Characterization of the Microbiome along the Gastrointestinal Tract of Growing Turkeys

Wilkinson, Toby; Cowan, A. A.; Vallin, Hannah; Onime, Lucy A.; Oyama, Linda; Cameron, Simon; Gonot, Charlotte; Moorby, J. M.; Waddams, Kate; Theobald, Vince J.; Leemans, David; Bowra, S.; Nixey, C.; Huws, Sharon

doi:10.3389/fmicb.2017.01089

Cited by 76 publications

(78 citation statements)

References 40 publications

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“…LEfSe analyses showed that the Clostridiaceae family (Firmicutes phylum) is abundant in the lower intestine of granivorous birds and Clostridium genus is predominant in the gizzard and upper intestine in frugivorous birds ( Fig 4D, 4E and 4F ), particularly in Buff-throated Saltator ( Fig 2 ). This family of bacteria is abundant in the ceca of granivorous chicken [ 13 , 28 ], neotropical birds [ 6 ], gastrointestinal tract of turkeys [ 29 ] and in vulture facial skin and hindgut samples [ 14 ]. The members of this bacterial family are associated with proteolytic activity and complex carbohydrate degradation, [ 30 – 32 ].…”

Section: Discussionmentioning

confidence: 99%

Comparison of gizzard and intestinal microbiota of wild neotropical birds

et al. 2018

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Gut bacterial communities have been shown to be influenced by diet, host phylogeny and anatomy, but most of these studies have been done in captive animals. Here we compare the bacterial communities in the digestive tract of wild birds. We characterized the gizzard and intestinal microbiota among 8 wild Neotropical bird species, granivorous or frugivorous species of the orders Columbiformes and Passeriformes. We sequenced the V4 region of the 16S rRNA gene in 94 collected samples from 32 wild birds from 5 localities, and compared bacterial communities by foraging guild, organ, locality and bird taxonomy. 16S rRNA gene-based sequencing data were examined using QIIME with linear discriminant analysis effect size (LEfSe) and metabolic pathways were predicted using PICRUSt algorism. We identified 8 bacterial phyla, dominated by Firmicutes, Actinobacteria and Proteobacteria. Beta diversity analyses indicated significant separation of gut communities by bird orders (Columbiformes vs. Passerifomes) and between bird species (p<0.01). In lower intestine, PICRUSt shows a predominance of carbohydrate metabolism in granivorous birds and xenobiotics biodegradation pathways in frugivorous birds. Gizzard microbiota was significantly richer in granivorous, in relation to frugivorous birds (Chao 1; non-parametric t-test, p<0.05), suggesting a microbial gizzard function, beyond grinding food. The results suggest that the most important factor separating the bacterial community structure was bird taxonomy, followed by foraging guild. However, variation between localities is also likely to be important, but this could not been assessed with our study design.

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Section: Discussionmentioning

confidence: 99%

Comparison of gizzard and intestinal microbiota of wild neotropical birds

et al. 2018

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“…Many studies have used high-throughput sequencing to investigate the gut microbial diversity of poultry. Among them, sequencing the rRNA gene of a gut microbiome is relatively simple and cost-effective, nonetheless understanding the function of the microbiome is key for understanding interrelationships with the host (Wilkinson et al 2017). In this study, we used an Illumina MiSeq approach to investigate bacterial community diversity within the duodenum (S), jejunum (K) and caecum (M) contents of 30-week-old (peak production stage) Jinghong laying hens.…”

Section: Discussionmentioning

confidence: 99%

Microbial community diversity of Jinghong laying hens at peak production based on 16S rRNA sequencing

