Enjoy perusing this beefy Microbiome Digest, which is heavy on information about plant/root/soil microbes, water/extremophile microbes, and new microbial techniques.
Events and jobs
Microbiome Symposium 2017 – September 11, Quadras Conference Center
General microbiome
Temperature, inocula and substrate: Contrasting electroactive consortia, diversity and performance in microbial fuel cells – E.S. Heidrich, Bioelectrochemistry
Effect of glucose on nitrogen removal and microbial community in anammox-denitrification system – Yujie Qin, Bioresource Technology
Horizontal Gene Transfer and Ecosystem Function Dynamics – Maarten van de Guchte, Trends in Microbiology
Pregnancy and early life
Patterns of Early-Life Gut Microbial Colonization during Human Immune Development: An Ecological Perspective – Isabelle Laforest-Lapointe, Frontiers in Microbiology
Maternal Gut Microbiome Biodiversity in Pregnancy – Marcela C. Smid, American Journal of Perinatology
Sphingolipid metabolism potential in fecal microbiome and bronchiolitis in infants: a case–control study – Kohei Hasegawa, BMC Research Notes
Adverse events in women and children who have received intrapartum antibiotic prophylaxis treatment: a systematic review – Farah Seedat, BMC Pregnancy and Childbirth
Human skin microbiome
Bacterial diversity in Buruli ulcer skin lesions: Challenges in the clinical microbiome analysis of a skin disease – Chloé Van Leuvenhaege, PLoS ONE
Human oral microbiome
16S rDNA analysis of periodontal plaque in chronic obstructive pulmonary disease and periodontitis patients – Wu X., Journal of Oral Microbiology
Porphyromonas gingivalis disturbs host-commensal homeostasis by changing complement function – Olsen I., Journal of Oral Microbiology
Human gut microbiome
The Present Status of Fecal Microbiota Transplantation and Its Value in the Elderly – Yao-Wen Cheng, Current Treatment Options in Gastroenterology
Fecal total iron concentration is inversely associated with fecal Lactobacillus in preschool children – Sasank Kalipatnapu, Gastroenterology
Long-term irritable bowel syndrome symptom control with reintroduction of selected FODMAPs – Ruth M. Harvie, World Journal of Gastroenterology
Distinct gut microbiota profiles in patients with primary sclerosing cholangitis and ulcerative colitis – Lukas Bajer, World Journal of Gastroenterology
Eubiotic properties of rifaximin: Disruption of the traditional concepts in gut microbiota modulation – Francesca Romana Ponziani, World Journal of Gastroenterology
Helicobacter pylori and gut microbiota in multiple sclerosis versus Alzheimer’s disease: 10 pitfalls of microbiome studies – Ah-Mee Park, Clinical and Experimental Neuroimmunology
Partners of patients with ulcerative colitis exhibit a biologically relevant dysbiosis in fecal microbial metacommunities – Guang-Lan Chen, World Journal of Gastroenterology
Animal Experiments
Oral administration of live- or heat-killed Candida albicansworsened cecal ligation and puncture sepsis in a murine model possibly due to an increased serum (1→3)-β-D-glucan – Wimonrat Panpetch, PLoS ONE
Cross-modulation of pathogen-specific pathways enhances malnutrition during enteric co-infection with Giardia lambliaand enteroaggregative Escherichia coli – Luther A. Bartelt, PLoS Pathogens
Animal microbiome
Changes in the Intestinal Microbiota of Gibel Carp (Carassius gibelio) Associated with Cyprinid herpesvirus2 (CyHV-2) Infection – Rong She, Current Microbiology
Diversity and stability of coral endolithic microbial communities at a naturally high pCO2 reef – Vanessa R. Marcelino, Molecular Ecology
Characterization of feather-degrading bacterial populations from birds’ nests – Potential strains for biomass production for animal feed – Maria Saarela, International Biodeterioration & Biodegradation
The impact of the bovine fecal microbiome on Escherichia coli O157:H7 prevalence and enumeration in naturally infected cattle – Minseok Kim, Journal of Applied Microbiology
Burying beetles regulate the microbiome of carcasses and use it to transmit a core microbiota to their offspring – Shantanu P. Shukla, Molecular Ecology
Plant, root, and soil microbiome
Elevated CO2 and nitrogen addition have minimal influence on the rhizospheric effects of Bothriochloa ischaemum – Lie Xiao, Scientific Reports
Soil nutritional status and biogeography influence rhizosphere microbial communities associated with the invasive tree Acacia dealbata – Casper N. Kamutando, Scientific Reports
Biotoxic impact of heavy metals on growth, oxidative stress and morphological changes in root structure of wheat (Triticum aestivum L.) and stress alleviation by Pseudomonas aeruginosa strain CPSB1 – Asfa Rizvi, Chemosphere
Use of microbial indicators combined with environmental factors coupled to metrology tools for discrimination and classification of Luzhou-flavored pit muds – Q.Y. Zhang, Journal of Applied Microbiology
Fertilization decreases compositional variation of paddy bacterial community across geographical gradient – Ruirui Chen, Soil Biology and Biochemistry
Effects of snow cover plus straw mulching on microorganisms in paddy soil during winter – Hao Zhang, Applied Soil Ecology
The Contribution of Pyrene Degrading Bacteria and Chemical Reagents to Scirpus triqueterPhytoremediation of Pyrene and Ni Co-contaminated Soil – Xiaoxin Hu, Water, Air, & Soil Pollution
