Shift of hindgut microbiota and microbial short chain fatty acids profiles in dairy calves from birth to pre-weaning

Song, Yang; Malmuthuge, Nilusha; Steele, M.A.; Guan, Le Luo

doi:10.1093/femsec/fix179

Cited by 71 publications

(101 citation statements)

References 61 publications

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“…First systematic investigations on the development of bacteria in the gut of newborn calves were carried out in the early 1960s (Smith and Crabb 1961;Smith 1965). Although there are some publications dealing with the calf's intestinal microbiome, there are only a few studies that cover the development within the first week of life (Takino et al 2017;Song et al 2018). This is surprising, considering that enteric infections in neonatal calves are amongst the major causes of calf mortality during the early stage of life (Bendali et al 1999).…”

Section: Introductionmentioning

confidence: 99%

Development of selected bacterial groups of the rectal microbiota of healthy calves during the first week postpartum

et al. 2019

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Aims:The intestinal microbiota of newborn calves is largely unexplored even if it is of great significance for their future health. Therefore, the aim of the study was to gain a better insight into the development dynamics of certain bacterial groups during the first week of life. Methods and Results: Faecal samples of healthy Simmental calves (dualpurpose breed; n = 80), bottle fed and raised in a dairy farm were taken immediately after birth and at 6/12/24/48/72/168 h (h) after birth. Samples were analysed using cultural, biochemical and molecular-biological methods. The aerobe, anaerobe, Enterobacteriaceae and Enterococcus counts of healthy calves increased significantly between 6 and 24 h postpartum (P <0Á05). Apart from the anaerobes, bacterial counts decreased after reaching a plateau at 24-48 h. Enterococcus faecalis was detected in significantly higher counts compared to E. faecium (P <0Á05). Lactobacilli developed more slowly and increased until day 7 after birth to a mean value of 6Á8 9 10 7 CFU per g. MALDI-TOF analysis of 2338 lactobacilli isolates resulted in 36 different species. Conclusions: Lactobacillus reuteri became the most common Lactobacillus sp. during the first week of life. Significance and Impact of the Study: This fact seems to be very important for the calf's intestinal health because L. reuteri is known to show in vitro bactericidal effects against bacterial pathogens and anti-infective activities against rotaviruses and Cryptosporidium parvum.

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Section: Introductionmentioning

confidence: 99%

Development of selected bacterial groups of the rectal microbiota of healthy calves during the first week postpartum

et al. 2019

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“…Together with other carbohydrate-utilizing bacteria, higher relative abundances of Blautia and Coprococcus were found by Song et al . in the gut of 3-week old dairy calves, which coincides with rumen development, solid intake and greater concentration of short-chain fatty acids [50]. These two genera were temporarily increased in calves that received enrofloxacin in our study, which may be considered a good, unpredicted side effect.…”

Section: Discussionmentioning

confidence: 61%

Effects of treatment with enrofloxacin or tulathromycin on fecal microbiota composition and function of dairy calves

