March 23, 2017

Today’s digest has quite a few papers in the human oral and gut microbiome with many interesting papers as the one from M. Lepczyńska addressing positive aspects of various diets on gut microbiota and its fight with parasites. In ‘Water microbiome’ you can take a look at Raquel S. Peixoto’s paper and beneficial microbes maintaining coral health, while in ‘Microbes in News’ you can read how team from Korea is tackling one of medicine’s most pressing problems – antibiotic resistance by using bacteria to fight bacteria.

General microbiome

Reduced microbial diversity in adult survivors of childhood acute lymphoblastic leukemia and microbial associations with increased immune activation – Ling Ling Chua -Microbiome

Pregnancy and early life

Manipulating the baby biome: What are the issues? – Lai-yang Lee – Australian and New Zealand Journal of Obstetrics and Gynaecology (ANZJOG)

Ex vivo infection of human placental chorionic villi explants with Trypanosoma cruzi and Toxoplasma gondii induces different Toll-like receptor expression and cytokine/chemokine profiles – Christian Castillo – American Journal of Reproductive Immunology (AJRI)

First foods and gut microbes – Martin F. Laursen – Frontiers in Microbiology

Reproductive microbiomes a new thread in the microbial network – Michael L. Power – Reproductive Sciences

Identical bacterial populations colonize premature infant gut, skin, and oral microbiomes and exhibit different in situ growth rates – Matthew R Olm – Genome Research

 
Human Oral

 
Differential responses of human dendritic cells to metabolites from the oral/airway microbiome – K. Whiteson – Clinical & Experimental Immunology

Candida albicans alters the bacterial microbiome of early in vitro oral biofilms – M. M. Janus – Journal of Oral Microbiology

Probiotic Lactobacillus reuteri has antifungal effects on oral Candida species in vitro – Mette Rose Jørgensen – Journal of Oral Microbiology

Porphyromonas gingivalis is the most abundant species detected in coronary and femoral arteries – J-L. C. Mougeot – Journal of Oral Microbiology

Oral microbiome in HIV-associated periodontitis – Noguera-Julian – Medicine

Quorum sensing of Streptococcus mutans is activated by Aggregatibacter actinomycetemcomitans and by the periodontal microbiome – Szymon P. Szafrański – BMC Genomics

Subgingival microbiota dysbiosis in systemic lupus erythematosus: association with periodontal status – Jôice Dias Corrêa – Microbiome
Human nearly-sterile sites 

Alterations in gastric microbiota after H. Pylori eradication and in different histological stages of gastric carcinogenesis – Tung Hiu Li – Scientific Reports

Human gut microbiome

Oral iron supplementation: Potential implications for the gut microbiome and metabolome in patients with CKD – Guus A. M. Kortman – Hemodialysis International

Hugonella massiliensis gen. nov., sp. nov., genome sequence, and description of a new strictly anaerobic bacterium isolated from the human gut – Ziena Elsawi – Microbiology Open

Gut microbiota: Neonatal gut microbiota induces lung immunity against pneumonia – Sabrina Tamburini – Nature Reviews Gastroenterology & Hepatology

*Review: Blastocystis: how do specific diets and human gut microbiota affect its development and pathogenicity? – M. Lepczyńska – European Journal of Clinical Microbiology & Infectious Diseases

Dysbiosis and compositional alterations with aging in the gut microbiota of patients with heart failure – Takehiro Kamo – PLOS One

Complex pectin metabolism by gut bacteria reveals novel catalytic functions – Didier Ndeh – Nature

Proteobacteria explain significant functional variability in the human gut microbiome – Patrick H. Bradley  – Microbiome

Animal experiments

Rice- or pork-based diets with similar calorie and content result in different rat gut microbiota – Xiaozhe Qi – International Journal of Food Sciences and Nutrition

Perturbation of microbiota in one-day old broiler chickens with antibiotic for 24 hours negatively affects intestinal immune development – Dirkjan Schokker – BMC Genomics

Effects of dietary administration of Shewanella xiamenensis A-1, Aeromonas veronii A-7, and Bacillus subtilis, single or combined, on the Grass Carp (Ctenopharyngodon idella) intestinal microbiota – Kai Hao – Probiotics and Antimicrobial Proteins

Plant, root, and soil microbiome

Pseudomonas sesami sp. nov., a plant growth-promoting Gammaproteobacteria isolated from the rhizosphere of Sesamum indicum L. – Munusamy Madhaiyan – Antonie van Leeuwenhoek

