Biology subjects

Keating, C.

Publications and source records attributed to Keating, C..

3 recordsLinked to original sources

bioRxiv2020

Circular Economy of Anaerobic Biofilm Microbiomes: A Meta-Analysis Framework for Re-exploration of Amplicon Sequencing Data

Use of high-throughput sequencing is widespread in efforts to understand the microbial communities in natural and engineered systems. Many built ecosystems, in particular those used for engineered wastewater treatment, have harnessed the metabolic capacity of complex microbial communities for the effective removal and recovery of organic pollutants. Recent efforts to better understand and precisely engineer such systems have increasingly used high-throughput sequencing to map the structure and function of wastewater treatment microbiomes. An enormous amount of data is readily available on online repositories such as the National Center for Biotechnology Information Short Read Archive (NCBI SRA). Here, we describe and provide an optimised meta-analysis workflow to utilise this resource to collate heterogenous studies together for anaerobic digestion research. We analysed 16S rRNA gene Illumina Miseq amplicon sequencing data from 31 anaerobic digestion studies (from high-rate digesters), including >1,300 samples. Additionally, we compare several methodological choices: extraction method, v-region, taxonomical database, and the classifier. We demonstrate that collation of data from multiple v-regions can be achieved by using only the taxa for which sequences are available in the reference databases, without losses in diversity trends. This is made possible by focusing on alternative strategies for taxonomic assignments, namely, bayesian lowest common ancestor (BLCA) algorithm which offers increased resolution to the traditional naive bayesian classifier (NBC). While we demonstrate this using an anaerobic digestion wastewater treatment dataset, this methodology can be translated to perform meta-analysis on amplicon sequences in any field. These findings not only provide a roadmap for meta-analysis in any field, but additionally provide an opportunity to reuse extensive data resources to ultimately advance knowledge of wastewater treatment systems. ImportanceIn this study, we have combined sequencing data from 31 individual studies with the purpose of identifying a meta-analysis workflow which can accurately collate data derived from sequencing different v-regions with minimal data loss and more accurate diversity patterns. While we have used Anaerobic Digestion (AD) communities for our proof-of-concept, our workflow (Fig 1) can be translated to any Illumina MiSeq meta-analysis study, in any field. Thereby, we provide the foundation for intensive data mining of existing amplicon sequencing resources. Such data-mining can provide a global perspective on complex microbial communities. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=110 SRC="FIGDIR/small/424166v1_fig1.gif" ALT="Figure 1"> View larger version (54K): org.highwire.dtl.DTLVardef@11fe518org.highwire.dtl.DTLVardef@f9a6eeorg.highwire.dtl.DTLVardef@3e5af0org.highwire.dtl.DTLVardef@1c45734_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1.C_FLOATNO Overview of the meta-analysis workflow to assess the protocols used in the analysis of AD microbiomes. C_FIG Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=120 SRC="FIGDIR/small/424166v1_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@1392216org.highwire.dtl.DTLVardef@1ecd922org.highwire.dtl.DTLVardef@a35894org.highwire.dtl.DTLVardef@c7fc0_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2020

Temporal changes in the gut microbiota in farmed Atlantic cod (Gadus morhua) outweigh the response to diet supplementation with macroalgae.

BackgroundAquaculture successfully meets global food demands for many fish species. However, aquaculture production of Atlantic cod (Gadus morhua) is modest in comparison to market demand. For cod farming to be a viable economic venture specific challenges on how to increase growth, health and farming productivity need to be addressed. Feed ingredients play a key role here. Macroalgae (seaweeds) have been suggested as a functional feed supplement with both health and economic benefits for terrestrial farmed animals and fish. The impact of such dietary supplements to cod gut integrity and microbiota, which contribute to overall fish robustness is unknown. The objective of this study was to supplement the diet of juvenile Atlantic cod with macroalgae and determine the impacts on fish condition and growth, gut morphology and hindgut microbiota composition (16S rRNA amplicon sequencing). Fish were fed one of three diets: control (no macroalgal inclusion), 10% inclusion of either egg wrack (Ascophyllum nodosum) or sea lettuce (Ulva rigida) macroalgae in a 12-week trial. ResultsThe results demonstrated there was no significant difference in fish condition, gut morphology or hindgut microbiota between the U. rigida supplemented fish group and the control group at any time-point. This contrasts with the A. nodosum treatment. Fish within this group were further categorised as either Normal or Lower Growth. Lower Growth individuals found the diet unpalatable resulting in reduced weight and condition factor combined with an altered gut morphology and microbiome relative to the other treatments. Excluding this group, our results show that the hindgut microbiota was largely driven by temporal pressures with the microbial communities becoming more similar over time irrespective of dietary treatment. The core microbiome at the final time-point consisted of the orders Vibrionales (Vibrio and Photobacterium), Bacteroidales (Bacteroidetes and Macellibacteroides) and Clostridiales (Lachnoclostridium). ConclusionsOur study indicates that U. rigida macroalgae can be supplemented at 10% inclusion levels in the diet of juvenile farmed Atlantic cod without any impact on fish condition or hindgut microbial community structure. We also conclude that 10% dietary inclusion of A. nodosum is not a suitable feed supplement in a farmed cod diet.

microbiology↗

bioRxiv2020

Indigenous Bacillus paramycoides and Alcaligenes faecalis: potential solution for the bioremediation of wastewaters

Farmers near towns and cities are using wide range of untreated wastewaters for crop irrigation in Pakistan due to severe freshwater shortage. The present study aimed to treat different types of wastewater including domestic, hospital, textile, pharmaceutical and mixed wastewaters using indigenous bacterial isolates to remove contaminants and render these wastewaters safer for irrigation. 37 bacterial strains were isolated from the 5 wastewater samples collected from different sites in Lahore, Pakistan. Under optimum growth conditions, the isolates D6, D7 and P1 showed maximum decolourisation potential of 96, 96, 93 %, respectively against hospital wastewater. GCMS analysis of the untreated hospital wastewater confirmed the presence of pharmaceutic pollutants i.e. Phenol, Salicylic acid, Caffeine, Naproxen, Octadecene and Diazepam. These organic compounds were biodegraded into derivate Ticlopidine in the case of isolate D6, derivatives Tetradecene and Griseofulvin in the case of isolate D7, and derivatives Lidocaine and Butalbital in the case of isolate P1. 16S rDNA sequencing was used to identify these isolates. Isolates D6 and D7 showed 100 and 99.86 % homology to Bacillus paramycoides, a novel strain from Bacillus cereus group (Liu et al., 2017). Isolate P1 showed 97.47 % homology to Alcaligenes faecalis. These strains therefore could represent a low-cost and low-tech alternative to bioremediate complex wastewaters prior to irrigation to support the achievement of the Sustainable Development Goal 6 - clean water and sanitation in Pakistan.

microbiology↗