Foditsch

Pereira

Siler

et al. 2019

Preprint

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16The increasing concerns with antimicrobial resistance highlights the need for studies 17 evaluating the impacts of antimicrobial use in livestock on antimicrobial resistance using new 18 sequencing technologies. Through shotgun sequencing, we investigated the changes in the fecal 19 microbiome composition and function, with a focus on functions related to antimicrobial 20 resistance, of dairy calves. Heifers 2 to 3 weeks old, which were not treated with antibiotics by the 21 farm before enrollment, were randomly allocated to one of three study groups: control (no 22 treatment), enrofloxacin, or tulathromycin. Fecal samples were collected at days 4, 14, 56 and 112 23 days after enrollment, and DNA extraction and sample preparation and sequencing was conducted. 2 24 The effect of antibiotic treatment on each taxon and functional level by time (including Day 0 as 25 a covariate) revealed few changes in the microbiota. At the genus level, enrofloxacin group had 26 higher abundance of Blautia, Coprococcus and Desulfovibrio and lower abundance of Bacteroides 27when compared to other treatment groups. The SEED database was used for functional analyses, 28 which showed that calves in the enrofloxacin group started with a higher abundance of "Resistance 29 to antibiotics and toxic compounds" function on Day 0, however an increase in antibiotic resistance 30 genes after treatment with enrofloxacin was not observed. "Resistance to Fluoroquinolones" and 31 "Erythromycin resistance", of relevance given the study groups, were not statistically different in 32 abundance between treatment groups. "Resistance to fluoroquinolones" increased during the study 33 period regardless of treatment group. Despite small differences over the first weeks between 34 treatment groups, at Day 112 the microbiota composition and functional profile was similar among 35 all study groups. These findings show that metaphylaxis treatment of dairy calves with either 36 enrofloxacin or tulathromycin have minimal impacts on the microbial composition and functional 37 microbiota of dairy calves over time. 38 39 40 42 45and resistance genes are present even in places that were never inhabited by humans [3,4] and in 46 wild animals [5]. However, the use of antibiotics in human and animal medicine, as well as in plant 3 47 agriculture and animal production systems, has resulted in an acceleration in the selection and 48 spread of antimicrobial resistance [1,6]. Antimicrobial resistant enteric bacteria can be transmitted 49 from livestock to humans through the fecal-oral route, or contamination in the food chain and 50 environment [1,7,8]. Together with prevention of disease and infectious agent transmission, the 51 prudent use of antibiotics is extremely important to preserve treatment effectiveness and decrease 52 the dissemination of resistant bacteria. 53Antimicrobials may be used to control and prevent the spread of the disease in production 54 animals at high risk of developing a bacterial infectious disease. This practice is referred to as 55 metaph...

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“…This may be explained by the difference of the spectrum between bacitracin and the antibiotics used on the veal farms, as bacitracin has a narrow spectrum, targeting Gram-positive bacteria, whereas E. coli is sensitive to antibiotics used during extended treatment (colistin, sulfonamides, tetracycline, trimethoprim). It may also be partially explained by the age of calves, as the microbiota change markedly between birth and the rst month of life [16,26].…”

Section: Discussionmentioning

confidence: 99%

Temporal dynamics of the fecal microbiota in veal calves in a 6-month field trial

Haenni

Nguyễn

Madec

et al. 2020

Preprint

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Background Little is known about maturation of calves’ gut microbiome in veal farms, in which animals are confined under intensive-farming conditions and the administration of collective antibiotic treatment in feed is common. We conducted a field study on 45 calves starting seven days after their arrival in three veal farms. We collected monthly fecal samples over six months and performed 16S rRNA gene sequencing and quantitative PCR of Escherichia coli to follow the dynamics of their microbiota, including that of their commensal E. coli populations. We used mixed-effect models to characterize the dynamics of α-diversity indices and numbers of E. coli, and searched for an effect of collective antibiotic treatments on the estimated parameters. On two farms, we also searched for associations between recommended daily doses of milk powder and bacterial abundance. Results There was high heterogeneity between calves’ microbiota upon their arrival at the farms, followed by an increase in similarity, starting at the first month. From the second month, 16 genera were detected at each sampling in all calves, representing 67.5% (± 9.9) of their microbiota. Shannon diversity index showed a two-phase increase, an inflection occurring at the end of the first month. Calves receiving antibiotics had a lower intercept estimate for Shannon index (-0.17 CI95%[0.27; -0.06], p = 0.003) and a smaller number of E. coli/ gram of feces during the treatment and in the 15 days following it (-0.37 log10 (E. coli/g) CI95%[-0.66; -0.08], p = 0.01) than unexposed calves. There were moderate to strong positive associations between the dose of milk powder and the relative abundances of the genera Megasphaera, Enterococcus, Dialister and Mitsuokella, and the number of E. coli (rs ≥ 0.40; Bonferroni corrected p < 0.05).Conclusions This observational study shows early convergence of the developing microbiota between veal calves and associations between the dose of milk powder and members of their microbiota. It suggests that administration of collective antibiotic treatment results in a reduction of diversity and size of the E. coli population and highlights the need for additional work to fully understand the impact of antibiotic treatment in the veal industry.

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Shift of hindgut microbiota and microbial short chain fatty acids profiles in dairy calves from birth to pre-weaning

Cited by 71 publications

References 61 publications

Development of selected bacterial groups of the rectal microbiota of healthy calves during the first week postpartum

Development of selected bacterial groups of the rectal microbiota of healthy calves during the first week postpartum

Effects of treatment with enrofloxacin or tulathromycin on fecal microbiota composition and function of dairy calves

Temporal dynamics of the fecal microbiota in veal calves in a 6-month field trial

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