April 15, 2017

Few interesting articles for your Saturday morning digest:   Urbanization alters the physicochemical environment: A new study suggests that urban soil archaeal and bacterial communities are not vulnerable to biodiversity loss, whereas global diversity loss of ectomycorrhizal fungi was observed.  Researchers believe they have found a method of hunting for buried landmines and explosive devices using a combination of engineered bacteria and lasers.    And another reason to be engaged in sports activities: a study highlights differences of microbiota and secondary metabolites in elite athletes.

General microbiome

Remote detection of buried landmines using a bacterial sensor – Shimshon Belkin – Nature Biotech

Next-generation approaches to understand and combat the antibiotic resistome – Terence S. Crofts – Nature Reviews

Human Oral Microbiome

Microbiomes of the normal middle ear and ears with chronic otitis media – Shujiro B. Minami – Laryngoscope

Human gut microbiome

The microbiome of professional athletes differs from that of more sedentary subjects in composition and particularly at the functional metabolic level– Wiley Barton – Gut

The MS-Associated Gut Microbiome – Sergio E Baranzini – Multiple Sclerosis Journal

Mental Health

Oral treatment with Lactobacillus rhamnosus attenuates behavioral deficits and immune changes in chronic social stress – Aadil Bharwani – BMC Medicine

Animal microbiome

Complete Genome Sequence of Akkermansia glycaniphila Strain PytT, a Mucin-Degrading Specialist of the Reticulated Python Gut – Janneke P. Ouwerkerk – Genome Announcements

Water and extremophile microbiome

Spatial variation in bacterial community in natural wetland-river-sea ecosystems
Hongxia Zhang – J. of Basic Microbiology

Built environment

Urbanization erodes ectomycorrhizal fungal diversity and may cause microbial communities to converge – Dietrich JE Schmidt -Nature Ecology & Evolution

Prebiotics

Prebiotic evaluation of red seaweed (Kappaphycus alvarezii) using in vitro colon model – DM Bajury – International Journal of Food Sciences and Nutrition

April 13, 2017

Profiles of ulcerative colitis patients’ microbiota after fecal microbiota transplantation, a bioinformatics software package for rarefaction analysis, an artist who uses sweat and bacteria to create scents and sculptures.

General microbiome

Review: Microbial metabolites in nutrition, healthcare and agriculture – Rajendra Singh – 3 Biotech

Review: Modified Mediterranean Diet for Enrichment of Short Chain Fatty Acids: Potential Adjunctive Therapeutic to Target Immune and Metabolic Dysfunction in Schizophrenia? – Jamie Joseph – Frontiers in Neuroscience

Human respiratory microbiome

The Nasopharyngeal Microbiota of Children with Respiratory Infections in Botswana – Matthew S Kelly – Pediatric Infectious Disease Journal

Human gut microbiome

* Microbial shifts and signatures of long-term remission in ulcerative colitis after faecal microbiota transplantation – Susana Fuentes – ISME Journal

Intestinal microbiome in children with severe and complicated acute viral gastroenteritis – Shih-Yen Chen – Scientific Reports

Unusual active site location and catalytic apparatus in a glycoside hydrolase family – Jose Munoz-Munoz – PNAS

Animal experiments

Enterococcus faecalis bacteriocin EntV inhibits hyphal morphogenesis, biofilm formation, and virulence of Candida albicans – Carrie E Graham – PNAS

The therapeutic protection of a living and dead Lactobacillus strain against aluminum-induced brain and liver injuries in C57BL/6 mice – Fengwei Tian & Leilei Yu – PLOS One

Microscale spatial analysis provides evidence for adhesive monopolization of dietary nutrients by specific intestinal bacteria – Yusuke Nagara – PLOS One

Review: Caspase recruitment domain 9, microbiota, and tryptophan metabolism: dangerous liaisons in inflammatory bowel diseases – Bruno Lamas – Current Opinion in Clinical Nutrition and Metabolic Care

Individual variation of natural D. melanogaster associated bacterial communities – Yun Wang – bioRxiv

Plant, root, and soil microbiome

A new polyketide glycoside from the rhizospheric Clonostachys rogersoniana associated with Panax notoginseng – Tian-Peng Yin – Journal of Asian Natural Products Research

Bacterial carbon use plasticity, phylogenetic diversity and the priming of soil organic matter – Ember M Morrissey – ISME Journal

