Spatial and temporal dynamics of microbiomes and resistomes in broiler litter stockpiles

Gupta, Chhedi Lal; Avidov, Ran; Kattusamy, Karuppasamy; Saadi, Ibrahim; Varma, V. Sudharsan; Blum, Shlomo E.; Zhu, Yan; Zhou, Xinyuan; Su, Jian‐Qiang; Laor, Yael; Cytryn, Eddie

doi:10.1016/j.csbj.2021.11.020

Cited by 5 publications

(4 citation statements)

References 83 publications

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“…Whereas some others documented that no positive effects on intestinal morphology of broilers fed diet supplemented with hydrolyzed yeast products was observed ( Baurhoo et al, 2009 ; Reisinger et al, 2012 ), which may be related to the composition of yeast hydrolysate and the farming conditions. Different farming conditions, such as farm environment, breeding mode, litter and so on, may have a certain impact on the microbial diversity and community in the intestinal of broilers, which will further affect the intestinal development and growth performance ( Gupta, et al, 2021 ; Xiao et al, 2021 ). Therefore, the actual application effect of the SCH needs to be evaluated according to its composition and the conditions of the applied farm.…”

Section: Discussionmentioning

confidence: 99%

Effects of Saccharomyces cerevisiae hydrolysate on growth performance, immunity function, and intestinal health in broilers

Lin¹,

Comi²,

Perricone³

et al. 2023

Poultry Science

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Section: Discussionmentioning

confidence: 99%

Effects of Saccharomyces cerevisiae hydrolysate on growth performance, immunity function, and intestinal health in broilers

Lin¹,

Comi²,

Perricone³

et al. 2023

Poultry Science

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“…Despite this, several aminoglycosides and tetracyclines ARGs was widely disseminated in food-producing animals litter and manure, particularly in the poultry sector and soil resistome [ 39 , 40 ]. Based on previous analogous investigations, the ARGs for tetracyclines and aminoglycosides antibiotics appeared highly abundant in organic fertilizer derived from poultry litter, being included in the “persistence resistome” characterized by low temporal fluctuations (over a 60-day period of composting) [ 41 ]. At the farm level, the relative abundance of tetracycline resistance genes increased with time in the poultry litter, irrespective of antibiotic treatment administrated during the rearing cycle [ 17 ].…”

Section: Discussionmentioning

confidence: 99%

Microbial Community and Abundance of Selected Antimicrobial Resistance Genes in Poultry Litter from Conventional and Antibiotic-Free Farms

Smoglica,

Farooq,

Ruffini

et al. 2023

Antibiotics

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In this study, a culture-independent approach was applied to compare the microbiome composition and the abundance of the antimicrobial resistance genes (ARGs) aadA2 for aminoglycosides, tet(A), tet(B), tet(K), and tet(M) for tetracyclines, and mcr-1 for colistin in broiler litter samples collected from conventional and antibiotic-free flocks located in Central Italy. A total of 13 flocks and 26 litter samples, collected at the beginning and at the end of each rearing cycle, were submitted to 16s rRNA sequence analysis and quantitative PCR for targeted ARGs. Firmicutes resulted in the dominant phylum in both groups of flocks, and within it, the Clostridia and Bacilli classes showed a similar distribution. Conversely, in antibiotic-free flocks, a higher frequency of Actinobacteria class and Clostridiaceae, Lactobacillaceae, Corynebacteriaceae families were reported, while in the conventional group, routinely treated with antibiotics for therapeutic purposes, the Bacteroidia class and the Enterobacteriaceae and Bacillaceae families were predominant. All investigated samples were found to be positive for at least one ARG, with the mean values of aadA2 and tet(A) the highest in conventional flocks by a significant margin. The results suggest that antibiotic use can influence the frequency of resistance determinants and the microbial community in poultry flocks, even though other environmental factors should also be investigated more deeply in order to identify additional drivers of antimicrobial resistance.

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“…When paired with additional sources of information, such as targeted amplification or longitudinal sequencing, SLRs are capable of resolving metagenomics to the strain level. In conjunction with high-throughput qPCR, LoopSeq has been used to associate antimicrobial resistance genes with specific species in environmental samples [20]. The long-read-like linkage information encoded in read clouds has been used to track single nucleotide variants in the human gut microbiome longitudinally, demonstrating that prioritizing depth of coverage over strict read length can be an optimal analysis strategy especially when the number of strains/haplotypes is an unknown variable [10].…”

Section: Applications Of Slr Sequencing In Metagenomicsmentioning

confidence: 99%

Ariadne: Synthetic Long Read Deconvolution Using Assembly Graphs

Meleshko

et al. 2021

Preprint

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Background: De novo assemblies are critical for capturing the genetic composition of complex samples. Linked-read sequencing techniques such as 10x Genomics' Linked-Reads, UST's TELL-Seq, Loop Genomics' LoopSeq, and BGI's Long Fragment Read combines 30 barcoding with standard short-read sequencing to expand the range of linkage resolution from hundreds to tens of thousands of base-pairs. The application of linked-read sequencing to genome assembly has demonstrated that barcoding-based technologies balance the ffs between long-range linkage, per-base coverage, and costs. Linkedreads come with their own challenges, chief among them the association of multiple long fragments with the same 30 barcode. The lack of a unique correspondence between a long fragment and a barcode, in conjunction with low sequencing depth, confounds the assignment of linkage between short-reads. Results: We introduce Ariadne, a novel linked-read deconvolution algorithm based on assembly graphs, that can be used to extract single-species read-sets from a large linked-read dataset. Ariadne deconvolution of linked-read clouds increases the proportion of read clouds containing only reads from a single fragment by up to 37.5-fold. Using these enhanced read clouds in de novo assembly significantly improves assembly contiguity and the size of the largest aligned blocks in comparison to the non-deconvolved read clouds. Integrating barcode deconvolution tools, such as Ariadne, into the postprocessing pipeline for linked-read technologies increases the quality of de novo assembly for complex populations, such as microbiomes. Ariadne is intuitive, computationally efficient, and scalable to other large-scale linked-read problems, such as human genome phasing.

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Spatial and temporal dynamics of microbiomes and resistomes in broiler litter stockpiles

Abstract: Graphical abstract

Cited by 5 publications

References 83 publications

Effects of Saccharomyces cerevisiae hydrolysate on growth performance, immunity function, and intestinal health in broilers

Effects of Saccharomyces cerevisiae hydrolysate on growth performance, immunity function, and intestinal health in broilers

Microbial Community and Abundance of Selected Antimicrobial Resistance Genes in Poultry Litter from Conventional and Antibiotic-Free Farms

Ariadne: Synthetic Long Read Deconvolution Using Assembly Graphs

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