July 27, 2017

General microbiome

Microbiota-host Transgenomic Metabolism, Bioactive Molecules from the Inside –  S Turroni – J. Med. Chem.

Cyanophages exhibit rhythmic infection patterns under light-dark cycles – R Liu – bioRxiv

The effect of aspartate supplementation on the microbial composition and innate immunity on mice – P Bin – Amino Acids

Clinical impact of pre-transplant gut microbial diversity on outcomes of allogeneic hematopoietic stem cell transplantation – N Doki – Annals of Hematology

Differentiating botulinum-neurotoxin-producing clostridia with a simple, multiplex PCR assay – CHD Williamson – Appl. Environ. Microbiol.

Review: Antimicrobial resistance in the next 30 years, humankind, bugs and drugs: a visionary approach – M Bassetti – Intensive Care Med.

Lactobacillus fermentum CECT 5716 and a reduction of the Staphylococcus load in breast milk which reduces the risk of infectious mastitis: evaluation of a health claim pursuant to Article 14 of Regulation (EC) No 1924/2006 – EFSA Panel – EFSA Journal

 

Human gut microbiome

Specific signatures of the gut microbiota and increased levels of butyrate in children treated with fermented cow’s milk containing heat-killed Lactobacillus paracasei CBA L74 – R Canani Berni – Appl. Environ. Microbiol.

Examining the gut bacteriome, virome, and mycobiome in glucose metabolism disorders: Are we on the right track? –  C Stefenaki – Metab.Clin.Exp.

 

Animal microbiome

Assessment of Cultivable Oral Bacterial Flora from Important Venomous Snakes of India and Their Antibiotic Susceptibilities – IK Shaikh – Current Microbiology

 

Plant, root and soil microbiome

Rhizosphere Sampling Protocols for Microbiome (16S/18S/ITS rRNA) Library Preparation and Enrichment for the Isolation of Drought Tolerance-Promoting Microbes – V Lakshmanan – Methods in Molecular Biology

Toward a Resilient, Functional Microbiome: Drought Tolerance-Alleviating Microbes for Sustainable Agriculture – V Lakshmanan – Methods in Molecular Biology

Review: Biochar-rhizosphere interactions – A review – S Głuszek – Pol J Microbiol.

Interactions between Pteris vittata L. genotypes and a polycyclic aromatic hydrocarbon (PAH)-degrading bacterium (Alcaligenes sp.) in arsenic uptake and PAH-dissipation – L Sun -Environmental Pollution

 

Built environment

The performance and microbial communities of biodegradation-electron transfer with sulfur metabolism integrated process for flue gas desulfurization wastewater treatment – C Wei – Bioprocess Biosyst Eng.

 

Techniques

Dual RNA-Seq of Lysobacter capsici AZ78 – Phytophthora infestans interaction shows the implementation of attack strategies by the bacterium and unsuccessful oomycete defense responses –  S Tomada – Environmental Microbiology

 

Microbes in news

Infant Gut Microbiome May Influence Cognitive Development – Whole Foods Magazine

HEALTHY BITES: The importance of a healthy gut – My Web Times

Why apartment dwellers need indoor plants – Phys.org

Algae cultivation technique could advance biofuels – Science Daily

Bacteria may explain why uncircumcised face higher HIV risk – UPI

Cafe shut down at LA Fitness that had Legionnaires’ bacteria – Orlando Sentinel

Link between Saharan Dust and Vibrio bacteria – Kiiitv.com

Life evolves adaptions to microgravity – Phys.org

Algal solution- Could Spirulina modify the microbiome to protect against age related damage – Nutra Ingredients

Penis Microbiome Could Enhance Risk of Infection with HIV – Invisiverse

Building Codes for Bacterial Cities – Quanta Magazine

Researchers offer new and novel paradigm for advancing research on beneficial microbes – Phys.org

15 facts about fecal transplants – The straight poop – Genetic Literacy Project

He thought he just had blisters from a hike. He had flesh-eating bacteria and nearly died – The Washington Post

$1.8 million NIH grant to Wayne State to aid in developing improved cholera treatments – EurekAlert

Investigator | High levels of E.Coli bacteria found at local shopping malls – WKYC

Beautiful and bizarre things to buy: From wall art to a probiotic deodorant – Livemint