Population and function analysis of cultivable bacteria associated with spores of arbuscular mycorrhizal fungus Gigaspora margarita – Liangkun Long – 3 Biotech

Water and extremophile microbiome

Exploring the ecological coherence between the spatial and temporal patterns of bacterioplankton in boreal lakes – Juan P. Niño García – Frontiers in Microbiology

Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems – Sean P Jungbluth – PeerJ

Bacterial community composition and dynamics spanning five years in freshwater bog lakes – Alexandra M Linz – bioRxiv

Occurrence of high-diversity metazoan- to microbial-dominated bioconstructions in a shallow Kimmeridgian carbonate ramp (Jabaloyas, Spain) – G San Miguel – Facies

Expression patterns of elemental cycling genes in the Amazon River Plume – Brandon M Satinsky – ISME Journal

Built environment

Comparison of microbial community shifts in two parallel multi-step drinking water treatment processes – Jiajiong Xu – Applied Microbiology and Biotechnology

Probiotics/prebiotics

Engineered probiotic Escherichia coli can eliminate and prevent Pseudomonas aeruginosa gut infection in animal models – In Young Hwang – Nature Communications

Review: Unraveling the Differences between Gram-Positive and Gram-Negative Probiotics in Modulating Protective Immunity to Enteric Infections – Sukumar Kandasamy – Frontiers in Immunology

Bioinformatics

* RTK: efficient rarefaction analysis of large datasets – Paul Saary – Bioinformatics

A geographically-diverse collection of 418 human gut microbiome pathway genome databases – Aria S Hahn – Scientific Data

Metabolomics

Indolepropionic acid and novel lipid metabolites are associated with a lower risk of type 2 diabetes in the Finnish Diabetes Prevention Study – Vanessa D de Mello – Scientific Reports

More microbes

Influences of dissolved oxygen concentration on biocathodic microbial communities in microbial fuel cells – Laura Rago – Bioelectrochemistry

Microbes in the news

Waste-munching bacteria could make nuclear stores safer – Sam Wong – New Scientist

‘Young poo’ makes aged fish live longer – Ewen Callaway – Nature

Microbiology: Gut microbes augment neurodegeneration – Daniel Erny – Nature

* This Artist Turns Sweat and Bacteria Into Art – Annie Tittiger – Wired

Science, publishing, and career

Why do scientists fabricate and falsify data? A matched-control analysis of papers containing problematic image duplications – Daniele Fanelli – bioRxiv

Amy’s non-microbiology picks

Human knockouts and phenotypic analysis in a cohort with a high rate of consanguinity – Danish Saleheen – Nature

April 9, 2017

Today’s digest features interesting research on how keystone microbial taxa regulate invasion of pathogens in agricultural systems. Also, interesting pre-print on how the gut microbiome influences the lifespan of fish.

Human gut microbiome

De novo assembly of microbial genomes from human gut metagenomes using barcoded short read sequences. Moss. E. Biorxiv

Review: Updating on Gut Microbiota and its Relationship with the Occurrence of Necrotizing Enterocolitis (Review). Hosny, M. Human Microbiome Journal

Supplementation of Diet with Galacto-oligosaccharides Increases Bifidobacteria, but not Insulin Sensitivity, in Obese Prediabetic Individuals. Canfora, E. Gastroenterology

Independence of Gut Bacterial Content and Neonatal Necrotizing Enterocolitis Severity Barron, LK. Journal of Pediatric Surgery

Evaluation of the impact of gut microbiota on uremic solute accumulation by a CE-TOFMS–based metabolomics approach. Mishima, E.Kidney International

Human skin microbiome

Semi-automated quantitative analysis of the human skin microbiome diversity  Kumagai, C. Journal of Dermatological Science

Human Skin Is the Largest Epithelial Surface for Interaction with Microbes. Gallo, R. Journal of Investigative Dermatology

Human milk microbiome

Human milk microbiome in urban and rural populations of India Yati, H. Meta Gene

Molecular Insight into Evolution of Symbiosis between Breast-Fed Infants and a Member of the Human Gut Microbiome Bifidobacterium longum.Yamada, C. Cell Chemical Biology

Food  microbiome

Microbial metabolites derived from colonic fermentation of non-digestible compounds. Tabernero, M. Current Opinion in Food Science

High relative humidity pre-harvest reduces post-harvest proliferation of Salmonella in tomatoes . Devleesschauwer, B. Food Microbiology

