SqueezeMeta, a highly portable, fully automatic metagenomic analysis pipeline

J Tamames, F Puente-Sánchez - Frontiers in microbiology, 2019 - frontiersin.org
The improvement of sequencing technologies has facilitated generalization of metagenomic
sequencing, which has become a standard procedure for analyzing the structure and …

Taking advantage of the genomics revolution for monitoring and conservation of chondrichthyan populations

S Johri, MP Doane, L Allen, EA Dinsdale - Diversity, 2019 - mdpi.com
Chondrichthyes (sharks, rays, skates and chimaeras) are among the oldest extant predators
and are vital to top-down regulation of oceanic ecosystems. They are an ecologically diverse …

'Genome skimming'with the MinION hand-held sequencer identifies CITES-listed shark species in India's exports market

S Johri, J Solanki, VA Cantu, SR Fellows… - Scientific reports, 2019 - nature.com
Abstract Chondrichthyes-sharks, rays, skates, and chimeras, are among the most threatened
and data deficient vertebrate species. Global demand for shark and ray derived products …

Open the SterivexTM casing: An easy and effective way to improve DNA extraction yields

P Cruaud, A Vigneron, MS Fradette… - Limnology and …, 2017 - Wiley Online Library
We describe an inexpensive, reliable, and easily executed improvement for the extraction of
DNA from SterivexTM filter units, that involves the separation of the SterivexTM filter from its …

Single-cell technologies in environmental omics

R Kodzius, T Gojobori - Gene, 2016 - Elsevier
Environmental studies are primarily done by culturing isolated microorganisms or by
amplifying and sequencing conserved genes. Difficulties understanding the complexity of …

The skin microbiome of the common thresher shark (Alopias vulpinus) has low taxonomic and gene function β‐diversity

MP Doane, JM Haggerty, D Kacev… - Environmental …, 2017 - Wiley Online Library
The health of sharks, like all organisms, is linked to their microbiome. At the skin interface,
sharks have dermal denticles that protrude above the mucus, which may affect the types of …

Giant kelp microbiome altered in the presence of epiphytes

AK James, CJ English, NJ Nidzieko… - Limnology and …, 2020 - Wiley Online Library
Characterizing patterns in the microbial communities associated with canopy‐forming kelps
is critical to understanding the mechanisms shaping macroalgal microbiomes. Using 16S …

On-site analysis of bacterial communities of the ultraoligotrophic South Pacific Gyre

G Reintjes, HE Tegetmeyer, M Bürgisser… - Applied and …, 2019 - Am Soc Microbiol
ABSTRACT The South Pacific Gyre (SPG) covers 10% of the ocean's surface and is often
regarded as a marine biological desert. To gain an on-site overview of the remote …

Microbiota composition and pulmonary surfactant protein expression as markers of death by drowning

SY Lee, SK Woo, SM Lee, EJ Ha… - Journal of forensic …, 2017 - Wiley Online Library
Pathological diagnosis of drowning remains a challenge for forensic science, because of a
lack of pathognomonic findings. We analyzed microbiota and surfactant protein in the lungs …

Ecology and biotechnological potential of bacteria belonging to the genus Pseudovibrio

S Romano - Applied and environmental microbiology, 2018 - Am Soc Microbiol
Members of the genus Pseudovibrio have been isolated worldwide from a great variety of
marine sources as both free-living and host-associated bacteria. So far, the available data …