The influence of environmental factors on communities of arbuscular mycorrhizal fungi associated with Chenopodium ambrosioides revealed by MiSeq sequencing investigation – Xihui Xu -Sceintific Reports

Compositional stability of the bacterial community in a climate-sensitive sub-Arctic peatland – James T. Weedon – Frontiers in Microbiology

Antibiotic and heavy metal tolerance of some indigenous bacteria isolated from petroleum contaminated soil sediments with a study – Jai Godheja – International Journal of Current Microbiology and Applied Science (IJCMAS)

Water and extremophile microbiome 

Genome reduction and microbe-host interactions drive adaptation of a sulfur-oxidizing bacterium associated with a cold seep sponge – Ren-Mao Tian – mSystems

Impact of hypoxia on gene expression patterns by the human pathogen, Vibrio vulnificus, and bacterial community composition in a North Carolina estuary – Britney L. Phippen – Geohealth

Distribution of anaerobic carbon monoxide dehydrogenase genes in deep subseafloor sediments – T. Hoshino – Letters in Applied Microbiology

Phytoplankton species richness, evenness, and production in relation to nutrient availability and imbalance – Sirpa Lehtinen – Limnology and Oceanography

Metagenomic and culture-dependent analysis of the bacterial diversity of a hot spring reservoir as a function of the seasonal variation – B. A. Kikani – International Journal of Environmental Research

Beneficial microorganisms for corals (BMC): Proposed mechanisms for coral health and resilience – Raquel S. Peixoto – Frontiers in Microbiology

High-throughput amplicon sequencing and stream benthic bacteria: identifying the best taxonomic level for multiple-stressor research – R. K. Salis – Scientific Reports

Highlighting of quorum sensing lux genes and their expression in the hydrothermal vent shrimp Rimicaris exoculata ectosymbiontic community. Possible use as biogeographic markers – Simon Le Bloa – PLOS One

Molecular insights on dissolved organic matter transformation by supraglacial microbial communities – Runa Antony – Environmental Science & Technology

An alternative polysaccharide uptake mechanism of marine bacteria – Greta Reintjes – ISME Journal

Viable cold-tolerant iron-reducing microorganisms in geographically diverse subglacial environments – Sophie L. Nixon – Biogeosciences

Different bacterial communities involved in peptide decomposition between normoxic and hypoxic coastal waters – Shuting Liu – Frontiers in Microbiology

Temperature- and size-scaling of phytoplankton population growth rates: Reconciling the Eppley curve and the metabolic theory of ecology – Colin T. Kremer – Limnology and Oceanography

Contrasting patterns of diversity of abundant and rare bacterioplankton in freshwater lakes along an elevation gradient – Huabing Li – Limnology and Oceanography

 Built environment 

Short-term effects of great cormorant droppings on water quality and microbial community of an artificial agricultural reservoir – Il Han – Journal of Environmental Quality

Probiotics / prebiotics

Review: Gut microbiota and bacterial translocation in digestive surgery: the impact of probiotics – Shunichiro Komatsu – Langenbeck’s Archives of Surgery

Techniques

MinION™ nanopore sequencing of environmental metagenomes: a synthetic approach – Bonnie L. Brown – Gigascience

Microbes in the news 

Diabetes patients can lower blood sugar through gut bacteria; fecal microbes found to have curative properties – The Science Times

Predatory bacteria as a new ‘living’ antibiotic -Phys Org

Achievements of the human microbiome project – News Medical Life Sciences

Warning: current ecological microbiome may be on the verge of disaster due to antibiotics – Nature World News

 

March 17, 2017

Circadian clocks are ubiquitous timing systems that induce rhythms of biological activities in synchrony with night and day.In the first highlighted paper the authors present the structural basis of the day-night transition in a cyanobacterial circadian clock. The second highlighted paper evaluated the effects of antibiotic treatment on the honeybee gut microbiome. The authors found that exposure to antibiotics significantly alters the honeybee gut microbial community structure and leads to decreased survival.