Plant and soil microbiome

Keystone microbial taxa regulate the invasion of a fungal pathogen in agro-ecosystems. Trivedi, P. Soil Biology and Biochemistry 

In-depth analysis of core methanogenic communities from high elevation permafrost-affected wetlands. Yang, S. Soil Biology and Biochemistry

Strigolactones in Plant Interactions with Beneficial and Detrimental Organisms: The Yin and Yang. López-Ráez, JA. Trends in Plant Science

Animal microbiome

Regulation of Life Span by the Gut Microbiota in The Short-Lived African Turquoise Killifish. Smith, P. Biorxiv

Factors influencing ruminal bacterial community diversity and composition and microbial fibrolytic enzyme abundance in lactating dairy cows with a focus on the role of active dry yeast. AlZahal, O. Journal of Dairy Science

Organochloride pesticides modulated gut microbiota and influenced bile acid metabolism in mice. Liu, Q. Environmental Pollution

Growth performance of the very small rotifer Proales similis is more dependent on proliferating bacterial community than the bigger rotifer Brachionus rotundiformis. Le, DVB.  Aquaculture

Evidence of Campylobacter jejuni reduction in broilers with early synbiotic administration Baffoni, L. International Journal of Food Microbiology

Raspberry pomace alters cecal microbial activity and reduces secondary bile acids in rats fed a high-fat diet. Fotschki, B.The Journal of Nutritional Biochemistry

Rumen microbial and fermentation characteristics are affected differently by acarbose addition during two nutritional types of simulated severe subacute ruminal acidosis in vitro. Wang, Y. Anaerobe.

Metabolomics 

Targeting aggression in severe mental illness: The predictive role of genetic, epigenetic, and metabolomic markers   Manchia, M. Progress in Neuro-Psychopharmacology and Biological Psychiatry

Prebiotics/Probiotics 

A three-stage continuous culture approach to study the impact of probiotics, prebiotics and fat intake on faecal microbiota relevant to an over 60 s population. Liu. Y.Journal of Functional Foods

 

April 5, 2017

Today’s digest features interesting research on the dynamic microbiome evolution in social bees and the alteration in quorum Sensing, cell motility, stress Response, and carbohydrate metabolism  of gut microbiome by the organophosphate pesticide Diazinon. Low dose penicillin in early life can induce long term changes in mice gut microbiota, brain cytokines and behavior. Interesting reviews on the microbiome and human biology, and role of gut microbiota in the development of hypertension, including that associated with obstructive sleep apnea.

General microbiome

*Review: The Microbiome and Human Biology – Rob Knight – Annual Review of Genomics and Human Genetics

*Dynamic microbiome evolution in social bees – Waldan K. Kwong – Science Advances

Anaerobic Bacterial Fermentation Products Increase Tuberculosis Risk in Antiretroviral-Drug-Treated HIV – Leopoldo N. Segal – Cell Host & Microbe

Pregnancy and early life

Vancomycin treatment is a risk factor for vancomycin-nonsusceptible Staphylococcus capitis sepsis in preterm neonates – Marine Butin – Clinical Microbiology and Infection

Human oral microbiome

Relative abundance of total subgingival plaque-specific bacteria in salivary microbiota reflects the overall periodontal condition in patients with periodontitis – Shinya Kageyama – Plos One

Review: Biofilm over teeth and restorations: What do we need to know? – Nancy J. Lin – Dental Materials

Human skin microbiome

Cutaneous Burn Injury Promotes Shifts in the Bacterial Microbiome in Autologous Donor Skin: Implications for Skin Grafting Outcomes – Jennifer K. Plichta – Shock

Human gut microbiome

Review : The gut microbiota: a possible factor influencing systemic lupus erythematosus – Hadar Neuman – Current Opinion in Rheumatology

*Organophosphate Diazinon Altered Quorum Sensing, Cell Motility, Stress Response, and Carbohydrate Metabolism of Gut Microbiome – Bei Gao -Toxicological Sciences

Baseline gut microbiota predicts clinical response and colitis in metastatic melanoma patients treated with ipilimumab – N. Chaput – Oncology

*Review: Obstructive Sleep Apnea-Induced Hypertension: Role of the Gut Microbiota – David J. Durgan – Current Hypertension Reports

Review: The Gut Microbiota and Alzheimer’s Disease – Chunmei Jiang – Journal of Alzheimer’s Disease