Guo

Wang

et al. 2018

Journal of Applied Animal Research

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In this study, the diversity within the duodenum (S), jejunum (K) and caecum (M) contents of the three different intestinal gut sections microbiota of 30-week-old (peak production stage) Jinghong laying hens were evaluated. The bacterial DNA was sequentially isolated and the V3 to V4 regions of 16S rRNA genes were amplified. Results showed that the average bacterial sequences from the duodenum, jejunum and caecum content were identified to be 175.33 ± 26.63, 64.00 ± 20.95 and 305.33 ± 4.16 OTUs, respectively. The inherent OTUs were found among duodenum (75), jejunum (2) and caecum (172). The caecum had the highest diversity (Shannon = 5.57 ± 0.06) among the three communities. Firmicutes (65.54%) and Proteobacteria (32.68%) were the predominant bacterial phyla in the duodenum content. Firmicutes (97.27%) was the most commonly detected phyla in the jejunum content. As to the caecum, the relatively prominent phyla were Bacteroidetes and Firmicutes and Fusobacteria, accounting for 48.70%, 28.91% and 15.93%, respectively. At the genus level, Lactobacillus, Helicobacter, Bacillus, Peptoclostridium and Campylobacter were the relatively abundant genera in the duodenum content, accounting for 51.76%, 28.07%, 5.89%, 5.04% and 1.70%, respectively. Within the jejunum content, Lactobacillus was the most commonly detected genera, which represent 96.26% of the total genera.

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“…16S rRNA gene sequences were processed as described by Wilkinson et al (2017) . Essentially, the CD-HIT-OTU pipeline ( Li et al, 2012 ) was used to denoise the sequences and remove low quality sequences, pyrosequencing errors and chimeras.…”

Section: Methodsmentioning

confidence: 99%

Using ‘Omic Approaches to Compare Temporal Bacterial Colonization of Lolium perenne, Lotus corniculatus, and Trifolium pratense in the Rumen

et al. 2018

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Understanding rumen plant–microbe interactions is central for development of novel methodologies allowing improvements in ruminant nutrient use efficiency. This study investigated rumen bacterial colonization of fresh plant material and changes in plant chemistry over a period of 24 h period using three different fresh forages: Lolium perenne (perennial ryegrass; PRG), Lotus corniculatus (bird’s foot trefoil; BFT) and Trifolium pratense (red clover; RC). We show using 16S rRNA gene ion torrent sequencing that plant epiphytic populations present pre-incubation (0 h) were substantially different to those attached post incubations in the presence of rumen fluid on all forages. Thereafter primary and secondary colonization events were evident as defined by changes in relative abundances of attached bacteria and changes in plant chemistry, as assessed using Fourier transform infrared (FTIR) spectroscopy. For PRG colonization, primary colonization occurred for up to 4 h and secondary colonization from 4 h onward. The changes from primary to secondary colonization occurred significantly later with BFT and RC, with primary colonization being up to 6 h and secondary colonization post 6 h of incubation. Across all 3 forages the main colonizing bacteria present at all time points post-incubation were Prevotella, Pseudobutyrivibrio, Ruminococcus, Olsenella, Butyrivibrio, and Anaeroplasma (14.2, 5.4, 1.9, 2.7, 1.8, and 2.0% on average respectively), with Pseudobutyrivibrio and Anaeroplasma having a higher relative abundance during secondary colonization. Using CowPI, we predict differences between bacterial metabolic function during primary and secondary colonization. Specifically, our results infer an increase in carbohydrate metabolism in the bacteria attached during secondary colonization, irrespective of forage type. The CowPI data coupled with the FTIR plant chemistry data suggest that attached bacterial function is similar irrespective of forage type, with the main changes occurring between primary and secondary colonization. These data suggest that the sward composition of pasture may have major implications for the temporal availability of nutrients for animal.

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Characterization of the Microbiome along the Gastrointestinal Tract of Growing Turkeys

Cited by 76 publications

References 40 publications

Comparison of gizzard and intestinal microbiota of wild neotropical birds

Comparison of gizzard and intestinal microbiota of wild neotropical birds

Microbial community diversity of Jinghong laying hens at peak production based on 16S rRNA sequencing

Using ‘Omic Approaches to Compare Temporal Bacterial Colonization of Lolium perenne, Lotus corniculatus, and Trifolium pratense in the Rumen

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