June 2, 2015

General human microbiome

The human microbiome in hematopoiesis and hematological disorders – Veronica E. Manzo and Ami S. Bhatt – Blood

Special issue of Microbial Ecology in Health and Disease: Editorial: We all need friends – Jørgen Valeur

Early Factors Leading to Later Obesity: Interactions of the Microbiome, Epigenome, and Nutrition – Lilly Chang, Josef Neu – Current Problems in Pediatric and Adolescent Health Care

Microbiome of pregnancy and birth

Opportunities to assess factors contributing to the development of the intestinal microbiota in infants living in developing countries – Dennis Lang – Microbial Ecology in Health and Disease

Review: Factors affecting infant gut microbiota and possible consequences for health
Merete Eggesbø – Microbial Ecology in Health and Disease

Human gut microbiome

Draft Genome Sequences of 24 Microbial Strains Assembled from Direct Sequencing from 4 Stool Samples – Patricio Jeraldo – Genome Announcements

Book Chapter: Physiology of Digestion and Absorption: The Functional Interdependence Between Food and the Gut – Stephen J. D. O’Keefe – The Principles and Practice of Nutritional Support

Review: With a little help from my enteric microbial friends – Ben Berkhout – Frontiers in Medicine

Editorial: AI-2 to the rescue against antibiotic-induced intestinal dysbiosis? – Zhongke Sun – Trends in Microbiology

Microbiome models

Evidence from Animal Models: Is a Restricted or Conventional Intestinal Microbiota Composition Predisposing to Risk for High-LET Radiation Injury? – Irene Maier – Radiation Research

Rumen Microbiome from Steers Differing in Feed Efficiency – Phillip R. Myer – PLOS ONE

Changes in the composition of intestinal fungi and their role in mice with dextran sulfate sodium-induced colitis – Xinyun Qiu – Scientific Reports

Microbiota prevents cholesterol loss from the body by regulating host gene expression in mice – Chun-Yan Zhong – Scientific Reports

Animal microbiome

Early-life establishment of the swine gut microbiome and impact on host phenotypes – Núria Mach – Environmental Microbiology Reports

Lifestyle Evolution in Cyanobacterial Symbionts of Sponges – Ilia Burgsdorf – mBio

Plant microbiome

Antagonistic interactions between endophytic cultivable bacterial communities isolated from the medicinal plant Echinacea purpurea – Isabel Maida – Environmental Microbiology

Soil microbiome

Distinct soil bacterial communities along a small-scale elevational gradient in alpine tundra – Congcong Shen – Frontiers in Microbiology

Carcass mass has little influence on the structure of gravesoil microbial communities – Sophie Weiss – International Journal of Legal Medicine

Impact of different cropping conditions and tillage practices on the soil fungal abundance of a Phaeozem luvico – Romina P. Gomez – Spanish Journal of Agricultural Research

Biological activity and microbial genetic diversity of bare-fallow and grassland soils – Anna Kot – Acta Agriculturae Scandinavica, Section B — Soil & Plant Science

Masters Thesis: Assessing soil microbial tolerance to salt – Arpita Maheshwari – Lund University

Water microbiome

Microbial metagenomics in the Baltic Sea: Recent advancements and prospects for environmental monitoring – Karolina Ininbergs – AMBIO

Characterizing microbial communities dedicated for conversion of coal to methane in situ and ex situ – Ji Zhang – International Journal of Coal Geology

Dynamics of the bacterial and archaeal communities in the northern South China Sea revealed by 454 pyrosequencing of the 16S rRNA gene – Xia Xiaomin – Deep Sea Research Part II: Topical Studies in Oceanography

Editorial: Microbial symbiosis of marine sessile hosts- diversity and function – Suhelen Egan – Frontiers in Microbiology

Review: Biodiversity, community structure and function of biofilms in stream ecosystems – Katharina Besemer – Research in Microbiology

Built environment microbiome

pecunia non olet? Screening Currency Notes for Microbial Pathogens and Antibiotic Resistance Genes Using a Shotgun Metagenomic Approach – Saakshi Jalali – PLOS ONE

Phages and viruses

Dark matter of the biosphere: The amazing world of bacteriophage diversity – Graham F. Hatfull – Journal of Virology

Bioinformatics and metagenomics

VirSorter: mining viral signal from microbial genomic data – Simon Roux – PeerJ

Denoising DNA deep sequencing data—high-throughput sequencing errors and their correction – David Laehnemann – Briefings in Bioinformatics

FCMM: A comparative metagenomic approach for functional characterization of multiple metagenome samples – Jongin Lee – Journal of Microbiological Methods

PuzzleCluster: A Novel Unsupervised Clustering Algorithm for Binning DNA Fragments in Metagenomics – Current Bioinformatics

Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi – Leho Tedersoo – MycoKeys

ANCOM: Analysis of composition of microbiomes: a novel method for studying microbial composition – Siddhartha Mandal – Microbial Ecology in Health and Disease

Transcriptomics and Metabolomics

MetabNet: an R package for metabolic association analysis of high-resolution metabolomics data – Karan Uppal – Frontiers in Bioengineering and Biotechnology

Meta-omics uncover temporal regulation of pathways across oral microbiome genera during in vitro sugar metabolism – Anna Edlund – ISME Journal

Review: Enteric short-chain fatty acids: microbial messengers of metabolism, mitochondria, and mind: implications in autism spectrum disorders – Derrick F. MacFabe – Microbial Ecology in Health and Disease


Co-extraction of DNA and PLFA from soil samples – Sheridan Brewer – Journal of Microbial Methods

Microbial ecology

Editorial: Flexible gene pools: hard to interpret the diversity often observed in microbial communities – Michael M. Desai – Science

Fine-scale diversity and extensive recombination in a quasisexual bacterial population occupying a broad niche – Michael J. Rosen – Science

Microbes in the news

Good craft beer can be spoiled by bacteria – Phys.org / American Society for Microbiology

Treating Koala STDs May also Quash Their Essential Gut Microbes – Katherine Harmon Courage – Scientific American

New study: Gut bacteria cooperate when life gets tough – EurekAlert

Metabolic activity and health of the skin microbiome – Medical Xpress / American Society for Microbiology

Is our first line of defense sleeping on the job? – Science Daily / American Society for Microbiology

Growing Up In an UnSterile World –The Importance of a Healthy Gut Through the Lifespan – Sarah Lobisco – Dr. Lobisco

Citizen Scientists Send Microbes Into Space – Science 2.0

Methanogens: Earth organisms survive under low-pressure Martian conditions – Science Daily

Why is the H-pylori bacteria developing a liking for Mumbai police? – Santosh Andhale – DNA India

Book review: The great microbial beauty – Vittorio Capozzi – Trends in Microbiology

Science, publishing, and career

Plagiarism is the most common cause of retractions in BioMed Central journals:
Retractions Often Due to Plagiarism: Study – Kerry Grens – The Scientist

Bik’s Picks: not-microbial science

Giant Sawfish Have Virgin Births, Rewrite Biology Textbooks – Charles Q. Choi – Live Science

These newly discovered marsupials basically sex each other to death – Elahe Izadi – Washington Post

Seals Help Scientists Probe Remote Seas – Discovery



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