Fecal Microbiota Transplantation

Fecal Microbiota Transplantation in Patients with Blood Disorders Inhibits Gut Colonization with Antibiotic-Resistant Bacteria: Results of a Prospective, Single-Center Study – Jaroslaw Bilinski – Clinical Infectious Diseases

Animal microbiome

Multi-Omics Analysis Reveals a Correlation between the Host Phylogeny, Gut Microbiota and Metabolite Profiles in Cyprinid Fishes – Tongtong Li – Frontiers in Microbiology

Diurnal Dynamics of Gaseous and Dissolved Metabolites and Microbiota Composition in the Bovine Rumen – Henk J. van Lingen – Frontiers in Microbiology

Microbial Biogeography and Core Microbiota of the Rat Digestive Tract – Dongyao Li – Scientific Reports

Animal experiments

Bifidobacterium in the gut microbiota confer resilience to chronic social defeat stress in mice – Chun Yang – Scientific Reports

Lack of Evidence That Selenium-Yeast Improves Chicken Health and Modulates the Caecal Microbiota in the Context of Colonization by Campylobacter jejuni – Alexandre Thibodeau – Frontiers in Microbiology

Review : Outstanding animal studies in allergy II: from atopic barrier and microbiome to allergen-specific immunotherapy – Erika Jensen-Jarolim – Current Opinion in Allergy & Clinical Immunology

Faecalibacterium prausnitzii treatment improves hepatic health and reduces adipose tissue inflammation in high-fat fed mice – Eveliina Munukka – ISME Journal

*Low-dose penicillin in early life induces long-term changes in murine gut microbiota, brain cytokines and behavior –  Sophie Leclercq – Nature Communications

Nod2 and Nod2-regulated microbiota protect BALB/c mice from diet-induced obesity and metabolic dysfunction – Ivan Rodriguez-Nunez – Scientific Reports

Plant, root, and soil microbiome

Aluminum-tolerant bacteria improve the plant growth and phosphorus content in ryegrass grown in a volcanic soil amended with cattle dung manure – María de la Luz Mora- Applied Soil Ecology

Invisible but consequential: root endophytic fungi have variable effects on belowground plant–insect interactions – Huyijuie Gan – Ecosphere

Land-use types and soil chemical properties influence soil microbial communities in the semiarid Loess Plateau region in China – Qin Tian – Scientific Reports

Phylogenetic conservation of substrate use specialization in leaf litter bacteria – Kristin L. Dolan – Plos ONE

Root biomass and exudates link plant diversity with soil bacterial and fungal biomass – Nico Eisenhauer – Scientific Reports

Water and extremophile microbiome

Discrimination of Four Marine Biofilm-Forming Bacteria by LC-MS Metabolomics and Influence of Culture Parameters – Laurie Favre – Journal of Proteome Research

Iron assimilation and utilization in anaerobic ammonium oxidizing bacteria – Christina Ferousi – Current Opinion in Chemical Biology

*Potential sources of bacteria colonizing the cryoconite of an Alpine glacier – Andrea Franzetti – PLOS ONE

Spatio-Temporal Variations of Marine Biofilm Communities Colonizing Artificial Substrata Including Antifouling Coatings in Contrasted French Coastal Environments – Jean-François Briand – Microbial Ecology

Metabolomics

Review: Metabolomics: Strategies to Define the Role of Metabolism in Virus Infection and Pathogenesis – Marianne Manchester – Advances in Virus Research

Effect of Major Royal Jelly Proteins on Spatial Memory in Aged Rats: Metabolomics Analysis in Urine – Di Chen -Journal of Agricultural and Food Chemistry

Food microbiology

Sourdough authentication: quantitative PCR to detect the lactic acid bacterial microbiota in breads – Erica Pontonio – Scientific Reports

Probiotics / prebiotics

Evaluation of Potential Probiotics Isolated from Human Milk and Colostrum – Quésia S. Damaceno – Probiotics and Antimicrobial Proteins

Bioinformatics

SLIMM: species level identification of microorganisms from metagenomes – Temesgen Hailemariam Dadi – PeerJ

Techniques

Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area – Kazuma Nakano – Human Cell

High-pressure microscopy for tracking dynamic properties of molecular machines – Masayoshi Nishiyama – Biophysical Chemistry

Gut Microbiome Standardization in Control and Experimental Mice – Kathy D. McCoy – Current Protocols in Immunology

Diastereomer-specific Quantification of Bioactive Hexosylceramides from Bacteria and Mammals – Johanna von Gerichten – Journal of Lipid Research