July 26, 2017

General microbiome

Microbiome analysis and confocal microscopy of used kitchen sponges reveal massive colonization by Acinetobacter, Moraxella and Chryseobacterium species – Massimiliano Cardinale – Scientific Reports

Review: The mother–offspring dyad: microbial transmission, immune interactions and allergy development – Maria C. Jenmalm – Journal of Internal Medicine

Human skin microbiome

The Skin Microbiome of Cohabiting Couples – Ashley A. Ross – mSystems

Animal microbiome

Influence of Host Plant on Thaumetopoea pityocampa Gut Bacterial Community – Cinzia P. Strano – Microbial Ecology

The time-course of broiler intestinal microbiota development after administration of cecal contents to incubating eggs – Erin E. Donaldson – PeerJ

Plant, root, and soil microbiome

Review: Sphingomonads in Microbe-Assisted Phytoremediation: Tackling Soil Pollution – Michael Gatheru Waigi – Trends in Biotechnology

Response of soil microbial community composition and function to a bottomland forest restoration intensity gradient – Michael S. Strickland – Applied Soil Ecology

Changes of soil microbial communities during decomposition of straw residues under different land uses – Hong Zhang – Journal of Arid Land

Water and extremophile microbiome

Metagenomics of urban sewage identifies an extensively shared antibiotic resistome in China – Jian-Qiang Su – Microbiome

An anaerobic ~3400 Ma shallow-water microbial consortium: presumptive evidence of Earth’s Paleoarchean anoxic atmosphere – J. William Schopf – Precambrian Research

Iron oxides alter methanogenic pathways of acetate in production water of high-temperature petroleum reservoir – Pan Pan – Applied Microbiology and Biotechnology

Food Microbiology

Editorial: Microbiology of Ethnic Fermented Foods and Alcoholic Beverages of the World – Jyoti P. Tamang – Frontiers in Microbiology

Probiotics / prebiotics

Specific signatures of the gut microbiota and increased levels of butyrate in children treated with fermented cow’s milk containing heat-killed Lactobacillus paracasei CBA L74 – Roberto Berni Canani – Applied and Environmental Microbiology

Phages and viruses

Review : The Human Virome – Implications for Clinical Practice in Transplantation Medicine – Susanna K. Tan – Journal of Clinical Microbiology

Anitha’s non-microbiology picks

Quantum tunneling takes time, new study shows

Perovskites power up the solar industry

Scientists develop fast chemistry that unlocks a new class of polymers

Medicine’s Movable Feast: What Jumping Genes Can Teach Us about Treating Disease

July 24, 2017

Here’s our Digest to start your Monday. The importance of managing the antibiotic resistance in perinatal and neonatal care, review on the plant-microbiota holobiont and poo bacteria found in three big fast food chains.

Jobs

Microbiology Lab Technician – Johnson County Community College – Overland Park, KS

Research Fellow – Microbiome Program Job – Mayo Clinic, Rochester MN

Pregnancy and infant microbiome

Book Chapter: Bacterial Infections in the Neonate – Morven S. Edwards & Carol J. Baker – Principles and Practice of Pediatric Infectious Diseases (Fifth Edition)

**Review: Antibiotic stewardship in perinatal and neonatal care Jayashree Ramasethu & Tetsuya Kawakita – Seminars in Fetal and Neonatal Medicine

Human liver microbiome

Sequencing the gut metagenome as a non-invasive diagnosis for advanced nonalcoholic steatohepatitis – Lixin Zhu et al. – Hepatology

Human gut microbiome

Comparative phenotypic analysis of “Clostridium neonatale” and Clostridium butyricum isolates from neonates – S. Schönherr-Helleca and G. Klein et al. – Anaerobe

The association of type II diabetes with gut microbiota composition – Fatemeh Navab-Moghadama et al. – Microbial Pathogenesis

The role of intestinal bacteria in the development and progression of gastrointestinal tract neoplasms – Kosuke Mima & Shuji Ogino et al. – Surgical Oncology

Review: The Microbiome in Crohn’s Disease : Role in Pathogenesis and Role of Microbiome Replacement Therapies – Sahil Khanna & Laura E. Raffals – Gastroenterology Clinics of North America

Review: The Gastric and Intestinal Microbiome: Role of Proton Pump Inhibitors – Artem Minalyan – Current Gastroenterology Reports

Animal experiments

The aerial parts of Salvia miltiorrhiza Bge. strengthen intestinal barrier and modulate gut microbiota imbalance in streptozocin-induced diabetic mice – Jun-Fei Gu et al. – Journal of Functional Foods