General microbiome

Biohybrid Microtube Swimmers Driven by Single Captured Bacteria – Morgan M. Stanton – Small

Structural basis of the day-night transition in a bacterial circadian clock – Roger Tseng – Science

Pregnancy and early life

Breast Milk Polyamines and Microbiota Interactions: Impact of Mode of Delivery and Geographical Location – C Gómez-Gallego  – Annals of Nutrition and Metabolism

 
Human respiratory microbiome

Modulation of behaviour and virulence of a high alginate expressing Pseudomonas aeruginosa strain from cystic fibrosis by oral commensal bacterium Streptococcus anginosus – RD Waite  – PLOS One

Human gut microbiome

Transfer of dysbiotic gut microbiota has beneficial effects on host liver metabolism – Simon Nicolas – Molecular Systems Biology

Fecal microbiota transplantation induces hepatitis B virus e-antigen (HBeAg) clearance in patients with positive HBeAg after long-term antiviral therapy – Yan-Dan Ren – Hepatology

The Microbiome and Host Behavior – Vuong HE – Annual Review of Neuroscience

Nonalcoholic Fatty Liver Disease, the Gut Microbiome, and Diet – Zeinab Mokhtari – Advances in Nutrition

Animal experiments

Intestinal transcriptome modulation by functional diets in rainbow trout: A high-throughput sequencing appraisal to highlight GALT immunomodulation – Ana Teresa Gonçalves – Fish & Shellfish Immunology

Effects of Gliadin consumption on the Intestinal Microbiota and Metabolic Homeostasis in Mice Fed a High-fat Diet – Li Zhang – Scientific Reports

Oral administration of synthetic porcine beta-defensin-2 improves growth performance and cecal microbial flora and down-regulates the expression of intestinal toll-like receptor-4 and inflammatory cytokines in weaned piglets challenged with enterotoxigenic Escherichia coli – Zhiru Tang – Animal Science Journal

RNA-Based Stable Isotope Probing Suggests Allobaculum spp. as Particularly Active Glucose Assimilators in a Complex Murine Microbiota Cultured In Vitro – Elena Herrmann – BioMed Research International

Animal microbiome

Antibiotic exposure perturbs the gut microbiota and elevates mortality in honeybees – Kasie Raymann – PLOS Biology

Plant, root, and soil microbiome

Accessing the Carbofuran Degradation Ability of Cultures From Natural River Biofilms in Different Environments – Chien-Jung Tien – CLEAN – Soil, Air, Water

Impact of Agri-Usable Nanocompounds on Soil Microbial Activity: An Indicator of Soil Health – Priyanka Khati – CLEAN – Soil, Air, Water

Complete genome sequence of Pseudomonas citronellolis P3B5, a candidate for microbial phyllo-remediation of hydrocarbon-contaminated sites – Mitja N.P. Remus-Emsermann – SIGS Standards in Genomic Sciences

Is the methanogenic community reflecting the methane emissions of river sediments?—comparison of two study sites – Prem Prashant Chaudhary – Microbiology Open

Water and extremophile microbiome

Characterizing and predicting cyanobacterial blooms in an 8-year amplicon sequencing time-course – Nicolas Tromas – bioRxiv

Effect of pesticides on microbial communities in container aquatic habitats – Ephantus J. Muturi – Scientific Reports

Serpentinization-Influenced Groundwater Harbors Extremely Low Diversity Microbial Communities Adapted to High pH – KI Twing – Frontiers in Microbiology

Dynamic Succession of Groundwater Sulfate-Reducing Communities during Prolonged Reduction of Uranium in a Contaminated Aquifer – Ping Zhang – Environmental Science & Technology

Reactivation of Deep Subsurface Microbial Community in Response to Methane or Methanol Amendment – Pauliina Rajala – Frontiers in Microbiology

Built environment

Nanoscale zero-valent iron/persulfate enhanced upflow anaerobic sludge blanket reactor for dye removal: Insight into microbial metabolism and microbial community – Fei Pan – Scientific reports

Probiotics / prebiotics

Achieving High Yield of Lactic Acid for Antimicrobial Characterization in Cephalosporin-Resistant Lactobacillus by the Co-Expression of the Phosphofructokinase and Glucokinase – Gong Y – Journal of Microbiology and Biotechnology

Phages and viruses

Inflammation boosts bacteriophage transfer between Salmonella spp.– Médéric Diard – Science

Bioinformatics

microclass: an R-package for 16S taxonomy classification – Kristian Hovde Liland – BMC Bioinformatics

Microbes in the news

Team finds new way that bacteria lay siege to neighboring cells by hijacking two factors involved in protein synthesis – Phys.Org

 

February 20, 2017

This Monday we have some quite interesting news about microbes! Microbes found inside giant crystals in caves in Chihuahua, Mexico, may have survived there for tens of thousands of years, while meadows of underwater seagrass plants might lower levels of harmful bacteria in nearby ocean waters making the whole ecosystem — from corals to fish to humans — healthier. Enjoy your reading..