Microbes in the news

Genetically engineered microbes make their own fertilizer, could feed the world’s poorest

The Next Plague (5) Bacteria: The Coming And Going And Coming Again Of Bacterial Plagues

Latest Helicobacter pylori breakthrough could lead to eradication of bacteria

Science, publishing, and career

Journal editor calls for ‘culture change’ around clinical trial data

Anitha’s non-microbiology picks

In the quest of Planet 9

March 31, 2017

Microbiome research

Potential role of fecal microbiota from patients with slow transit constipation in the regulation of gastrointestinal motility – Xiaolong Ge, Scientific Reports

Opinion: Gut microbiome as a clinical tool in gastrointestinal disease management: are we there yet? – Eamonn M. M. Quigley – Nature Reviews Gastroenterology & Hepatology

Relevance of secretor status genotype and microbiota composition in susceptibility to rotavirus and norovirus infections in humans  – Jesús Rodríguez-Díaz – Scientific Reports

Milk Fat Globule Membrane Supplementation in Formula Modulates the Neonatal Gut Microbiome and Normalizes Intestinal Development – Ganive Bhinder – Scientific Reports

Critical Review: Microbiota-Gut-Brain Axis: Modulator of Host Metabolism and Appetite – Marcel van de Wouw – The Journal of Nutrition

Comparison of stool versus rectal swab samples and storage conditions on bacterial community profiles – Christine M. Bassis – BMC Microbiology

Ethnic and diet-related differences in the healthy infant microbiome – Jennifer C. Stearns – Genome Medicine (BMC)

Intestinal Barrier Function and the Gut Microbiome Are Differentially Affected in Mice Fed a Western-Style Diet or Drinking Water Supplemented with Fructose – Valentina Volynets – The Journal of Nutrition

The gut microbiota of insecticide-resistant insects houses insecticide-degrading bacteria: A potential source for biotechnological exploitation – Luis Gustavo de Almeida – PLOS One

Probiotics / Synbiotics

A comparative characterization of different host-sourced Lactobacillus ruminis strains and their adhesive, inhibitory, and immunomodulating functions – Xia Yu – Frontiers in Microbiology

Rice bran and Probiotics Alter the Porcine Large Intestine and Serum Metabolomes for Protection Against Human Rotavirus Diarrhea  – Nora Jean Nealon – Frontiers in Microbiology

Development of a synbiotic beverage enriched with bifidobacteria strains and fortified with whey proteins – Federico Baruzzi – Frontiers in Microbiology

Inferring Microbial Interactions in the Gut of the Hong Kong Whipping Frog (Polypedates megacephalus) and a Validation Using Probiotics – Francis Cheng-Hsuan Weng – Frontiers in Microbiology

The effects of probiotic and synbiotic supplementation on metabolic syndrome indices in adults at risk of type 2 diabetes: study protocol for a randomized controlled trial – Nazila Kassaian – Trials (BMC)

Good Bugs vs Bad Bugs: Evaluation of Inhibitory Effect of Selected Probiotics against Enterococcus faecalis – Aarti A Bohora – The Journal of Contemporary Dental Practice (PDF here)

Probiotic bacteria prevent Salmonella – induced suppression of lymphoproliferation in mice by an immunomodulatory mechanism – R. Doug Wagner – BMC Microbiology

Exogenous lactobacilli mitigate microbial changes associated with grain fermentation (corn, oats, and wheat) by equine fecal microflora ex vivo – Brittany E. Harlow – PLOS One

 

Pathogens

Methicillin resistant Staphylococcus aureus emerged long before the introduction of methicillin in to clinical practice – Catriona Harkins – BioRxiv

Azathioprine, Mercaptopurine, and 5-Aminosalicylic Acid Affect the Growth of IBD-Associated Campylobacter Species and Other Enteric Microbes – Fang Liu –  Frontiers in Microbiology

Untargeted metabolomics analysis reveals key pathways responsible for the synergistic killing of colistin and doripenem combination against Acinetobacter baumannii – Mohd Hafidz Mahamad Maifiah – Scientific Reports

 

Other Genomics / Metagenomics

Untangling Genomes of Novel Planctomycetal and Verrucomicrobial Species from Monterey Bay Kelp Forest Metagenomes by Refined Binning – John Vollmers – Frontiers in Microbiology