Intervention of probiotic L. reuteri fermented milk as an adjuvant to combat protein energy malnourishment induced gut disturbances in albino mice – S. Garg et al. – Journal of Functional Foods

Western Diet–Induced Dysbiosis in Farnesoid X Receptor Knockout Mice Causes Persistent Hepatic Inflammation after Antibiotic Treatment – Prasant K. Jena et al. – The American Journal of Pathology

The title seems an overstatement: Microbial regulation of hippocampal miRNA expression: Implications for transcription of kynurenine pathway enzymes – Gerard M. Moloney et al. – Behavioural Brain Research

Helicobacter species are potent drivers of colonic T cell responses in homeostasis and inflammation – Jiani N. Chai et al. – Science Immunology

Press: How ‘Bad’ Gut Bacteria Can Change Their Evil Ways – Christopher Wanjek – LiveScience

Animal microbiome

Exploring a possible link between the intestinal microbiota and feed efficiency in pigs – Ursula M. McCormack et al. – Applied and Environmental Microbiology

Press: PIG MICROBIOME MAKEUP MAY INFLUENCE ANIMAL GROWTH RATE – Julie Wolf – ASM

Plant, root and soil microbiome

Review: Insights into plant phosphate sensing and signaling – Byung-Kook Ham et al. – Current Opinion in Biotechnology

Responses of rice paddy micro-food webs to elevated CO2 are modulated by nitrogen fertilization and crop cultivars – Zhengkun Hu et al. – Soil Biology and Biochemistry

**Review: Understanding the holobiont: the interdependence of plants and their microbiome – Carmen Sánchez-Cañizares et al. – Current Opinion in Microbiology

Water and extremophile microbiome

Operation-driven heterogeneity and overlooked feed-associated populations in global anaerobic digester microbiome – Ran Mei et al. – Water Research

Preprint: Cytosine methylation within marine sediment microbial communities: potential epigenetic adaptation to the environment – Ian M. Rambo – bioRxiv

Phages and viruses

Bacteriophages in the human gut: our fellow travelers throughout life and potential biomarkers of heath or disease – Babak Bakhshinejad & Saeedeh Ghiasvand – Virus Research

Microbes in the news

Florida man contracts flesh-eating bacteria through blisters from hiking
Cherise Leclerc – WMUR9

Florida Seawater Bacteria Case Count Rises – Sherri Lonon – Patch

Shock as lab tests find of poo bacteria in products at McDonald’s, KFC and Burger King – Zara Whelan – Daily Post

Vaginal Probiotics Could Slow Zika & Other STD Infections – Sheryl Wood – Invisiverse

NASA Identifies What Kind of Fungi Could Grow in a Mars Habitat – Cynthia Wallentine – Invisiverse

July 22, 2017

General microbiome

Evolutionary genetic analysis uncovers multiple species with distinct habitat preferences and antibiotic resistance phenotypes in the Stenotrophomonas maltophilia complex – LE Ochoa-Sanchez – bioRxiv

ReviewRegulation of inflammation by microbiota interactions with the host – JM Blanders – Nature Immunology

Dramatic expansion of microbial groups that shape the global sulfur cycle – K Anantharaman – bioRxiv

The importance of species identity and interactions on multifunctionality depends on how ecosystem functions are valued – EM Slade – Ecology

The potential of anti-infectives and immunomodulators as therapies for asthma and asthma exacerbations – MR Edwards – Allergy

Pest categorisation of Pseudocercospora angolensis – EPH – EFSA Journal

Vascular complications in diabetes: old messages, new thoughts – JM Forbes – Diabetologia

Deciphering functional diversification within the lichen microbiota by meta-omics – T Cernava – Microbiome

 

Human oral microbiome

Saliva and tooth biofilm bacterial microbiota in adolescents in a low caries community – L Erikkson – Scientific Reports

 

Animal microbiome

Using MinION to characterize dog skin microbiota through full-length 16S rRNA gene sequencing approach – A Cusco – bioRxiv

Context-dependent Requirements for FimH and Other Canonical Virulence Factors in Gut Colonization by Extraintestinal Pathogenic Escherichia coli – CW Russell – bioRxiv

Graded replacement of maize grain with molassed sugar beet pulp modulated ruminal microbial community and fermentation profile in vitro – M Münnich – J Sci Food Agric.

