Welcome to Animal Microbiome

Huws, Sharon

doi:10.1186/s42523-019-0003-5

Cited by 11 publications

(12 citation statements)

References 2 publications

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“…It is well-known that age, sex, husbandry and management practices, season, circadian rhythm, geography etc. can cause microbiome variation between populations [ 13 , 14 ]. Due to our one-pen study design mimicking a production broiler house on a smaller scale, the enormous microbiome differences we observed between Big and Small broilers cannot be attributed to such confounding effects.…”

Section: Discussionmentioning

confidence: 99%

“…A plethora of factors are involved in shaping the microbial gut community. If not carefully considered and controlled, these influences can confound the study [ 13 , 14 ]. Animals housed together share microbiomes to a large extent due to the shared local environment and behaviours such as coprophagy and pecking/preening activities.…”

Section: Introductionmentioning

confidence: 99%

“…Animals housed together share microbiomes to a large extent due to the shared local environment and behaviours such as coprophagy and pecking/preening activities. This can result in a so-called cage or pen effect [ 14 , 15 ], meaning that a pen-specific microbiome is developed within a single pen of animals. This phenomenon is a potentially confounding factor that may mask the effect under study, e.g.…”

Section: Introductionmentioning

confidence: 99%

“…This phenomenon is a potentially confounding factor that may mask the effect under study, e.g. the effect of a feed additive intervention on the microbiome [ 14 ]. A sound solution is to spread out the confounding variable across a statistically appropriate number of pens replicated in the trial design and either housing the animals individually, pooling samples from each pen or subsampling one or more birds from each pen.…”

Section: Introductionmentioning

confidence: 99%

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The link between broiler flock heterogeneity and cecal microbiome composition

Lundberg

Scharch²,

Sandvang

2021

anim microbiome

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Background Despite low genetic variation of broilers and deployment of considerate management practices, there still exists considerable body weight (BW) heterogeneity within broiler flocks which adversely affects the commercial value. The purpose of this study was to investigate the role of the cecal microbiome in weight differences between animals. Understanding how the gut microbiome may contribute to flock heterogeneity helps to pave the road for identifying methods to improve flock uniformity and performance. Results Two hundred eighteen male broiler chicks were housed in the same pen, reared for 37 days, and at study end the 25 birds with highest BW (Big) and the 25 birds with lowest BW (Small) were selected for microbiome analysis. Cecal contents were analyzed by a hybrid metagenomic sequencing approach combining long and short read sequencing. We found that Big birds displayed higher microbial alpha diversity, higher microbiome uniformity (i.e. lower beta diversity within the group of Big birds), higher levels of SCFA-producing and health-associated bacterial taxa such as Lachnospiraceae, Faecalibacterium, Butyricicoccus and Christensenellales, and lower levels of Akkermansia muciniphila and Escherichia coli as compared to Small birds. Conclusion Cecal microbiome characteristics could be linked to the size of broiler chickens. Differences in alpha diversity, beta diversity and taxa abundances all seem to be directly associated with growth differences observed in an otherwise similar broiler flock.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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The link between broiler flock heterogeneity and cecal microbiome composition

Lundberg

Scharch²,

Sandvang

2021

anim microbiome

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“…In this light, while antimicrobials susceptibility testing is commonly employed in the practice and remains a mainstay for appropriate drug selection. The pharmacodynamics of the drugs should be further considered in the choice of the individual antimicrobial administration [ 17 ].…”

Section: Introductionmentioning

confidence: 99%

Changes in the Fecal Microbiota Associated with a Broad-Spectrum Antimicrobial Administration in Hospitalized Neonatal Foals with Probiotics Supplementation

Freccero

Lanci

Mariella

et al. 2021

Animals

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There is a wide array of evidence across species that exposure to antibiotics is associated with dysbiosis, and due to their widespread use, this also raises concerns also in medicine. The study aimed to determine the changes on the fecal microbiota in hospitalized neonatal foals administered with broad-spectrum antimicrobials and supplemented probiotics. Fecal samples were collected at hospital admission (Ta), at the end of the antimicrobial treatment (Te) and at discharge (Td). Feces were analysed by next-generation sequencing of the 16S rRNA gene on Illumina MiSeq. Seven foals treated with IV ampicillin and amikacin/gentamicin were included. The mean age at Ta was 19 h, the mean treatment length was 7 days and the mean time between Te and Td was 4.3 days. Seven phyla were identified: Actinobacteria, Bacteroidetes, Firmicutes, Fusobacteria, Proteobacteria, TM7 and Verrucomicrobia. At Ta, Firmicutes (48.19%) and Proteobacteria (31.56%) were dominant. The alpha diversity decreased from Ta to Te, but it was the highest at Td. The beta diversity was higher at Ta than at Te and higher at Td than at Te. An increase in Akkermansia over time was detected. The results suggest that the intestinal microbiota of neonatal foals rapidly returns to a high diversity after treatment. It is possible that in foals, the effect of antimicrobials is strongly influenced or overshadowed by the time-dependent changes in the developing gut microbiota.

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