Genome-Scale Reconstruction of the Metabolic Network in Oenococcus oeni to Assess Wine Malolactic Fermentation – Sebastián N. Mendoza – Frontiers in Microbiology

Comparative genomics of transport proteins in probiotic and pathogenic Escherichia coli and Salmonella enterica strains – Jimmy Do – Microbial Pathogenesis (Elsevier)

 

Bioinformatics

STITCHER 2.0: primer design for overlapping PCR applications  – Damien M. O’Halloran – Scientific Reports

 

Evolution

Phylogenomic evolutionary surveys of subtilase superfamily genes in fungi – Juan Li – Scientific Reports

Evolutionary dynamics on any population structure – Benjamin Allen – Nature

On the origins of oxygenic photosynthesis and aerobic respiration in Cyanobacteria – Rochelle M. Soo – Science

A perspective article about the latter paper here: How Cyanobacteria went green by Robert E. Blankenship

Structural reconstruction of protein ancestry – Romain Rouet – PNAS

 

March 30, 2017

Midgut microbiome of a vector for leishmaniasis, reviews on the human oral microbiome, using microfluidics to visualize live root-bacteria interactions, new open-access publishing project from the Gates Foundation.

General microbiome

Lotka-Volterra pairwise modeling fails to capture diverse pairwise microbial interactions – Babak Moment – eLIFE

Human oral microbiome

Review: Oral Microbiome and Nitric Oxide: the Missing Link in the Management of Blood Pressure – Nathan S. Bryan – Current Hypertension Reports

Review: Microbiota, Immune Subversion, and Chronic Inflammation – Carolyn D Kramer – Frontiers in Microbiology

Human gut microbiome

Highlight: Shaping the gut microbiome from the pancreas – Wei Wong – Science Signaling

Review: Mechanisms and consequences of intestinal dysbiosis – G. Adrienne Weiss – Cellular and Molecular Life Sciences

Animal experiments

Metaproteogenomics Reveals Taxonomic and Functional Changes between Cecal and Fecal Microbiota in Mouse – Alessandro Tanca – Frontiers in Microbiology

Helminth-induced alterations of the gut microbiota exacerbate bacterial colitis – C Su – Mucosal Immunology

Sex-related alterations of gut microbiota composition in the BTBR mouse model of autism spectrum disorder – Lorena Coretti – Scientific Reports

Milk Fat Globule Membrane Supplementation in Formula Modulates the Neonatal Gut Microbiome and Normalizes Intestinal Development – Ganive Bhinder – Scientific Reports

Gut metagenomic analysis reveals prominent roles of Lactobacillus and cecal microbiota in chicken feed efficiency – Wei Yan – Scientific Reports

Animal microbiome

An integrated overview of the midgut bacterial flora composition of Phlebotomus perniciosus, a vector of zoonotic visceral leishmaniasis in the Western Mediterranean Basin – Wael Fraihi – PLOS Neglected Tropical Diseases

Plant, root, and soil microbiome

Live imaging of root–bacteria interactions in a microfluidics setup – Hassan Massalha – PNAS

Mechanisms of nitrogen deposition effects on temperate forest lichens and trees – Therese S. Carter – Ecosphere

Research priorities for harnessing plant microbiomes in sustainable agriculture – Posy E Busby – PLOS Biology

Fe plaque-related aquatic uranium retention via rhizofiltration along a redox-state gradient in a natural Phragmites australis Trin ex Steud. wetland – Weqing Wang – Environmental Science and Pollution Research

Functional and phylogenetic diversity of cultivable rhizobacterial endophytes of sorghum [Sorghum bicolor (L.) Moench] – Venkadasamy Govindasamy – Antonie van Leeuwenhoek

Enhanced growth of halophyte plants in biochar-amended coastal soil: roles of nutrient availability and rhizosphere microbial modulation – Hao Zheng – Plant, Cell & Environment

Water and extremophile microbiome

Metagenomic Analysis of a Complex Community Present in Pond Sediment – Vivek Negi – Journal of Genomics

Probiotics/prebiotics

The preliminary study of prebiotic potential of Polish wild mushroom polysaccharides: the stimulation effect on Lactobacillus strains growth – Renata Nowak – European Journal of Nutrition

Probiotics may delay the progression of nonalcoholic fatty liver disease by restoring the gut microbiota structure and improving intestinal endotoxemia – Li Xue – Scientific Reports

Bioinformatics

MIPE: A metagenome-based community structure explorer and SSU primer evaluation tool – Bin Zou – PLOS One

