Metagenomes and Assembled Genomes from Diarrhea-Affected Cattle (Bos taurus)

Ateba, Tshepiso Pleasure; Alayande, Kazeem Adekunle; Mwanza, Mulunda

doi:10.1128/mra.01411-20

Cited by 3 publications

(2 citation statements)

References 11 publications

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“…Indeed, higher Streptococcus prevalence has been reported to correlate with quantitative diarrhea outcomes except in DEC infections [ 47 ]. Besides, Flavobacterium is a common species among bacterial communities in diarrhea-affected cattle [ 48 ]. In the first phase (1–7 days), Enterobacteriaceae/ E. coli-Shigella were not enriched in the D_1 group compared with those of H_1.…”

Section: Discussionmentioning

confidence: 99%

Gut microbiota-derived ursodeoxycholic acid from neonatal dairy calves improves intestinal homeostasis and colitis to attenuate extended-spectrum β-lactamase-producing enteroaggregative Escherichia coli infection

Yang

et al. 2022

Microbiome

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Background Antimicrobials are often used to prevent and treat diarrhea induced by enteroaggregative Escherichia coli (EAEC) in young ruminants. However, drug overuse or misuse accelerates the spread of multidrug-resistant extended-spectrum β-lactamase (ESBL)-producing E. coli. Thus, supplementary foods as alternatives to antibiotics are needed to prevent colibacillus diarrhea in neonatal dairy calves. Ursodeoxycholic acid (UDCA), a therapeutic bile acid, helps alleviate colitis. However, how UDCA helps alleviate ESBL-EAEC-induced clinical symptoms and colitis remains unclear. Results We investigated the microbial profiles and metabolites of healthy and diarrheic neonatal calves to determine microbial and metabolite biomarkers in early-life development. Both the gut microbiota communities and their associated metabolites differed between healthy and diarrheic calves. Commensal Butyricicoccus, Faecalibacterium, Ruminococcus, Collinsella, and Coriobacterium were key microbial markers that distinguished healthy and diarrheic gut microbiomes. Random forest machine-learning algorithm and Spearman correlation results indicated that enriched UDCA, short-chain fatty acids (SCFAs), and other prebiotics were strongly positively correlated with these five bacterial genera. We explored the effect of ursodiol on bacterial growth, cell adherence, and lipopolysaccharide-treated Caco-2 cells. Adding ursodiol induced direct antibacterial effects, suppressed proinflammatory effects, and reduced cell integrity damage. Oral ursodiol delivery to neonatal mice exhibited significant antibacterial effects and helped maintain colonic barrier integrity in mouse models of peritonitis sepsis and oral infection. UDCA supplementation attenuated colitis and recovered colonic SCFA production. To validate this, we performed fecal microbiota transplantations to inoculate ESBL-EAEC-infected neonatal mice. Microbiotas from UDCA-treated neonatal mice ameliorated colitis and hindgut commensal bacterial damage compared with that of the microbiotas from the control and placebo mice, as evidenced by colonization of abundant bacteria, including Oscillospiraceae, Ruminococcaceae, Lachnospiraceae, and Clostridia_UCG-014, and upregulated SCFA production. Conclusions This study provided the first evidence that UDCA could confer diarrhea resistance in ESBL-EAEC-infected newborn dairy calves. UDCA blocked bacterial growth and invasion both in vitro and in vivo, alleviated commensal bacterial dysbiosis during ESBL-EAEC infection in neonatal mouse models of sepsis and colitis via the TGR5-NF-κB axis, and upregulated SCFA production in the hindgut digesta. Our findings provide insight into the UDCA-mediated remission of ESBL-EAEC infections and the potential role of UDCA as an antibiotic alternative.

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Section: Discussionmentioning

confidence: 99%

Gut microbiota-derived ursodeoxycholic acid from neonatal dairy calves improves intestinal homeostasis and colitis to attenuate extended-spectrum β-lactamase-producing enteroaggregative Escherichia coli infection

Yang

et al. 2022

Microbiome

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“…Gallibacterium is associated with a wide range of pathological changes in poultry (Persson and Bojesen, 2015 ), thus indicating the potential risks of intestinal infections in neonatal calves. Flavobacterium is detected to be a common species among the bacterial communities in diarrhea-affected cattle (Ateba et al, 2021 ). Further studies are needed to probe into the mutual influence of these microbial markers on improved gut health in young ruminants.…”

Section: Discussionmentioning

confidence: 99%

Temporal Changes in Fecal Unabsorbed Carbohydrates Relative to Perturbations in Gut Microbiome of Neonatal Calves: Emerging of Diarrhea Induced by Extended-Spectrum β-lactamase-Producing Enteroaggregative Escherichia coli

Chen

et al. 2022

Front. Microbiol.

