A microbial gene catalog of anaerobic digestion from full-scale biogas plants

Ma, Shichun; Jiang, Fan; Huang, Yan; Zhang, Yan; Wang, Sen; Fan, Haibo; Liu, Bo; Li, Qiang; Yin, Lei; Wang, Hengchao; Liu, Hangwei; Ren, Yingxue; Li, Shuqu; Cheng, Lei; Fan, Wei; Deng, Yu

doi:10.1093/gigascience/giaa164

Cited by 34 publications

(47 citation statements)

References 57 publications

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“…PCoA analysis confirmed the variation of the difference in profile and composition of detected pathways in all sample groups by 4 distinct clusters. The dominance of methane metabolic pathways in the AD treatment was consistent with previous findings (Guo et al, 2015; Ma et al, 2021). This is directly linked to the high abundance of methanogenic archaea in the microbial community.…”

Section: Discussionsupporting

confidence: 92%

Data based slurry treatment decision tree to minimise antibiotic resistance and pathogen transfer while maximising nutrient recycling

Thuy

Nolan

Hayes

et al. 2022

Preprint

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Direct application of pig slurry to agricultural land introduces pathogens, antibiotic resistant bacteria, or genes, to the envi-ronment. With global environmental sustainability policies mandating a reduction in synthetic fertilization and a commit-ment to a circular economy it is imperative to find effective on-farm treatments of slurry that maximizes its fertilization val-ue and minimizes risk to health and the environment. We compared the effect of storage, composting, and anaerobic diges-tion on pig slurry microbiome, resistome and nutrient content using shotgun metagenomic sequencing and HT-qPCR arrays. Our results identified that each treatment method had advantages and disadvantages, depending on the parameter measured. Storage and composting were optimal for the removal of human pathogens and anaerobic digestion (AD) for the reduction in antimicrobial resistance (AMR) genes and mobile genetic elements. The nitrogen content was increased in storage and AD and reduced in composting. Our data indicates that composting provided the reduction in risk to human health and the envi-ronment. Network analysis revealed reducing Proteobacteria and Bacteroidetes while increasing Firmicutes reduced AMR content. This novel study provides a data driven decision tree to determine the optimal treatment for best practice to mini-mize pathogen, AMR, and optimum nutrient transfer from slurry to environment.

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Section: Discussionsupporting

confidence: 92%

Data based slurry treatment decision tree to minimise antibiotic resistance and pathogen transfer while maximising nutrient recycling

Thuy

Nolan

Hayes

et al. 2022

Preprint

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show abstract

“…KEGG and eggNOG annotations were aligned against the corresponding databases using DIAMOND (v0.8.28.90), by taking the best hit with the criteria of E value < 1e−5. Annotation of CAZymes families was aligned against the CAZy database using the hmmscan tool of HMMER (v3.2.1), by taking the best hit with the threshold of E value < 1e−18 and coverage >0.35 [ 84 ].…”

Section: Methodsmentioning

confidence: 99%

Adaptation of gut microbiome and host metabolic systems to lignocellulosic degradation in bamboo rats

Xiao

Liang

et al. 2022

The ISME Journal

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Bamboo rats ( Rhizomys pruinosus ) are among the few mammals that lives on a bamboo-based diet which is mainly composed of lignocellulose. However, the mechanisms of adaptation of their gut microbiome and metabolic systems in the degradation of lignocellulose are largely unknown. Here, we conducted a multi-omics analysis on bamboo rats to investigate the interaction between their gut microbiomes and metabolic systems in the pre- and post-weaning periods, and observed significant relationships between dietary types, gut microbiome, serum metabolome and host gene expression. For comparison, published gut microbial data from the famous bamboo-eating giant panda ( Ailuropoda melanoleuca ) were also used for analysis. We found that the adaptation of the gut microbiome of the bamboo rat to a lignocellulose diet is related to a member switch in the order Bacteroidales from family Bacteroidaceae to family Muribaculaceae , while for the famous bamboo-eating giant panda, several aerobes and facultative anaerobes increase after weaning. The conversion of bacteria with an increased relative abundance in bamboo rats after weaning enriched diverse carbohydrate-active enzymes (CAZymes) associated with lignocellulose degradation and functionally enhanced the biosynthesis of amino acids and B vitamins. Meanwhile, the circulating concentration of short-chain fatty acids (SCFAs) derived metabolites and the metabolic capacity of linoleic acid in the host were significantly elevated. Our findings suggest that fatty acid metabolism, including linoleic acid and SCFAs, are the main energy sources for bamboo rats in response to the low-nutrient bamboo diet.

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“…The first three steps are conducted by the bacterial community which, despite the great variation across different conditions, is dominated by the phylum Firmicutes , usually followed by Bacteroidetes and Proteobacteria . Archaeal species, mostly belonging to the phylum Euryarchaeota , are involved in the conversion of simple molecules to methane and usually account for a much smaller part of the community [ 3 ]. The microbial species present and their balance are crucial for optimisation of biogas production, and they have been extensively studied in the last two decades [ 4 ].…”

Section: Introductionmentioning

confidence: 99%

Analysis of the anaerobic digestion metagenome under environmental stresses stimulating prophage induction

et al. 2022

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Background The viral community has the potential to influence the structure of the microbiome and thus the yield of the anaerobic digestion process. However, the virome composition in anaerobic digestion is still under-investigated. A viral induction experiment was conducted on separate batches undergoing a series of DNA-damaging stresses, in order to coerce temperate viruses to enter the lytic cycle. Results The sequencing of the metagenome revealed a viral community almost entirely composed of tailed bacteriophages of the order Caudovirales. Following a binning procedure 1,092 viral and 120 prokaryotic genomes were reconstructed, 64 of which included an integrated prophage in their sequence. Clustering of coverage profiles revealed the presence of species, both viral and microbial, sharing similar reactions to shocks. A group of viral genomes, which increase under organic overload and decrease under basic pH, uniquely encode the yopX gene, which is involved in the induction of temperate prophages. Moreover, the in-silico functional analysis revealed an enrichment of sialidases in viral genomes. These genes are associated with tail proteins and, as such, are hypothesised to be involved in the interaction with the host. Archaea registered the most pronounced changes in relation to shocks and featured behaviours not shared with other species. Subsequently, data from 123 different samples of the global anaerobic digestion database was used to determine coverage profiles of host and viral genomes on a broader scale. Conclusions Viruses are key components in anaerobic digestion environments, shaping the microbial guilds which drive the methanogenesis process. In turn, environmental conditions are pivotal in shaping the viral community and the rate of induction of temperate viruses. This study provides an initial insight into the complexity of the anaerobic digestion virome and its relation with the microbial community and the diverse environmental parameters.

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A microbial gene catalog of anaerobic digestion from full-scale biogas plants

Cited by 34 publications

References 57 publications

Data based slurry treatment decision tree to minimise antibiotic resistance and pathogen transfer while maximising nutrient recycling

Data based slurry treatment decision tree to minimise antibiotic resistance and pathogen transfer while maximising nutrient recycling

Adaptation of gut microbiome and host metabolic systems to lignocellulosic degradation in bamboo rats

Analysis of the anaerobic digestion metagenome under environmental stresses stimulating prophage induction

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