Metabolomics

Gas chromatography/mass spectrometry metabolomics of urine and serum from nonhuman primates exposed to ionizing radiation: Impacts on the tricarboxylic acid cycle and protein metabolism – Evan L Pannkuk – Journal of Proteome Research

Techniques

Review: Pretreatment methods of lignocellulosic biomass for anaerobic digestion – Farrukh Raza Amin – AMB Express

Comparison of Standard Culture-Based Method to Culture-Independent Method for Evaluation of Hygiene Effects on the Hand Microbiome – C Zapka – mBio

More microbes

Depleting Mycobacterium tuberculosis of the transcription termination factor Rho causes pervasive transcription and rapid death – Laure Botella – Nature Communications

A Pseudomonas T6SS effector recruits PQS-containing outer membrane vesicles for iron acquisition – Jinshui Lin – Nature Communications

Indole-Induced Activities of β-Lactamase and Efflux Pump Confer Ampicillin Resistance in Pseudomonas putida KT2440 – Jisun Kim – Frontiers in Microbiology

Microbes in the news

Microbiome: Puppy power – Sujata Gupta – Nature (Outlook section)

Biological underpinnings of chronic fatigue syndrome begin to emerge – Amy Maxmen – Nature (News section)

Bacteria from sewage are infecting coral reefs – Elena Motivans – ZME Science

Key research priorities for agricultural microbiomes identified – Phys Org

Viral Bacterial Parasites Called Phages Drive Co-Evolution of Gut Microbiome – MedicalResearch.com

MSU, Shedd Aquarium partnering to create healthier aquatic homes – EurekAlert

Painting with bacteria is a thing and BUGSS will show you how – Stephen Babcock – Technical.ly Baltimore

Microbes on the market

Marrone Bio Innovations and Evogene Advance Novel Bacteria and Related Proteins Beyond Discovery into Insecticidal Product Development Phase – GlobeNewswire – Yahoo!Finance

Science, publishing, and career

Gates Foundation announces open-access publishing venture – Declan Butler – Nature (News section)

The readability of scientific texts is decreasing over time – Pontus Plavén-Sigray – bioRxiv

Amy’s non-microbiology picks

Iron minerals within specific microfossil morphospecies of the 1.88 Ga Gunflint Formation – Kevin Lepot – Nature Communications

March 22, 2017

Today’s digest features interesting review articles on the role of microbiome in health and disease, heart failure, and how the respiratory tract microbiota act as gatekeepers to respiratory health. Also, we have original research articles on the response of bacterial communities in oil-contaminated marine waters to addition of chemical and biological dispersants. Also, a very fascinating article in Harvard Business review on the gender bias against junior female scientists. Not surprising!! Enjoy.

General microbiome

*Review: The role of the microbiome in human health and disease: an introduction for clinicians – Vincent B Young – British Medical Journal

*Review: Targeting the Microbiome in Heart Failure – Allyson Zabell – Current Treatment Options in Cardiovascular Medicine

Gastric microbiota features associated with cancer risk factors and clinical outcomes: A pilot study in gastric cardia cancer patients from Shanxi, China – Guoqin Yu – international Journal of Cancer

Pregnancy and early life

Late preterm birth has direct and indirect effects on infant gut microbiota development during the first six months of life – M Forsgren – Acta Pediatrica

Vaginal microbiome

Characterization of vaginal Lactobacillus species by rplK -based multiplex qPCR in Russian women – Vladimir V. Demkin – Anaerobe

Human oral microbiome

Changes in salivary microbiota increase volatile sulfur compounds production in healthy male subjects with academic-related chronic stress – Bruno Dias Nani – Plos One

Candida albicans biofilm heterogeneity does not influence denture stomatitis but strongly influences denture cleansing capacity – Lindsay E. O’Donnell – Journal of Medical Microbiology

Oral Bacterial Infections : Diagnosis and Management – Glendee Reynolds-Campbell – Dental Clinics of North America

Human respiratory microbiome

*The microbiota of the respiratory tract: gatekeeper to respiratory health – Wing Ho Man – Nature Reviews Microbiology

Human gut microbiome

Editorial : Infant colic is still a mysterious disorder of the microbiota–gut–brain axis – Anna Pärtty – Acta Pediatrica

Review: More Flavor for Flavonoid-Based Interventions? – Nadeem O. Kaakoush – Trends in Molecular Medicine