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Early gut microbiota development and colonization are crucial for the long-term health and performance of ruminants. However, cognition among these microbiota is still vague, particularly among the neonatal dairy calves. Here, extended-spectrum β-lactamase-producing enteroaggregative E. coli (ESBL-EAEC)-induced temporal changes in diversity, stability, and composition of gut microbiota were investigated among the neonatal female calves, with the view of discerning potential biomarkers of this arising diarrhea cases in local pastures. Nearly, 116 newborn calves were enrolled in this time period study during their first 2 weeks of life, and a total of 40 selected fecal samples from corresponding calves were used in this study. The results revealed that differentiated gut microbiome and metabolome discerned from neonatal calves were accompanied by bacterial infections over time. Commensal organisms like Butyricicoccus, Faecalibacterium, Ruminococcus, Collinsella, and Coriobacterium, as key microbial markers, mainly distinguish “healthy” and “diarrheic” gut microbiome. Random forest machine learning algorithm indicated that enriched fecal carbohydrates, including rhamnose and N-acetyl-D-glucosamine, and abundant short-chain fatty acids (SCFAs) existed in healthy ones. In addition, Spearman correlation results suggested that the presence of Butyricicoccus, Faecalibacterium, Collinsella, and Coriobacterium, key commensal bacteria of healthy calves, is positively related to high production of unabsorbed carbohydrates, SCFAs, and other prebiotics, and negatively correlated to increased concentrations of lactic acid, hippuric acid, and α-linolenic acid. Our data suggested that ESBL-EAEC-induced diarrhea in female calves could be forecasted by alterations in the gut microbiome and markedly changed unabsorbed carbohydrates in feces during early lives, which might be conducive to conduct early interventions to ameliorate clinical symptoms of diarrhea induced by the rising prevalence of ESBL-EAEC.

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Metagenomic and metabolomic analyses reveal the role of gut microbiome-associated metabolites in diarrhea calves

Shi,

Wang,

Yan

et al. 2023

mSystems

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Calf diarrhea is a multifactorial disease that affects the cattle industry and accounts for more than 50% of calf mortality. Although there is evidence of an association between altered gut microbiota and diarrhea, remarkably little is known about the microbial and metabolic mechanisms underlying the link between gut microbiota dysbiosis and the occurrence of calf diarrhea. Here, we performed fecal metagenomic and metabolomic studies on fecal samples from diarrheic and healthy calves of Xia-nan cattle breed. Results revealed that composition of the gut microbiome and metabolome was remarkably altered in diarrheic calves, and gut microbial alterations were associated with diarrhea and linked to the changes in metabolites. Metabolite profiles showed that diarrheic calves exhibited a marked decrease in some purines (adenosine, adenine, 2'-deoxyguanosine, allantoate, deoxyinosine, and deoxyguanosine) and arachidonic acid (prostaglandin F2α and prostaglandin E2) compared to healthy calves. Purine-producing microbial species, including Lactiplantibacillus plantarum, Campylobacter coli , Treponema porcinum , Klebsiella pneumoniae , and Phocaeicola coprophilus , were significantly reduced in diarrheic calves compared to healthy calves, whereas the arachidonic acid-producing species such as Neisseria gonorrhoeae , Staphylococcus aureus , and Clostridiales bacterium exhibited a marked increase. These microbial signatures were closely associated with the metabolic dysbiosis of purine and arachidonic acid in diarrhea calves. Our study showed that gut microbiota-driven metabolic disorders of purine or arachidonic acid were associated with calf diarrhea. The findings prove that altered gut microbiota plays a role in diarrhea pathogenesis and indicate that gut microbiota-targeted therapies could be useful for both prevention and treatment of diarrhea. IMPORTANCE Calf diarrhea is of great concern to the global dairy industry as it results in significant economic losses due to lower conception rates, reduced milk production, and early culling. Although there is evidence of an association between altered gut microbiota and diarrhea, remarkably little is known about the microbial and metabolic mechanisms underlying the link between gut microbiota dysbiosis and the occurrence of calf diarrhea. Here, we used fecal metagenomic and metabolomic analyses to demonstrate that gut microbiota-driven metabolic disorders of purine or arachidonic acid were associated with calf diarrhea. These altered gut microbiotas play vital roles in diarrhea pathogenesis and indicate that gut microbiota-targeted therapies could be useful for both prevention and treatment of diarrhea.

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Metagenomes and Assembled Genomes from Diarrhea-Affected Cattle (Bos taurus)

Cited by 3 publications

References 11 publications

Gut microbiota-derived ursodeoxycholic acid from neonatal dairy calves improves intestinal homeostasis and colitis to attenuate extended-spectrum β-lactamase-producing enteroaggregative Escherichia coli infection

Gut microbiota-derived ursodeoxycholic acid from neonatal dairy calves improves intestinal homeostasis and colitis to attenuate extended-spectrum β-lactamase-producing enteroaggregative Escherichia coli infection

Temporal Changes in Fecal Unabsorbed Carbohydrates Relative to Perturbations in Gut Microbiome of Neonatal Calves: Emerging of Diarrhea Induced by Extended-Spectrum β-lactamase-Producing Enteroaggregative Escherichia coli

Metagenomic and metabolomic analyses reveal the role of gut microbiome-associated metabolites in diarrhea calves

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