Microbial Communities in Different Tissues of Atta sexdens rubropilosa Leaf-cutting Ants – AS Vieira – Current Microbiology

Fecal excretion of Maillard reaction products and the gut microbiota composition of rats fed with bread crust or bread crumb – C Helou – Food & Function

The salivary microbiome as an indicator of carcinogenesis in patients with oropharyngeal squamous cell carcinoma: A pilot study – A Wolf – Scientific Reports

16S rRNA gene-based association study identified microbial taxa associated with pork intramuscular fat content in feces and cecum lumen – S Fang – BMC Microbiology

 

Plant, root and soil microbiome

Environmental drivers of viral community composition in Antarctic soils identified by viromics – EM Adriaenssens – Microbiome

 

Water microbiome and extremophiles

Metabolic Network Analysis and Metatranscriptomics Reveals Auxotrophies and Nutrient Sources of the Cosmopolitan Freshwater Microbial Lineage acI – JJ Hamilton – bioRxiv

 

Techniques

Effective identification of Lactobacillus casei group species: genome-based selection of the gene mutL as the target of a novel multiplex PCR assay – B Bottari – Microbiology

Comparative analysis of vaginal microbiota sampling using 16S rRNA gene analysis – S Virtanen – PLoS One

 

Microbes in news

UCONN RESEARCH: IN FROGS, EARLY ACTIVITY OF GUT MICROBIOME SHAPES LATER HEALTH – UConn

Fecal bacteria found in drinks at UK branches of McDonald’s, Burger King and KFC – D Reid – CNBC

Google’s Verily Trying to Debug Fresno with Bacteria-Treated Mosquitoes – C Wallentine – Invisiverse

South Florida hiker contracts flesh-eating bacteria – R Lowe – WSVN

 

 

July 21, 2017

Today’s digest is short and sweet. An interesting study of the microbial community composition inside the Internation Space Station using WGS. And, how a microbiologist is saving prairie dogs.

General Microbiome and Microbiology

Microbial metal resistance and metabolism across dynamic landscapes: high-throughput environmental microbiology

Carlson H.F1000Research

Animal and insect microbiome

Population-Specific Responses to Interspecific Competition in the Gut Microbiota of Two Atlantic Salmon (Salmo salar) Populations

He X. Microbial Ecology

Plant, soil, and air microbiome

Metabarcoding: A powerful tool to investigate microbial communities and shape future plant protection strategies

Abdelfattah A.Biological Control

 Microbial functional diversity covaries with permafrost thaw‐induced environmental heterogeneity in tundra soil

Yuan MM.Global Change Biology

Marine and inland waters

Sulfide-Induced Dissimilatory Nitrate Reduction to Ammonium Supports Anaerobic Ammonium Oxidation (Anammox) in an Open-Water Unit Process Wetland

Jones ZL Applied and Environmental Microbiology

 The effects of phosphorus limitation on carbon metabolism in diatoms

Brembu T. Philosophical  Transaction of the Royal  Society B

Genetic and metabolic engineering in diatoms

Huang W. Philosophical  Transaction of the Royal  Society B

Built Microbiome

Microalgal hydrogen production-a review

Khetkorn W. Bioresource Technology

Whole metagenome profiles of particulates collected from the International Space Station

Nicholas AB.Microbiome, 2017

Microbes in the news

How a wildlife biologist became a plague-chaser in the American Southwest

STAT

July 20, 2017

A study of chemical interactions between fungi and ants by imaging mass spectrometry, characterization of forty-six Arthrobacter phages, influence of fruit fungal infestation on vertebrate fruit preferences.

Human gut microbiome

The essential genomic landscape of the commensal Bifidobacterium breve UCC2003 – Lorena Ruiz – Scientific Reports

Animal experiments

Fat binding capacity and modulation of the gut microbiota both determine the effect of wheat bran fractions on adiposity – Francesco Suriano – Scientific Reports

Effects of dietary supplementation with two alternatives to antibiotics on intestinal microbiota of preweaned calves challenged with Escherichia coli K99 – Yanliang Bi – Scientific Reports

Animal microbiome

Imaging mass spectrometry and MS/MS molecular networking reveals chemical interactions among cuticular bacteria and pathogenic fungi associated with fungus-growing ants – Cristopher A Boya P – Scientific Reports