Investigating whether light intensity can modify decomposition rates in peatlands through control of the ‘enzymic latch’ – Christian Dunn, Ecological Engineering
Analysis of microbiota in rhizosphere, water and gut of grass carp (Ctenopharyngodon idella) in ponds treated with artificial floating beds – Jian Li, Water and Environment Journal
Scaling from the growth chamber to the greenhouse to the field: Demonstration of diminishing effects of mitigation of salinity in peppers inoculated with plant growth-promoting bacterium and humic acids – Macario Bacilio, Applied Soil Ecology
Disease management of tomato through PGPB: current trends and future perspective – Vipin Kumar Singh, 3 Biotech
Soil bacteria and archaea change rapidly in the first century of Fennoscandian boreal forest development – Stephanie A. Yarwood, Soil Biology and Biochemistry
Leaf litterfall decomposition of pedunculate (Quercus robur L.) and sessile (Q. petraea [Matt.] Liebl.) oaks and their hybrids and its impact on soil microbiota – Girmantė Jurkšienė, Dendrobiology
On the controls of abundance for soil-dwelling organisms on the Tibetan Plateau – Ke Zhao, Ecosphere
Water and extremophile microbiome
Microbial planktonic communities in the Red Sea: high levels of spatial and temporal variability shaped by nutrient availability and turbulence – John K. Pearman, Scientific Reports
Characterization of a highly efficient antibiotic-degrading metallo-β-lactamase obtained from an uncultured member of a permafrost community – Marcelo Monteiro Pedroso, Metallomics
Polycyclic aromatic hydrocarbons (PAHs) enrich their degrading genera and genes in human-impacted aquatic environments – Ke Yuan, Environmental Pollution
Spatial autocorrelation of microbial communities atop a debris-covered glacier is evidence of a supraglacial chronosequence – Jack L. Darcy, FEMS Microbiology Ecology
Eco-friendly and efficient in situ restoration of the constructed sea stream by bioaugmentation of a microbial consortium – Jangyeon Yoo, Korean Journal of Microbiology
Identification of two organohalide-respiring Dehalococcoidiaassociated to different dechlorination activities in PCB-impacted marine sediments – Andrea Nuzzo, Microbial Cell Factories
Draft genome sequence of the halophilic Halobacillus mangroviKTB 131 isolated from Topan salt of the Jeon-nam in Korea – Mingyeong Woo, Genomics Data
First draft genome sequence of a strain from the genus Fusibacter isolated from Salar de Ascotán in Northern Chile – Antonio E. Serrano, Extended Genome Report
Draft Genome Sequence of the Deep-Sea Bacterium Moritella sp. JT01 and Identification of Biotechnologically Relevant Genes – Robert Cardoso de Freitas, Marine Biotechnology
Bacterial and Archaeal Diversity in Hypersaline Cyanobacterial Mats Along a Transect in the Intertidal Flats of the Sultanate of Oman – Janina C. Vogt, Microbial Ecology
Bacterial and fungal communities and contribution of physicochemical factors during cattle farm waste composting – Huhe, Microbiology Open
Built environment
Bioprotection of the built environment and cultural heritage – Geoffrey Michael Gadd, Microbial Biotechnology
Food microbiology
Food waste conversion to microbial polyhydroxyalkanoates – Chad Nielsen, Microbial Biotechnology
Insect frass in stored cereal products as a potential source of Lactobacillus sanfranciscensis for sourdough ecosystem – Federica Boiocchi, Journal of Applied Microbiology
Probiotics
Evaluation of Probiotic Diversity from Soybean (Glycine max) Seeds and Sprouts Using Illumina-Based Sequencing Method – Yali Huang, Probiotics and Antimicrobial Proteins
Bioinformatics
Visibiome: an efficient microbiome search engine based on a scalable, distributed architecture – Syafiq Kamarul Azman, BMC Bioinformatics
Techniques
Inferring Past Environments from Ancient Epigenomes – David Gokhman, Microbial Ecology and Evolution
Comparison of DNA extraction methods used to detect bacterial and yeast DNA from spiked whole blood by real-time PCR – Libera M. Dalla-Costa, Journal of Microbiological Methods
Understanding the fundamental mechanisms of biofilms development and dispersal: BIAM (Biofilm Intensity and Architecture Measurement), a new tool for studying biofilms as a function of their architecture and fluorescence intensity – Marine Baudin, Journal of Microbiological Methods
Comparison of sequencing the D2 region of the large subunit ribosomal RNA gene (MicroSEQ®) versus the internal transcribed spacer (ITS) regions using two public databases for identification of common and uncommon clinically relevant fungal species – S. Arbefeville, Journal of Microbiological Methods
The feasibility of improved live-dead distinction in qPCR-based microbial source tracking – Laura Seidel, Journal of Microbiological Methods
Comparison of two bioinformatics tools used to characterize the microbial diversity and predictive functional attributes of microbial mats from Lake Obersee, Antarctica – Hyunmin Koo, Journal of Microbiological Methods
Multiplex polymerase chain reaction for identification of Escherichia coli, Escherichia albertii and Escherichia fergusonii – Rebecca L. Lindsey, Journal of Microbiological Methods
Nontargeted virus sequence discovery pipeline and virus clustering for metagenomic data – David Paez-Espino, Nature Protocols
SigTree: A Microbial Community Analysis Tool to Identify and Visualize Significantly Responsive Branches in a Phylogenetic Tree – John R. Stevens, Computational and Structural Biotechnology Journal