Metagenomics of Antimicrobial and Heavy Metal Resistance in the Cecal Microbiome of Fattening Pigs Raised without Antibiotics

Tunsagool, Paiboon; Mhuantong, Wuttichai; Tangphatsornruang, Sithichoke; Am-In, Nutthee; Chuanchuen, Rungtip; Luangtongkum, Taradon; Suriyaphol, Gunnaporn

doi:10.1128/aem.02684-20

Cited by 20 publications

(42 citation statements)

References 64 publications

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“…Captivity and free-range are the main rearing condition for sika deer, and it is valuable to evaluate how the present practices affect environmental antibiotic resistance transmission. Unlike the composition of gut microbiota, the predominant phyla in antibiotic-resistant bacteria were Firmicutes and Proteobacteria (rather than Firmicutes and Bacteroidetes ), indicating that Proteobacteria played a more important role in the abundance of ARGs than Bacteroidetes ( 36 ). We found abundant antibiotic resistances in the fecal microbiome of sika deer, and tet Q and lnu C dominated the AROs.…”

Section: Discussionmentioning

confidence: 99%

“…According to the RDA of tetracycline resistance, tet Q, tet X, and tet W/N/W were related to the dominant genus Prevotella in the captive deer. Previous studies have reported that tet Q genes can be isolated from Prevotella strains in sick and healthy humans ( 36 , 39 ). lnu C is a lincosamide resistance gene, which is induced by clindamycin and lincomycin ( 40 ).…”

Section: Discussionmentioning

confidence: 99%

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Differences in Fecal Microbiome and Antimicrobial Resistance between Captive and Free-Range Sika Deer under the Same Exposure of Antibiotic Anthelmintics

Zhang

et al. 2021

Microbiol Spectr

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We used a metagenomic approach to investigate whether and how captive and free-range impact the microbial communities and antimicrobial resistance in sika deer. The results provide solid evidence of the significant impacts on the microbial composition and function in captive and free-range sika deer. Interestingly, although the sika deer had the same exposure to antibiotic anthelmintics, the antimicrobial resistances were affected by the breeding environment.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Differences in Fecal Microbiome and Antimicrobial Resistance between Captive and Free-Range Sika Deer under the Same Exposure of Antibiotic Anthelmintics

Zhang

et al. 2021

Microbiol Spectr

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“…As a new addition to the UK market, it is unknown how consumers perceive 'raised without antibiotics' labelled products and whether the presence of such labels influence food choice. Research surrounding 'raised without antibiotics' labels in the UK has been exclusively based on analytical techniques, focusing on the identification of food-borne pathogens in 'raised without antibiotics' labelled foods (Tunsagool et al, 2021). Thus, to the best of our knowledge, this is the first study of its kind to investigate consumer knowledge and perceptions towards antimicrobial use in agriculture and willingness to buy 'raised without antibiotics' labelled meat.…”

Section: Introductionmentioning

confidence: 99%

Consumers' perceptions and willingness to purchase pork labelled ‘raised without antibiotics’

et al. 2022

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“…This also explains why the number (115 ARGs) and diversity of ARGs detected in the present study was much lower than in a previous study (250 ARGs) using the same short reads that were used to assemble the MAGs here (11) as well as in the metagenome co-assembly (897 ARGs; data not shown). Despite the limitations associated with ARG binning we were able to provide genomic context for 115 ARGs including several that are relatively abundant in the swine gut such as erm(B), tet (44), tet(Q), and tet(W) (35)(36)(37)(38).…”

Section: Many Of Thementioning

confidence: 99%

Novel insights into the pig gut microbiome using metagenome-assembled genomes

Holman¹,

Kommadath²,

Tingley

et al. 2022

Preprint

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Pigs are among the most numerous and intensively farmed food-producing animals in the world. The gut microbiome plays an important role in the health and performance of swine and changes rapidly after weaning. Here, fecal samples were collected from pigs at 7 different times points from 7 to 140 days of age. These swine fecal metagenomes were used to assemble 1,150 dereplicated metagenome-assembled genomes (MAGs) that were at least 90% complete and had less than 5% contamination. These MAGs represented 472 archaeal and bacterial species, and the most widely distributed MAGs were the uncultured species Collinsella sp002391315, Sodaliphilus sp004557565, and Prevotella sp000434975. Weaning was associated with a decrease in the relative abundance of 69 MAGs (e.g. Escherichia coli) and an increase in the relative abundance of 140 MAGs (e.g. Clostridium sp000435835, Oliverpabstia intestinalis). Genes encoding for the production of the short-chain fatty acids acetate, butyrate, and propionate were identified in 68.5%, 18.8%, and 8.3% of the MAGs, respectively. Carbohydrate-active enzymes associated with the degradation of arabinose oligosaccharides and mixed-linkage glucans were predicted to be most prevalent among the MAGs. Antimicrobial resistance genes were detected in 327 MAGs, including 59 MAGs with tetracycline resistance genes commonly associated with pigs such as tet(44), tet(Q), and tet(W). Overall, 82% of the MAGs were assigned to species that lack cultured representatives indicating that a large portion of the swine gut microbiome is still poorly characterized. The results here also demonstrate the value of MAGs in adding genomic context to gut microbiomes.ImportanceMany of the bacterial strains found in the mammalian gut are difficult to culture and isolate due to their various growth and nutrient requirements that are frequently unknown. Here, we assembled strain-level genomes from short metagenomic sequences, so-called metagenome-assembled genomes (MAGs), that were derived from fecal samples collected from pigs at multiple time points. The majority of these MAGs represented bacterial species that have yet to be cultured or described thus underlining the need for cultivation studies that isolate and describe novel bacterial species. The genomic context of a number of antimicrobial resistance genes commonly detected in swine was also determined. In addition, our study connected taxonomy with potential metabolic functions such as carbohydrate degradation and short-chain fatty acid production.

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Metagenomics of Antimicrobial and Heavy Metal Resistance in the Cecal Microbiome of Fattening Pigs Raised without Antibiotics

Cited by 20 publications

References 64 publications

Differences in Fecal Microbiome and Antimicrobial Resistance between Captive and Free-Range Sika Deer under the Same Exposure of Antibiotic Anthelmintics

Differences in Fecal Microbiome and Antimicrobial Resistance between Captive and Free-Range Sika Deer under the Same Exposure of Antibiotic Anthelmintics

Consumers' perceptions and willingness to purchase pork labelled ‘raised without antibiotics’

Novel insights into the pig gut microbiome using metagenome-assembled genomes

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