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A functional approach to characterising the microbial communities underpinning low temperature anaerobic digestion (2015)

Gunnigle, Eoin

A functional approach to characterising the microbial communities underpinning low temperature anaerobic digestion (2015)

Gunnigle, Eoin

Abstract:

Low-temperature anaerobic digestion (LTAD) presents a sustainable, cost-efficient technology for the treatment of a vast array of wastewater streams. However, this microbially-mediated process requires further understanding and experimental characterisation if large-scale application of LTAD is to be realised. The objective of this thesis was to employ a functional-based approach to characterise the microbial communities underpinning low-temperature anaerobic digestion. Firstly, the key microbial functional groups present in end-point samples taken from three, laboratory-scale, expanded granular sludge bed (EGSB) bioreactors; R1 (37°C), R2 (15°C) and R3 (7°C) were characterised. Metaproteomics, in conjunction with 16S rRNA gene phylogenetic approaches (clone libraries, qPCR), was applied to record microbial community composition and metaproteomic profiles as a function of bioreactor operating temperature. Clone libraries indicated a predominance of the Chloroflexi (21%) and ¿-Prote...

http://hdl.handle.net/10379/5044

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Archaebiotics: archaea as pharmabiotics for treating chronic disease in humans? (2017)

Ben Hania, Wajdi; Ballet, Nathalie; Vandeckerkove, Pascal; Ollivier, Bernard; O'To...

Archaebiotics: archaea as pharmabiotics for treating chronic disease in humans? (2017)

Ben Hania, Wajdi; Ballet, Nathalie; Vandeckerkove, Pascal; Ollivier, Bernard; O'Toole, Paul W.; Brugère, Jean-François

Abstract:

Recent findings highlight the role of the human gut microbiota in various disorders. For example, atherosclerosis frequently seems to be the consequence of gut microbiota–derived metabolism of some dietary components. Pharmabiotics (i.e., live/dead microbes and microbe-derived substances) and probiotics (live microorganisms with a health benefit when administered in adequate amounts) are a means to counteract these deleterious effects. Among the latter, microbes now being used or, being currently developed, are bacteria and eukaryotes (yeasts), so omitting the third domain of life—the archaea, despite their unique properties that could be of great interest to human health. Here, we promote the idea that some specific archaea are potential next-generation probiotics. This is based on an innovative example of the bioremediation of a gut microbial metabolite. Indeed, besides the fact that they are archaea (i.e. originating from a domain of life from which no pathogens of humans/animals...

http://hdl.handle.net/10468/5161

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Characterization of the ruminal fermentation and microbiome in lambs supplemented with hydrolysable and condensed tannins (2018)

Salami, Saheed A.; Valenti, Bernardo; Bella, Marco; O'Grady, Michael N.; Luciano, ...

Characterization of the ruminal fermentation and microbiome in lambs supplemented with hydrolysable and condensed tannins (2018)

Salami, Saheed A.; Valenti, Bernardo; Bella, Marco; O'Grady, Michael N.; Luciano, Giuseppe; Kerry, Joseph P.; Jones, Eleanor; Priolo, Alessandro; Newbold, Charles J.

Abstract:

This study characterised the response of ruminal fermentation and the rumen microbiome in lambs fed commercial vegetal sources of hydrolysable tannins (HT) and condensed tannins (CT). Forty-four lambs (19.56 ± 2.06 kg) were randomly assigned to either a concentrate diet (CON, n = 8) or CON supplemented with 4% of two HT [chestnut (Castanea sativa, HT-c) and tara (Caesalpinia spinosa, HT-t)] and CT [mimosa (Acacia negra, CT-m) and gambier (Uncaria gambir, CT-g)] extracts (all, n = 9) for 75 days pre-slaughter. Tannin supplementation did not influence ruminal fermentation traits. Quantitative PCR demonstrated that tannins did not affect the absolute abundance of ruminal bacteria or fungi. However, CT-m (-12.8%) and CT-g (-11.5%) significantly reduced the abundance of methanogens while HT-t (-20.7%) and CT-g (-20.8%) inhibited protozoal abundance. Ribosomal amplicon sequencing revealed that tannins caused changes in the phylogenetic structure of the bacterial and methanogen communities...

http://hdl.handle.net/10468/5792

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Distribution, localization, and phylogeny of abundant populations of crenarchaeota in anaerobic granular sludge (2018)

Collins, G.; O'Connor, L.; Mahony, T.; Gieseke, A.; de Beer, D.; O'Flaherty, V.

Distribution, localization, and phylogeny of abundant populations of crenarchaeota in anaerobic granular sludge (2018)

Collins, G.; O'Connor, L.; Mahony, T.; Gieseke, A.; de Beer, D.; O'Flaherty, V.