Pregnancy and early life

Adenoid bacterial colonization in a paediatric population – João Subtil – European Archives of Oto-Rhino-Laryngology

Human gut microbiome

Review: NLRP6: A Multifaceted Innate Immune Sensor – Maayan Levy – Trends in Immunology

Prebiotic inulin-type fructans induce specific changes in the human gut microbiota – Doris Vandeputte – Gut

Gut microbial profile is altered in primary biliary cholangitis and partially restored after UDCA therapy – Ruqi Tang – Gut

Multidonor intensive faecal microbiota transplantation for active ulcerative colitis: a randomised placebo-controlled trial – Sudarshan Paramsothy – The Lancet

Reinforcement of intestinal epithelial barrier by arabinoxylans in overweight and obese subjects: A randomized controlled trial: Arabinoxylans in gut barrier – Bouke N. Salden – Clinical Nutrition

Diet-induced obesity, gut microbiota and bone, including alveolar bone loss – Sathima Eaimworawuthikul – Archives of Oral Biology

Animal experiments

Dietary Prebiotics and Bioactive Milk Fractions Improve NREM Sleep, Enhance REM Sleep Rebound and Attenuate the Stress-Induced Decrease in Diurnal Temperature and Gut Microbial Alpha Diversity – Robert S. Thompson – Frontiers in  Behavioral Neuroscience

Plant, root, and soil microbiome

Plant community and nitrogen deposition as drivers of α- and β-prokaryotic diversity in reconstructed oil-sands soils and natural boreal forest soils – Jacynthe Masse – Applied and Environmental Microbiology

Plant-microbial association in petroleum and gas exploration sites in the state of Assam, north-east India—significance for bioremediation – Hemen Sarma – Environmental Science and Pollution Research

The choice of the DNA extraction method may influence the outcome of the soil microbial community structure analysis – Sylwia Zielińska – Microbiology Open

Water and extremophile microbiome

Seagrass ecosystems reduce exposure to bacterial pathogens of humans, fishes, and invertebrates – Joleah B. Lamb – Science

Phages and viruses

Cyanophage-encoded lipid-desaturases: oceanic distribution, diversity and function – Sheila Roitman – bioRxiv

Techniques

Effects of gelling agent and extracellular signaling molecules on the culturability of marine bacteria – Anita Mac Rygaard – Applied and Environmental Microbiology

A tool named Iris for versatile high-throughput phenotyping in microorganisms – George Kritikos – Nature Microbiology

Microbes in the news 

Microbes survived inside giant cave crystals for up to 50,000 years – Science News

Three-way dance between herbivores, plants and microbes unveiled  – Phys.org

Synthetic antibiotic developed by Sask. researchers to combat drug-resistant bacteria – CBC News

Salmonella ‘can kill cancer’: How bacteria that cause food poisoning could be used to attack tumour cells – Colin Fernandez for Daily Mail, UK

Brazilian peppertree packs power to knock out antibiotic-resistant bacteria – Science Daily

Bacteria Hysteria

Drug-resistant deadly bacteria more widespread than previously thought, study finds – News Medical

 

January 16, 2017

Environmental pollutants have become an increasingly common health hazard. The possible effects of environmental pollutants on gut microbiota and their subsequent effects on health is discussed in highlighted review.

Pregnancy and early life

Antibiotics in Pregnancy Increase Children’s Risk of Otitis Media and Ventilation Tubes – Tine Marie Pedersen – The journal of Pediatrics

Human skin microbiome

Insights into the mast cell–microbiome connection in the skin – Alon Y. Hershko – Journal of Allergy and Clinical Immunology

Microbiota fingerprints lose individually identifying features over time – David Wilkins – Microbiome

Human vaginal microbiome

Association between preterm labor and genitourinary tract infections caused by Trichomonas vaginalis, Mycoplasma hominis, Gram-negative bacilli, and coryneforms – Alaa El-Dien M.S. Hosny – Journal of the Chinese Medical Association

The Vaginal Microbiota and Urinary Tract Infection – Ann E. Stapleton – Microbiol Spectrum

Human nearly-sterile sites 

Metabolic profiles of exudates from chronic leg ulcerations – Adam Junka – Journal of Pharmaceutical and Biomedical Analysis

Human oral microbiome

Review: Ecology of the Oral Microbiome: Beyond Bacteria – Jonathon L. Baker – Trends in Microbiology

On-going Mechanical Damage from Mastication Drives Homeostatic Th17 Cell Responses at the Oral Barrier – Nicolas Dutzan – Immunity

