Introduction to Microbial Quantitation, Community Profiling, and Array Approaches

2016 ◽  
pp. 1-5
Author(s):  
Josh D. Neufeld
Keyword(s):  
Community Profiling

Culture‐enriched community profiling improves resolution of the vertebrate gut microbiota

2021 ◽  
Author(s):  
Samantha L. Goldman ◽  
Jon G. Sanders ◽  
Weiwei Yan ◽  
Anthony Denice ◽  
Margaret Cornwall ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Community Profiling

scholarly journals White Syndrome-Affected Corals Have a Distinct Microbiome at Disease Lesion Fronts

2016 ◽  
Vol 83 (2) ◽  
Author(s):  
F. Joseph Pollock ◽  
Naohisa Wada ◽  
Gergely Torda ◽  
Bette L. Willis ◽  
David G. Bourne
Keyword(s):  
Disease Ecology ◽  
Tissue Loss ◽  
Coral Tissue ◽  
Health States ◽  
Host Coral ◽  
Tissue Samples ◽  
Content Type ◽  
White Syndrome ◽  
Community Profiling

ABSTRACT Coral tissue loss diseases, collectively known as white syndromes (WSs), induce significant mortality on reefs throughout the Indo-Pacific, yet definitive confirmation of WS etiologies remains elusive. In this study, we integrated ecological disease monitoring, bacterial community profiling, in situ visualization of microbe-host interactions, and cellular responses of the host coral through an 18-month repeated-sampling regime. We assert that the observed pathogenesis of WS lesions on acroporid corals at Lizard Island (Great Barrier Reef) is not the result of apoptosis or infection by Vibrio bacteria, ciliates, fungi, cyanobacteria, or helminths. Histological analyses detected helminths, ciliates, fungi, and cyanobacteria in fewer than 25% of WS samples, and helminths and fungi were also observed in 12% of visually healthy samples. The abundances of Vibrio-affiliated sequences (assessed using 16S rRNA amplicon sequencing) did not differ significantly between health states and never exceeded 3.3% of reads in any individual sample. In situ visualization detected Vibrio bacteria only in summer WS lesion samples and revealed no signs of these bacteria in winter disease samples (or any healthy tissue samples), despite continued disease progression year round. However, a 4-fold increase in Rhodobacteraceae-affiliated bacterial sequences at WS lesion fronts suggests that this group of bacteria could play a role in WS pathogenesis and/or serve as a diagnostic criterion for disease differentiation. While the causative agent(s) underlying WSs remains elusive, the microbial and cellular processes identified in this study will help to identify and differentiate visually similar but potentially distinct WS etiologies. IMPORTANCE Over the past decade, a virulent group of coral diseases known as white syndromes have impacted coral reefs throughout the Indian and Pacific Oceans. This article provides a detailed case study of white syndromes to combine disease ecology, high-throughput microbial community profiling, and cellular-scale host-microbe visualization over seasonal time scales. We provide novel insights into the etiology of this devastating disease and reveal new diagnostic criteria that could be used to differentiate visually similar but etiologically distinct forms of white syndrome.

scholarly journals hilldiv: an R package for the integral analysis of diversity based on Hill numbers

2019 ◽  
Author(s):  
Antton Alberdi ◽  
M Thomas P Gilbert
Keyword(s):  
Phylogenetic Trees ◽  
R Package ◽  
Diversity Partitioning ◽  
Diet Reconstruction ◽  
Functional Correlation ◽  
Community Profiling ◽  
High Throughput Dna Sequencing ◽  
Multi Level ◽  
Diversity Profile ◽  
Hill Numbers

AbstractHill numbers provide a powerful framework for measuring, comparing and partitioning the diversity of biological systems as characterised using high throughput DNA sequencing approaches. In order to facilitate the implementation of Hill numbers into such analyses, whether focusing on diet reconstruction, microbial community profiling or more general ecosystem characterisation analyses, we present a new R package. ‘Hilldiv’ provides a set of functions to assist analysis of diversity based on Hill numbers, using count tables (e.g. OTU, ASV) and associated phylogenetic trees as inputs. Multiple functionalities of the library are introduced, including diversity measurement, diversity profile plotting, diversity comparison between samples and groups, multi-level diversity partitioning and (dis)similarity measurement. All of these are grounded in abundance-based and incidence-based Hill numbers, and can accommodate phylogenetic or functional correlation among OTUs or ASVs. The package can be installed from CRAN or Github, and tutorials and example scripts can be found in the package’s page (https://github.com/anttonalberdi/hilldiv).

scholarly journals Diversity, host-specificity and stability of sponge-associated fungal communities of co-occurring sponges

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4965 ◽  
Author(s):  
Mary T.H.D. Nguyen ◽  
Torsten Thomas
Keyword(s):  
Host Specificity ◽  
Horizontal Transmission ◽  
Critical Role ◽  
Fungal Species ◽  
Fungal Communities ◽  
Sponge Species ◽  
Fungal Community Composition ◽  
Potential Core ◽  
Community Profiling ◽  
Surrounding Seawater

Fungi play a critical role in a range of ecosystems; however, their interactions and functions in marine hosts, and particular sponges, is poorly understood. Here we assess the fungal community composition of three co-occurring sponges (Cymbastela concentrica, Scopalina sp., Tedania anhelans) and the surrounding seawater over two time points to help elucidate host-specificity, stability and potential core members, which may shed light into the ecological function of fungi in sponges. The results showed that ITS-amplicon-based community profiling likely provides a more realistic assessment of fungal diversity in sponges than cultivation-dependent approaches. The sponges studied here were found to contain phylogenetically diverse fungi (eight fungal classes were observed), including members of the family Togniniaceae and the genus Acrostalagmus, that have so far not been reported to be cultured from sponges. Fungal communities within any given sponge species were found to be highly variable compared to bacterial communities, and influenced in structure by the community of the surrounding seawater, especially considering temporal variation. Nevertheless, the sponge species studied here contained a few “variable/core” fungi that appeared in multiple biological replicates and were enriched in their relative abundance compared to seawater communities. These fungi were the same or highly similar to fungal species detected in sponges around the world, which suggests a prevalence of horizontal transmission where selectivity and enrichment of some fungi occur for those that can survive and/or exploit the sponge environment. Our current sparse knowledge about sponge-associated fungi thus indicate that fungal communities may perhaps not play as an important ecological role in the sponge holobiont compared to bacterial or archaeal symbionts.

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