protozoa | Microbiome Digest

Single cell genomics, metagenomics and bioinformatics, primers for protozoa detection, and Bik’s Picks.
Microbial detection

Clinical PathoScope: rapid alignment and filtration for accurate pathogen identification in clinical samples using unassembled sequencing data – Allyson L Byrd – BMC Bioinformatics

“Clinical PathoScope is the only pathogen identification method currently available that can identify multiple pathogens from mixed samples and distinguish between very closely related species and strains in samples with very few reads per pathogen. “

Metagenomics

Recent advances in genomic DNA sequencing of microbial species from single cells – Roger S. Lasken & Jeffrey S. McLean – Nature Review Genetics

“With the advent of single-cell sequencing, genomes of uncultivated species are rapidly filling in unsequenced branches of the microbial phylogenetic tree.”

Employing whole genome mapping for optimal de novo assembly of bacterial genomes
Basil Britto Xavier – BMC Research Notes

“Utilising several assembly tools based on de Bruijn graphs like Velvet, SPAdes and IDBA, we demonstrate that at the optimal N50, mis-assemblies do occur, even when using the multi-k-mer approaches of SPAdes and IDBA. “

Protozoal components of microbiome

Design and Validation of Four New Primers for Next-Generation Sequencing To Target the 18S rRNA Genes of Gastrointestinal Ciliate Protozoa – Suzanne L. Ishaq and André-Denis G. Wright – Applied and Environmental Microbiology

“PCR amplicons of 394 to 498 bases were generated from three primer sets, sequenced using Roche 454 pyrosequencing with Titanium, and analyzed using the BLAST database (NCBI) and MOTHUR version 1.29.”

Microbes in the news

What Causes Antibiotic Resistance? Video Answers This In Awesome Animation – Kevin Wu – Inquisitr.com

“Kevin Wu details the evolution of this problem that present a big challenge for the future of medicine in this amazing animated video uploaded on YouTube.”

Women in Science

Harassment in Science, Replicated – Christie Aschwanden – The New York Times

“The findings are depressingly similar to the data some colleagues and I collected this year from an online questionnaire sent to science writers. “

Bik’s Picks

Comparative population genomics reveals the domestication history of the peach (Prunus persica) and human influences on perennial fruit crops – Ke Cao – Genome Biology

“We perform large-scale resequencing of 10 wild and 74 cultivated peach varieties, including 9 ornamental, 23 breeding, and 42 landrace lines. We identify 4.6 million SNPs, a large number of which could explain the phenotypic variation in cultivated peach.”

Grizzly bears master healthy obesity – Meghan Rosen – Science News

“Though the animals beef up before hibernating, they may avoid diabetes by tweaking signals in fat cells, researchers report in the Aug. 5 Cell Metabolism.”

Natural light in office boosts health – Science Daily

“Office workers with more natural light exposure at the office had longer sleep duration, better sleep quality, more physical activity and better quality of life compared to office workers with less light exposure in the workplace, a study shows.”

[hr]

Protozoa detection in fecal samples from children, airway microbiome, and Staphylococcus transmission between mother and child.

Oral microbiome

Intercellular communications in multispecies oral microbial communities – Lihong Guo – Frontiers in Microbiology

“This review will summarize the evidence that oral microbes participate in intercellular communications with co-inhabitants through cell contact-dependent physical interactions, metabolic interdependencies, as well as coordinative signaling systems to establish and maintain balanced microbial communities.”

Respiratory microbiome

Airway Microbiome Dynamics in Exacerbations of Chronic Obstructive Pulmonary Disease – Yvonne J. Huang – Journal of Clinical Microbiology

“In this study, temporal changes in the airway microbiome before, at the onset of, and after an acute exacerbation were examined in 60 sputum samples collected from subjects enrolled in a longitudinal study of bacterial infection in COPD.”

Time between Collection and Storage Significantly Influences Bacterial Sequence Composition in Sputum Samples from Cystic Fibrosis Respiratory Infections – Leah Cuthbertson – Journal of Clinical Microbiology

“Samples were treated with propidium monoazide to distinguish live from dead cells prior to DNA extraction, and 16S rRNA gene pyrosequencing was used to characterize their bacterial compositions.”

Gut microbiome

The devil lies in the details: How variations in polysaccharide fine-structure impact the physiology and evolution of gut microbes – Eric C. Martens – Journal of Molecular Biology

“Here, we review the recent literature on this topic and posit that numerous, subtle variations in polysaccharides diversify the spectrum of available nutrient niches, each of which may be best filled by a subset of microorganisms that possess the corresponding proteins to recognize and degrade different carbohydrates”

Pregnancy and birth

Detection of intestinal protozoa in paediatric patients with gastrointestinal symptoms by multiplex real-time PCR – L. Maas – Clinical Microbiology and Infection

“The performance of a multiplex real-time PCR for the detection of Blastocystis, Dientamoeba fragilis, Giardia lamblia, Cryptosporidium species and Entamoeba species in faecal samples was evaluated in an observational prospective study.”

Transmission of Staphylococcus aureus between mothers and infants in an African setting – F. Schaumburg – Clinical Microbiology and Infection

“We aimed to investigate the transmission of S. aureus between mothers and their newborns during the first year after delivery in an African setting. In a longitudinal cohort study, colonization of Gabonese mother–infant pairs was assessed at delivery and after 1, 9 and 12 months.”

Commentary: Travelling within the fetal gut: simple rules for an arduous journey
Qiling Xu – BMC Microbiology

“A recent paper in BMC Biology addresses this issue with live imaging of gut explants from mouse embryos.”

[hr]