Plant, root, and soil microbiome

Population structure of an orchid mycorrhizal fungus with genus-wide specificity – M P Ruibal – Scientific Reports

Water and extremophile microbiome

Review: Cultivation of microbes from the deep-sea environments – Zenghu Zhang – Deep Sea Research Part II: Topical Studies in Oceanography

Food microbiology

Fungal infestation boosts fruit aroma and fruit removal by mammals and birds – Josep E Peris – Scientific Reports

Pre-print: Resilience mechanisms of small intestinal lactobacilli to the toxicity of soybean oil fatty acids – Sara C Di Rienzi – bioRxiv

Probiotics/prebiotics

Dietary lipid content reorganizes gut microbiota and probiotic L. rhamnosus attenuates obesity and enhances catabolic hormonal milieu in zebrafish – Silvia Falcinelli – Scientific Reports

Phages and viruses

Tales of diversity: Genomic and morphological characteristics of forty-six Arthrobacter phages – Karen K Klyczek – PLOS ONE

Pre-print: Isolation and characterization of BpL1, a broad acting lytic bacteriophage against Brucella – Vimlesh Gupta – bioRxiv

Microbes in the news

Bac-for good: Bacteria passed between generations benefits you more than others – Phys.org

Microbes on the market

Verily Releases Bacteria-Infected Mosquitoes To Fight Zika And Dengue: Is Wolbachia Technique Safe For Humans? – Allan Adamson – Tech Times

Science, career, and publishing

Climate scientists flock to France’s call – Declan Butler – Nature

July 18, 2017

A short Digest today, but with very interesting papers. Strain diversity implicated in atopic dermatitis, infant gut microbiome associated with cognitive development? And the sourdough microbiome.

General microbiology

Use of oxygen isotopes to differentiate between nitrous oxide produced by fungi or bacteria during denitrification – Lena Rohe et al. – Rapid Communications in Mass Spectrometry

Human skin microbiome

Staphylococcus aureus and Staphylococcus epidermidis strain diversity underlying pediatric atopic dermatitis – Allyson Byrd et al. – Science Translational Medicine

Human gut-microbiome-brain axis

Infant Gut Microbiome Associated with Cognitive Development – Alexander L. Carlson et al. – Biological Psychiatry

Press: In baby’s dirty diapers, the clues to baby’s brain development – UNC Health Care – EurekaAlert

Animal experiments

Peripartum Antibiotics Promote Gut Dysbiosis, Loss of Immune Tolerance, and Inflammatory Bowel Disease in Genetically Prone Offspring – Jun Miyoshi et al. – Cell Reports

Press: Higher IBD Risk in Offspring Associated With Antibiotic Use in Pregnancy – IDSE News Staff – IDSE

Microbes in the news

More Than Bread: Sourdough As a Window Into The Microbiome – Marcus Woo – NPR

Promising but take caution: Probiotics and Weight Loss – Philip J. Gregory – Medscape

Review article discusses potential role, benefits of non-rhizobia bacteria in root nodules of legume – Phys.org

Microbes on the market

Enterome, Nestlé Health Science Launch Microbiome Diagnostics Partners to Develop New IBD Treatments – Carolina Henriques – IBD News Today

Essential Science: Big investments for human microbiome research – Tim Sandle – Digital Journal

July 16, 2017

Events and jobs
Postdoctoral Fellow – Astrobiology – University of Florida

Microbiology Laboratory Manager – Cranleigh Scientific, Northamptonshire, England

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

July 6, 2017

The microbiota of spotted hyenas, a review of potential interactions between olfactory sensation and the microbiome-gut-brain axis, phylogenetic analysis of host-microbe symbioses to examine the evolution of dependence over time.

General microbiome

Synthetic Microbial Ecology: Engineering Habitats for Modular Consortia – Sami Ben Said – Frontiers in Microbiology

The evolution of host-symbiont dependence – Roberta M Fisher – Nature Communications

Review: The microbiota revolution: Excitement and caution – Maria Rescigno – European Journal of Immunology

Review: The Microbiome and Blood Pressure: Can Microbes Regulate Our Blood Pressure? – Souhaila Al Khodor – Frontiers in Pediatrics

Human oral microbiome

Suppression of αvβ6 Integrin Expression by Polymicrobial Oral Biofilms in Gingival Epithelial Cells – Jiarui Bi – Scientific Reports

Proteomic shifts in multi-species oral biofilms caused by Anaeroglobus geminatus – Kai Bao – Scientific Reports