Perspectives : New Frontiers in Fibers: Innovative and Emerging Research on the Gut Microbiome and Bone Health – Taylor C. Wallace – Journal of the American College of Nutrition

Does the Gut Microbiota Influence Immunity and Inflammation in Multiple Sclerosis Pathophysiology? – Monika Adamczyk-Sowa – Journal of Immunology Research

The Role of Intestinal Alkaline Phosphatase in Inflammatory Disorders of Gastrointestinal Tract – Jan Bilski – Mediators of Inflammation

The Gut Microbiome, Energy Homeostasis, and Implications for Hypertension – Ruth A. Riedl – Current Hypertension Reports

Fecal Microbiota Transplantation

Commentary: A proposed definition of microbiota transplantation for regulatory purposes – Diane E. Hoffmann – Gut Microbes

Review: Novel Indications for Fecal Microbial Transplantation: Update and Review of the Literature – Nathaniel Aviv Cohen – Digestive Diseases and Sciences

Animal microbiome

Review: Role of the microbiome in swine respiratory disease – Megan C. Niederwerder – Veterinary Microbiology

Comparative composition, diversity, and abundance of oligosaccharides in early lactation milk from commercial dairy and beef cows – William M. Sischo – Journal of Dairy Science

Comparative analysis of fecal microbial communities in cattle and Bactrian camels – Liang Ming – Plos One

Sheep fed with banana leaf hay reduce ruminal protozoa population – Cláudio Eduardo Silva Freitas – Tropical Animal Health and Production

Metabolomics

Review: Metabolomic-guided discovery of Alzheimer’s disease biomarkers from body fluid – Che Nor Adlia Enche Ady – Journal of Neuroscience Research

Animal experiments

The farming environment protects mice from allergen-induced skin contact hypersensitivity – C. P. Frossard – Clinical and Experimental Allergy

Metabolomics insights into diabetes nephropathy and protective effects of Radix Scutellariae on rats using ultra-high performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry – Lihui Men – RSC Advances

Plant, root, and soil microbiome

Root plant growth promoting rhizobacteria inoculations increase ferric chelate reductase (FC-R) activity and Fe nutrition in pear under calcareous soil conditions – Muzaffer İpek – Scientia Horticulturae

Bacterial diversity of the rhizosphere and nearby surface soil of rice (Oryza sativa) growing in the Camargue (France) – Jorge R. Osman – Rhizosphere

Structure and function of the bacterial communities during rhizoremediation of hexachlorobenzene in constructed wetlands – Cuiping Zhang – Environmental Science and Pollution Research

Water and extremophile microbiome
Characterization of spatial distribution of the bacterial community in the South Sea of Korea – Ji-Hui Seo – Plos One

Diversity and community structure of cyanobacteria and other microbes in recycling irrigation reservoirs – Ping Kong – Plos One

*Response of the bacterial community in oil-contaminated marine water to the addition of chemical and biological dispersants – Camila Rattes de Almeida Couto – Journal of Environmental Management

Probiotics / prebiotics

Lactobacillus johnsonii supplementation attenuates respiratory viral infection via metabolic reprogramming and immune cell modulation – W. Fonseca- Mucosal Immunology

Identification of the key excreted molecule by Lactobacillus fermentum related to host iron absorption – Ana González – Food Chemistry

Effect of 8-weeks prebiotics/probiotics supplementation on alcohol metabolism and blood biomarkers of healthy adults: a pilot study – Christopher Irwin – European Journal of Nutrition

Bioinformatics

Making big data smart—how to use metagenomics to understand soil quality – Gisle Vestergaard – Biology and Fertility of Soils

Techniques

SILVA, RDP, Greengenes, NCBI and OTT — how do these taxonomies compare? – Monika Balvočiūtė – BMC Genomics

Comparative evaluation of four bacteria-specific primer pairs for 16S rRNA gene surveys – Sofie Thijs – Frontiers in Microbiology

Microbes in the news

Asthma: Researchers discover how exposure to microbes protects against asthma

Rainy Day? Microbes May Be at Play

Building A Brewery, Chapter 4: For the Love of Microbes

Science, publishing, and career 

*Junior Female Scientists Aren’t Getting the Credit They Deserve “despite evidence that women on average, may perform better than men in early stage of their careers”

Anitha’s non-microbiology picks

How Pluto’s haze could explain its red spots

Cancer cells cast a sweet spell on the immune system

Actinide chemistry expands to new oxidation states