis – Toko Sawabe – Journal of Infection and Public Health

Summary of Sloan symposium: healthy buildings 2015-Europe – Hal Levin – Microbiome

Waste microbiology

Characterization of a microbial consortium that converts mariculture fish waste to biomethane – Brigit Quinn – Aquaculture

More microbiology

Ankyrin-mediated self-protection during cell invasion by the bacterial predator Bdellovibrio bacteriovorus – Carey Lambert – Nature Communications

Phages and viruses

In retrospect: A century of phage lessons – Forest Rohwer & Anca M. Segall – Nature

Science, publishing, and career

Scientific Misconduct: Red Flags: Warning signs that scandal might be brewing in your lab – John R. Thomas Jr – The Scientist

Explaining Retractions: Editors and publishers should use a standardized form to detail why they are pulling papers from the scientific literature – Hervé Maisonneuve and Evelyne Decullier – The Scientist

Self Correction: What to do when you realize your publication is fatally flawed – Kerry Grens – The Scientist

Microbes in the news

Why It’s Time to Map the Microbiome (Kavli Roundtable) – Alan Brown, The Kavli Foundation – LiveScience

Scientists Argue Appendix Might Not Be ‘Irrelevant’ to Our Health, Propose This as the Organ’s Current Function – Liz Klimas – The Blaze

Immune cells make appendix ‘silent hero’ of digestive health – Walter and Eliza Hall Institute – EurekAlert

Bugs Against Disease: Could bacteria help fight colorectal cancer? A collaborative group of Tufts researchers hope to find out – Jacqueline Mitchell – Tufts Now

New research: Intestinal bacteria are affected by antidiabetic drugs – EurekAlert
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December 1, 2015

Posted on by

African gut microbiota and Entamoeba colonization, cuticular bacteria in social spiders, Arabidopsis leaf and root microbiota, the mineralosphere, bacteria in operating rooms and on a university campus.

Pregnancy and birth

The role of gut microbiota in fetal methylmercury exposure: insights from a pilot study – Sarah E. Rothenberg – Toxicology Letters

Human respiratory microbiome

Corticosteroid therapy and airflow obstruction influence the bronchial microbiome, which is distinct from that of bronchoalveolar lavage in asthmatic airways – Darcy R. Denner – The Journal of Allergy and Clinical Immunology

Human gut microbiome

Variation in Rural African Gut Microbiota Is Strongly Correlated with Colonization by Entamoeba and Subsistence – Elise R. Morton – PLOS Genetics

Not yet on Nature website: Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota – Forslund K – Nature

Gut microbiome in health and disease: Linking the microbiome-gut-brain axis and environmental factors in the pathogenesis of systemic and neurodegenerative diseases – Shivani Ghaisas – Pharmacology & Therapeutics

Book Chapter: Microbiome in the Critically Ill – Meredith Barrett – Nutrition Support for the Critically Ill

Review: The gut microbiome, diet, and links to cardiometabolic and chronic disorders – Judith Aron-Wisnewsky & Karine Clément – Nature Reviews Nephrology

Microbiome and bioreactor models

A distributed cell division counter reveals growth dynamics in the gut microbiota –
Cameron Myhrvold – Nature Communications

Polymicrobial Oral Infection with Four Periodontal Bacteria Orchestrates a Distinct Inflammatory Response and Atherosclerosis in ApoEnull Mice – Sasanka S. Chukkapalli – PLOS ONE

Aflatoxin B1 induced compositional changes in gut microbial communities of male F344 rats – Jincheng Wang – Toxicological Sciences

PhD thesis: Advanced Computational Tools for Analyzing Microbial Communities for Energy Production Environments – Adam Robbins-Pianka – University of Colorado at Boulder

Escherichia coli Nissle 1917 enhances bioavailability of serotonin in gut tissues through modulation of synthesis and clearance – Jonathan Nzakizwanayo – Scientific Reports

Animal microbiome

Cuticular bacteria appear lethal to social spiders in mixed but not monoculture inoculations – Carl N. Keiser – Current Zoology

Plant, root, and soil microbiome

Not yet on Nature website: Functional overlap of the Arabidopsis leaf and root microbiota – Bai Y – Nature

The Mineralosphere Concept: Mineralogical Control of the Distribution and Function of Mineral-associated Bacterial Communities – Stephane Uroz – Trends in Microbiology

Impact of lowland rainforest transformation on diversity and composition of soil prokaryotic communities in Sumatra (Indonesia) – Dominik Schneider – Frontiers in Microbiology

The assessment of epiphytic yeast diversity in sugarcane phyllosphere in Thailand by culture-independent method – Rujikan Nasanit – Fungal Biology

Changes in soil physicochemical and microbial properties along elevation gradients in two forest soils – Lei Hu – Scandinavian Journal of Forest Research

Influence of Cadmium and Glucose on Soil Microbial Communities – Aliya Gilmullina – American Journal of Applied Sciences

Convergence of microbial assimilations of soil carbon, nitrogen, phosphorus, and sulfur in terrestrial ecosystems – Xiaofeng Xu – Scientific Reports

Water microbiome

Reverse transcriptase genes are highly abundant and transcriptionally active in marine plankton assemblages – Magali Lescot – ISME Journal

Impact of a wastewater treatment plant on microbial community composition and function in a hyporheic zone of a eutrophic river – Siavash Atashgahi – Scientific Reports

Built environment microbiology

The first microbial environment of infants born by C-section: the operating room microbes – Hakdong Shin – Microbiome

Microbial biogeography of a university campus – Ashley A. Ross and Josh D. Neufeld – Microbiome

Only on Pubmed as of now: Biofilms in churches built in grottoes – Cennamo P – Science of the Total Environment

Molecular Analysis of Microbial Community Structures in Nigerian Oil Production and Processing Facilities in order to Access Souring Corrosion and Methanogenesis – Chuma Okoro – Corrosion Science

Water heater temperature set point and water use patterns influence Legionella pneumophila and associated microorganisms at the tap – William J. Rhoads – Microbiome

Food microbiology

Selection of aroma compounds for the differentiation of wines obtained by fermenting musts with starter cultures of commercial yeast strains – Florin Vararu – Food Chemistry

Metagenomics and bioinformatics

MetaQUAST: evaluation of metagenome assemblies – Alla Mikheenko – Bioinformatics

Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires – Eugen Bauer – Microbiome

Book Chapter: Predicting the Metagenomics Content with Multiple CART Trees – Dante Travisany – Mathematical Models in Biology

Enhanced virome sequencing using targeted sequence capture – Todd N. Wylie – Genome Research

Biofilms and infection

Multi-species biofilms in ecology, medicine, and biotechnology – A. N. Nozhevnikova – Microbiology

Bacterial infection remodels the DNA methylation landscape of human dendritic cells –
Alain Pacis – Genome Research

Survival with a Helping Hand: Campylobacter and Microbiota – Ivana Indikova – Frontiers in Microbiology

Microbes in the news

Microbiome Startup uBiome Will Sequence Poop for the CDC – Sarah Zhang – Wired

Dr. Elizabeth Lindsey, gastroenterologist: FACES of Nashville – Liza Graves – Style

Microbiome Monday: The Bacteria and “The Guinea Pig Doctor” – American Museum of Natural History

The beloved pioneer bread that smells like feet and breaks food safety rules – Natalie Zarrelli – Atlas Obscura

Peer review

Want me to review your manuscript for free? Then be polite… – Ian M Mackay – Virology Down Under
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