Salivary Gluten Degradation and Oral Microbial Profiles in Health and Celiac Disease – Na Tian  – Applied and Environmental Microbiology

Human gut microbiome

Expert review: Management of Clostridium difficile Infection in Inflammatory Bowel Disease: Expert Review from the Clinical Practice Updates Committee of the AGA Institute – Sahil Khanna – Clinical Gastroenterology and Hepatology

Review: Effects of environmental pollutants on gut microbiota – Yuanxiang Jin – Environmental Pollution

Impact of dietary pattern of the fecal donor on in vitro fermentation properties of whole grains and brans – Sandrayee Brahma – Journal of Functional Foods

Review: The role of the gut microbiota in sepsis – Bastiaan W Haak – The Lancet Gastroenterology & Hepatology

Gut microbiota interactions with the immunomodulatory role of vitamin D in normal individuals – Renata V. Luthold – Metabolism

Angelakisella massiliensis” gen. nov., sp. nov., a new bacterial species isolated from human ileum – Morgane Mailhe – New Microbes and New Infections

Helicobacter pylori–related metabolic syndrome as predictor of progression to esophageal carcinoma in a subpopulation-based Barrett’s esophagus cohort – Jannis Kountouras – Gastrointestinal Endoscopy

Impact of dietary pattern of the fecal donor on in vitro fermentation properties of whole grains and brans – Sandrayee Brahma – Journal of Functional Foods

Absence of intestinal microbiota increases ß-cyclodextrin stimulated reverse cholesterol transport – Rima H. Mistry – Molecular Nutrition & Food Research

European consensus conference on faecal microbiota transplantation in clinical practice – Giovanni Cammarota – Gut
Animal experiments

Gd-DTPA-induced dynamic metabonomic changes in rat biofluids – Chuanling Wan – Magnetic Resonance Imaging

Increasing dietary nitrate has no effect on cancellous bone loss or fecal microbiome in ovariectomized rats – Melissa N. Conley – Molecular Nutrition & Food Research

Animal microbiome

Improved growth rate and disease resistance in olive flounder, Paralichthys olivaceus, by probiotic Lactococcus lactis WFLU12 isolated from wild marine fish – Thanh Luan Nguyen – Aquaculture

Plant, root, and soil microbiome

The effects of tree species and substrate on carbon sequestration and chemical and biological properties in reforested post-mining soils – Agnieszka Józefowska – Geoderma

Impacts of inorganic and organic fertilization treatments on bacterial and fungal communities in a paddy soil – Jichen Wang – Applied Soil Ecology

Water and extremophile microbiome

Effects of the halophilic fungi Cladosporium sphaerospermum, Wallemia sebi, Aureobasidium pullulans and Aspergillus nidulans on halite formed on sandstone surface – Maisa M.A. Mansour – International Biodeterioration & Biodegradation

Epiphytic Planctomycetes communities associated with three main groups of macroalgae – Joana Bondoso – FEMS Microbiology Ecology

Floc formation reduces the pH stress experienced by microorganisms living in alkaline environments -C.J. Charles – Applied and Environmental Microbiology

Capturing compositional variation in denitrifying communities: A multiple primer approach that includes autotrophic denitrifying Epsilonproteobacteria – S.A. Murdock  – Applied and Environmental Microbiology

Waste and pollution microbiology

Review: Aerobic and anaerobic fungal metabolism and Omics insights for increasing polycyclic aromatic hydrocarbons biodegradation – Sevcan Aydin – Fungal Biology Reviews

Built environment 

Biological invasion in the indoor environment: the spread of Eurotium halophilicum on library materials – Andrea Polo – International Biodeterioration & Biodegradation

Review: Integrated management of the risks of stored grain spoilage by seedborne fungi and contamination by storage mould mycotoxins – An update – Francis Fleurat-Lessard – Journal of Stored Products Research

Food microbiology

Impact of environmental conditions and process modifications on microbial diversity, fermentation efficiency and chemical profile during the fermentation of mezcal in Oaxaca – Manuel R. Kirchmayr – LWT – Food Science and Technology

Anti-aging and redox state regulation effects of A-type proanthocyanidins-rich cranberry concentrate and its comparison with grape seed extract in mice – Jingjing Jiao – Journal of Functional Foods

Probiotics / prebiotics

Probiotic mixture improves fatty liver disease by virtue of its action on lipid profiles, leptin, and inflammatory biomarkers – Hessah Mohammed Al-muzafar – BMC Complementary and Alternative Medicine