Abstract:

Eight anaerobic granular sludges were surveyed for Crenarchaeota using rRNA gene cloning. Microbial arrangement and substrate uptake patterns were elucidated by fluorescent in situ hybridization and beta imaging. Group 1.3 Crenarchaeota represented up to 50% of Archaea and 25% of the total microbiota in five sludges. Crenarchaeota were localized in close association with methanogenic Archaea.

http://hdl.handle.net/10379/8982

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Human methanogen diversity and incidence in healthy and diseased colonic groups using mcrA gene analysis (2008)

Scanlan, Pauline D.; Shanahan, Fergus; Marchesi, Julian R.

Human methanogen diversity and incidence in healthy and diseased colonic groups using mcrA gene analysis (2008)

Scanlan, Pauline D.; Shanahan, Fergus; Marchesi, Julian R.

Abstract:

Background: The incidence and diversity of human methanogens are insufficiently characterised in the gastrointestinal tract of both health and disease. A PCR and clone library methodology targeting the mcrA gene was adopted to facilitate the two-fold aim of surveying the relative incidence of methanogens in health and disease groups and also to provide an overview of methanogen diversity in the human gastrointestinal tract. Results: DNA faecal extracts (207 in total) from a group of healthy controls and five gastrointestinal disease groups were investigated. Colorectal cancer, polypectomised, irritable bowel syndrome and the control group had largely equivalent numbers of individuals positive for methanogens (range 45-50%). Methanogen incidence in the inflammatory bowel disease groups was reduced, 24% for ulcerative colitis and 30% for Crohn's disease. Four unique mcrA gene restriction fragment length polymorphism profiles were identified and bioinformatic analyses revealed tha...

http://hdl.handle.net/10468/970

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Methanosarcina play an important role in anaerobic co-digestion of the seaweed Ulva lactuca: metagenomics structure and predicted metabolism of functional microbial communities. (2015)

FitzGerald, Jamie A.; Allen, Eoin; Wall, David M.; Jackson, Stephen A.; Murphy, Jerry D...

Methanosarcina play an important role in anaerobic co-digestion of the seaweed Ulva lactuca: metagenomics structure and predicted metabolism of functional microbial communities. (2015)

FitzGerald, Jamie A.; Allen, Eoin; Wall, David M.; Jackson, Stephen A.; Murphy, Jerry D.; Dobson, Alan D. W.

Abstract:

Macro-algae represent an ideal resource of third generation biofuels, but their use necessitates a refinement of commonly used anaerobic digestion processes. In a previous study, contrasting mixes of dairy slurry and the macro-alga Ulva lactuca were anaerobically digested in mesophilic continuously stirred tank reactors for 40 weeks. Higher proportions of U. lactuca in the feedstock led to inhibited digestion and rapid accumulation of volatile fatty acids, requiring a reduced organic loading rate. In this study, 16S pyrosequencing was employed to characterise the microbial communities of both the weakest (R1) and strongest (R6) performing reactors from the previous work as they developed over a 39 and 27-week period respectively. Comparing the reactor communities revealed clear differences in taxonomy, predicted metabolic orientation and mechanisms of inhibition, while constrained canonical analysis (CCA) showed ammonia and biogas yield to be the strongest factors differentiating th...

http://hdl.handle.net/10468/3557

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Use of lactic acid bacteria to reduce methane production in ruminants, a critical review (2019)

Doyle, Natasha; Mbandlwa, Philiswa; Kelly, William J.; Attwood, Graeme; Li, Yang; Ross,...

Use of lactic acid bacteria to reduce methane production in ruminants, a critical review (2019)

Doyle, Natasha; Mbandlwa, Philiswa; Kelly, William J.; Attwood, Graeme; Li, Yang; Ross, R. Paul; Stanton, Catherine; Leahy, Sinead

Abstract:

Enteric fermentation in ruminants is the single largest anthropogenic source of agricultural methane and has a significant role in global warming. Consequently, innovative solutions to reduce methane emissions from livestock farming are required to ensure future sustainable food production. One possible approach is the use of lactic acid bacteria (LAB), Gram positive bacteria that produce lactic acid as a major end product of carbohydrate fermentation. LAB are natural inhabitants of the intestinal tract of mammals and are among the most important groups of microorganisms used in food fermentations. LAB can be readily isolated from ruminant animals and are currently used on-farm as direct-fed microbials (DFMs) and as silage inoculants. While it has been proposed that LAB can be used to reduce methane production in ruminant livestock, so far research has been limited, and convincing animal data to support the concept are lacking. This review has critically evaluated the current litera...

http://hdl.handle.net/10468/8748