Human vaginal microbiome

Quantifying the human vaginal community state types (CSTs) with the species specificity index – Zhanshan Ma – PeerJ

Animal experiments

Effects of iron supplementation on growth, gut microbiota, metabolomics and cognitive development of rat pups – Erica E Alexeev – PLOS ONE

Review: Disruptive physiology: olfaction and the microbiome-gut-brain axis – John Bienenstock – Biological Reviews Cambridge Philosophical Society

Effects of melanin from Sepiella Maindroni ink (MSMI) on the intestinal Microbiome of mice – Hui Dong – BMC Microbiology

Animal microbiome

The Intestinal Eukaryotic and Bacterial Biome of Spotted Hyenas: The Impact of Social Status and Age on Diversity and Composition – Emanuel Heitlinger – Frontiers in Cellular and Infection Microbiology

Plant, root, and soil microbiome

Perspective: The deep, hot biosphere: Twenty-five years of retrospection – Daniel R Colman – PNAS

Draft Genome Sequence of Pseudomonas koreensis CI12, a Bacillus cereus “Hitchhiker” from the Soybean Rhizosphere – Gabriel L Lozano – Genome Announcements

Warmer winters increase the rhizosphere carbon flow to mycorrhizal fungi more than to other microorganisms in a temperate grassland – Johanna Birgander – Global Change Biology

Negative plant-phyllosphere feedbacks in native Asteraceae hosts – a novel extension of the plant-soil feedback framework – Briana K Whitaker – Ecology Letters

Water and extremophile microbiome

Size and composition of subseafloor microbial community in the Benguela upwelling area examined from intact membrane lipid and DNA analysis – Thomas W Evans – Organic Geochemistry

FurukawaMarine microbes as a valuable resource for brand new industrial biocatalysts – Azadeh Beygmoradi – Biocatalysts and Agricultural Biotechnology

Antagonistic Interactions and Biofilm Forming Capabilities Among Bacterial Strains Isolated from the Egg Surfaces of Lake Sturgeon (Acipenser fulvescens) – M Fujimoto – Microbial Ecology

Probiotics/prebiotics

Effects of the probiotic Bifidobacterium animalis subsp. lactis on the non-surgical treatment of periodontitis. A histomorphometric, microtomographic and immunohistochemical study in rats – Milla S T Ricoldi – PLOS ONE

Phages and viruses

Virus-host relationships of marine single-celled eukaryotes resolved from metatranscriptomics – Mohammad Moniruzzaman – Nature Communications

Occurrence of Bacillus thuringensis Bacteriophages in the Egyptian Arid Soil – Amel S M Abo-Senna – International Journal of Virology and Molecular Biology

Bioinformatics

A conceptual framework for quality assessment and management of biodiversity data – Allan Koch Veiga – PLOS ONE

Techniques

SParticle, an algorithm for the analysis of filamentous microorganisms in submerged cultures – Joost Willemse – bioRxiv

Mapping-based all-RNA-information sequencing analysis (ARIseq) pipeline simultaneously revealed taxonomic composition, gene expression, and their correlation in an acidic stream ecosystem – Arisa Tsuboi – bioRxiv

More microbes

Review: Metabolic engineering pathways for rare sugars biosynthesis, physiological functionalities, and applications – A review – Muhammad Bilal – Critical Reviews in Food Science and Nutrition

Microbes in the news

Microbes aren’t the enemy, they’re a big part of who we are – Amy Loughman – Medical Xpress

What Cheese Can Tell Us About Antibiotic Resistance – Jason Tetro – Huffington Post Canada

Cases of recurrent Clostridium difficile infection are soaring – Medical Xpress

Helium ions reveal how viruses attack bacteria – ScienceDaily

July 3, 2017

 

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

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

 
Human respiratory microbiome

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

 
Human gut microbiome

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

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

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

 
Animal microbiome 

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

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

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

 
Plant, root, and soil microbiome

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

 

Water and extremophile microbiome

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

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

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

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

 
Food microbiology

 

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

 

Probiotics / prebiotics

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

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

 
Phages and viruses

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

 
Biotechnology

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

 
Microbes in the news

 
A new approach to tackling drug-resistant bacteria

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

 
Microbes on the market (news about biotech companies)

 
New Belgian Biotech will use Microorganisms to Replace Pesticides and Fertilizers