Milk microbiome in dairy cattle and the challenges of low microbial biomass and exogenous contamination

Abstract Background The blanket usage of antimicrobials at the end of lactation (or “drying off”) in dairy cattle is under increasing scrutiny due to concerns about antimicrobial resistance. To lower antimicrobial usage in dairy farming, farmers are now encouraged to use “selective dry cow therapy”...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Jolinda Pollock, Susannah J. Salter, Rebecca Nixon, Michael R. Hutchings
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Veterinary medicine SF600-1100 Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/19fd21c46717434dab0eff84c9fa4c3e
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:19fd21c46717434dab0eff84c9fa4c3e
record_format	dspace
spelling	oai:doaj.org-article:19fd21c46717434dab0eff84c9fa4c3e2021-11-21T12:29:02ZMilk microbiome in dairy cattle and the challenges of low microbial biomass and exogenous contamination10.1186/s42523-021-00144-x2524-4671https://doaj.org/article/19fd21c46717434dab0eff84c9fa4c3e2021-11-01T00:00:00Zhttps://doi.org/10.1186/s42523-021-00144-xhttps://doaj.org/toc/2524-4671Abstract Background The blanket usage of antimicrobials at the end of lactation (or “drying off”) in dairy cattle is under increasing scrutiny due to concerns about antimicrobial resistance. To lower antimicrobial usage in dairy farming, farmers are now encouraged to use “selective dry cow therapy” whereby only cows viewed as at high risk of mastitis are administered antimicrobial agents. It is important to gain a better understanding of how this practice affects the udder-associated microbiota and the potential knock-on effects on antimicrobial-resistant bacterial populations circulating on the farm. However, there are challenges associated with studying low biomass environments such as milk, due to known contamination effects on microbiome datasets. Here, we obtained milk samples from cattle at drying off and at calving to measure potential shifts in bacterial load and microbiota composition, with a critical assessment of contamination effects. Results Several samples had no detectable 16S rRNA gene copies and crucially, exogenous contamination was detected in the initial microbiome dataset. The affected samples were removed from the final microbiome analysis, which compromised the experimental design and statistical analysis. There was no significant difference in bacterial load between treatments (P > 0.05), but load was lower at calving than at drying off (P = 0.039). Escherichia coli counts by both sequence and culture data increased significantly in the presence of reduced bacterial load and a decreasing trend of microbiome richness and diversity. The milk samples revealed diverse microbiomes not reflecting a typical infection profile and were largely comprised of gut- and skin-associated taxa, with the former decreasing somewhat after prolonged sealing of the teats. Conclusions The drying off period had a key influence on microbiota composition and bacterial load, which appeared to be independent of antimicrobial usage. The interactions between drying off treatment protocol and milk microbiome dynamics are clearly complex, and our evaluations of these interactions were restricted by low biomass samples and contamination effects. Therefore, our analysis will inform the design of future studies to establish whether different selection protocols could be implemented to further minimise antimicrobial usage.Jolinda PollockSusannah J. SalterRebecca NixonMichael R. HutchingsBMCarticleVeterinary medicineSF600-1100MicrobiologyQR1-502ENAnimal Microbiome, Vol 3, Iss 1, Pp 1-10 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Veterinary medicine SF600-1100 Microbiology QR1-502
spellingShingle	Veterinary medicine SF600-1100 Microbiology QR1-502 Jolinda Pollock Susannah J. Salter Rebecca Nixon Michael R. Hutchings Milk microbiome in dairy cattle and the challenges of low microbial biomass and exogenous contamination
description	Abstract Background The blanket usage of antimicrobials at the end of lactation (or “drying off”) in dairy cattle is under increasing scrutiny due to concerns about antimicrobial resistance. To lower antimicrobial usage in dairy farming, farmers are now encouraged to use “selective dry cow therapy” whereby only cows viewed as at high risk of mastitis are administered antimicrobial agents. It is important to gain a better understanding of how this practice affects the udder-associated microbiota and the potential knock-on effects on antimicrobial-resistant bacterial populations circulating on the farm. However, there are challenges associated with studying low biomass environments such as milk, due to known contamination effects on microbiome datasets. Here, we obtained milk samples from cattle at drying off and at calving to measure potential shifts in bacterial load and microbiota composition, with a critical assessment of contamination effects. Results Several samples had no detectable 16S rRNA gene copies and crucially, exogenous contamination was detected in the initial microbiome dataset. The affected samples were removed from the final microbiome analysis, which compromised the experimental design and statistical analysis. There was no significant difference in bacterial load between treatments (P > 0.05), but load was lower at calving than at drying off (P = 0.039). Escherichia coli counts by both sequence and culture data increased significantly in the presence of reduced bacterial load and a decreasing trend of microbiome richness and diversity. The milk samples revealed diverse microbiomes not reflecting a typical infection profile and were largely comprised of gut- and skin-associated taxa, with the former decreasing somewhat after prolonged sealing of the teats. Conclusions The drying off period had a key influence on microbiota composition and bacterial load, which appeared to be independent of antimicrobial usage. The interactions between drying off treatment protocol and milk microbiome dynamics are clearly complex, and our evaluations of these interactions were restricted by low biomass samples and contamination effects. Therefore, our analysis will inform the design of future studies to establish whether different selection protocols could be implemented to further minimise antimicrobial usage.
format	article
author	Jolinda Pollock Susannah J. Salter Rebecca Nixon Michael R. Hutchings
author_facet	Jolinda Pollock Susannah J. Salter Rebecca Nixon Michael R. Hutchings
author_sort	Jolinda Pollock
title	Milk microbiome in dairy cattle and the challenges of low microbial biomass and exogenous contamination
title_short	Milk microbiome in dairy cattle and the challenges of low microbial biomass and exogenous contamination
title_full	Milk microbiome in dairy cattle and the challenges of low microbial biomass and exogenous contamination
title_fullStr	Milk microbiome in dairy cattle and the challenges of low microbial biomass and exogenous contamination
title_full_unstemmed	Milk microbiome in dairy cattle and the challenges of low microbial biomass and exogenous contamination
title_sort	milk microbiome in dairy cattle and the challenges of low microbial biomass and exogenous contamination
publisher	BMC
publishDate	2021
url	https://doaj.org/article/19fd21c46717434dab0eff84c9fa4c3e
work_keys_str_mv	AT jolindapollock milkmicrobiomeindairycattleandthechallengesoflowmicrobialbiomassandexogenouscontamination AT susannahjsalter milkmicrobiomeindairycattleandthechallengesoflowmicrobialbiomassandexogenouscontamination AT rebeccanixon milkmicrobiomeindairycattleandthechallengesoflowmicrobialbiomassandexogenouscontamination AT michaelrhutchings milkmicrobiomeindairycattleandthechallengesoflowmicrobialbiomassandexogenouscontamination
_version_	1718418929604362240

Milk microbiome in dairy cattle and the challenges of low microbial biomass and exogenous contamination

Ejemplares similares