Human Microbiome

Genome reconstruction and characterisation of extensively drug-resistant bacterial pathogens through direct metagenomic sequencing of human faeces – Mu et al. – BioRxiv

Oropharyngeal and Sputum Microbiomes Are Similar Following Exacerbation of Chronic Obstructive Pulmonary Disease – Liu et al. – Frontiers in Microbiology

Segal’s Law, 16S rRNA gene sequencing, and the perils of foodborne pathogen detection within the American Gut Project – Pettengill & Rand – PeerJ

Unexplored diversity and strain-level structure of the skin microbiome associated with psoriasis – Tett et al. – npj Biofilms and Microbiomes

Rosacea and its association with enteral microbiota in Korean females – Nam et al. – Experimental Dermatology

Review: The role of microbiota, and probiotics and prebiotics in skin health – Maguire & Maguire – Archives of Dermatological Research

Human age and skin physiology shape diversity and abundance of Archaea on skin – Moissl-Eichinger et al. – Scientific Reports

Microbial Signatures Associated with Oropharyngeal and Oral Squamous Cell Carcinomas – Banerjee et al. – Scientific Reports

 

Animal Microbiome

Gut Dysbiosis and Adaptive Immune Response in Diet-induced Obesity vs. Systemic Inflammation – Pindjakova et al. – Frontiers in Microbiology

Characterization of the Microbiome along the Gastrointestinal Tract of Growing Turkeys –  Wilkinson et al. – Frontiers in Microbiology

Diet-induced reconstruction of mucosal microbiota associated with alterations of epithelium lectin expression and regulation in the maintenance of rumen homeostasis – Shen et al. – Scientific Reports

Fatty acid composition and phospholipid types used in infant formulas modifies the establishment of human gut bacteria in germ-free mice –  Guldhammer Nejrup et al. – Scientific Reports

Microbiota-derived butyrate suppresses group 3 innate lymphoid cells in terminal ileal Peyer’s patches – Kim et al. – Scientific Reports

Early-life gut microbial colonization shapes Th1/Th2 balance in asthma model in BALB/c mice – Qin et al. – BMC Microbiology

The development of lower respiratory tract microbiome in mice – Singh et al. – Microbiome (BMC)

 

Pathogen research

Genetic indicators of drug resistance in the highly repetitive genome of Trichomonas vaginalis – Bradic et al. – Genome Biology and Evolution

Metabolic and fitness determinants for in vitro growth and intestinal colonization of the bacterial pathogen Campylobacter jejuni – Gao et al. – PLoS Biology

Review: Periodontal diseases – Kinane et al. – Nature Reviews Disease Primer

 

Soil and Water Microbiome

Culture-Independent Analyses Reveal Novel Anaerolineaceae as Abundant Primary Fermenters in Anaerobic Digesters Treating Waste Activated Sludge – McIlroy et al. – Frontiers in Microbiology

Nitrogen enrichment impacts on boreal litter decomposition are driven by changes in soil microbiota rather than litter quality – Maaroufi et al. – Scientific Reports

 

Bioinformatics

CD-HIT-OTU-MiSeq, an Improved Approach for Clustering and Analyzing Paired End MiSeq 16S rRNA Sequences – Li et al. – BioRxiv

Divide and Conquer (DC) BLAST: fast and easy BLAST execution within HPC environments – Yim​ & Cushman – PeerJ

BGDMdocker: a Docker workflow for data mining and visualization of bacterial pan-genomes and biosynthetic gene clusters – Cheng et al. – PeerJ Preprints

 

Evolution

Phylogenetic Tracings of Proteome Size Support the Gradual Accretion of Protein Structural Domains and the Early Origin of Viruses from Primordial Cells – Nasir et al. – Frontiers in Microbiology

Pan-genome and phylogeny of Bacillus cereus sensu lato – Bazinet – BioRxiv

TreeTime: maximum likelihood phylodynamic analysis – Sagulenko et al. – BioRxiv

 

Other

Review: Fungal and Bacterial Pigments: Secondary Metabolites with Wide Applications –  Morris et al. – Frontiers in Microbiology

A Highly Efficient CRISPR-Cas9-Mediated Large Genomic Deletion in Bacillus subtilis – So et al. – Frontiers in Microbiology