16S rRNA amplicon sequencing characterization of caecal microbiome composition of broilers and free-range slow-growing chickens throughout their productive lifespan

Ocejo, Medelin; Oporto, Beatriz; Hurtado, Ana

doi:10.1038/s41598-019-39323-x

Cited by 129 publications

(161 citation statements)

References 63 publications

(104 reference statements)

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“…When analysing the abundance of MAGs between birds from different lines, consuming either a vegetable diet or a diet containing fish meal, we found significant differences in the microbial communities based on both line and diet. This agrees with previous studies where significant differences have been described in the intestinal microbiota of chickens from different lines, including those from faster and slower growing lines [73][74][75]. Differences have also previously been observed in the microbiota when feeding chickens a diet supplemented with fish meal [34,35].…”

Section: Discussionsupporting

confidence: 92%

Assembly of hundreds of novel bacterial genomes from the chicken caecum

et al. 2020

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Background: Chickens are a highly important source of protein for a large proportion of the human population. The caecal microbiota plays a crucial role in chicken nutrition through the production of short-chain fatty acids, nitrogen recycling, and amino acid production. In this study, we sequence DNA from caecal content samples taken from 24 chickens belonging to either a fast or a slower growing breed consuming either a vegetable-only diet or a diet containing fish meal. Results: We utilise 1.6 T of Illumina data to construct 469 draft metagenome-assembled bacterial genomes, including 460 novel strains, 283 novel species, and 42 novel genera. We compare our genomes to data from 9 European Union countries and show that these genomes are abundant within European chicken flocks. We also compare the abundance of our genomes, and the carbohydrate active enzymes they produce, between our chicken groups and demonstrate that there are both breed-and diet-specific microbiomes, as well as an overlapping core microbiome. Conclusions: This data will form the basis for future studies examining the composition and function of the chicken caecal microbiota.

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Section: Discussionsupporting

confidence: 92%

Assembly of hundreds of novel bacterial genomes from the chicken caecum

et al. 2020

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“…2 and 3). Additionally, the age of the animal was the variable that had the highest in uence over the microbiota variation, in agreement with previous studies [48,50]. This is a key evidence suggesting that microbiota approximations done under controlled environments do not differ largely from farming conditions.…”

Section: Discussionsupporting

confidence: 90%

Salmonella Phage cocktail, its effects and benefits on the gut of chickens in a commercial farm.

Clavijo¹,

Morales²,

Flores³

et al. 2020

Preprint

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BackgroundThe microbiota of broiler chicken gut affects positively or negatively the health, metabolism and immunity of chickens thus it has a significant impact on the animal productivity. Phages, host-specific parasites of bacterial cells, are a promising antimicrobial alternative that selectively target pathogens without disturbing the microbiota. The aim of the study is further characterizing the behaviour of phages and its effect on the commensal microbial community.MethodsWe used 16S rRNA gene amplicon sequencing to evaluate the effect of SalmoFree® (a phage cocktail against Salmonella) on the microbiota of the cecum of broilers reared in a commercial farming system. Two field trials were carried out including 2 control and 2 experimental houses. Phages were incorporated in the broilers’ drinking water using three doses at the grower stage. The core microbiome, differentially abundant taxa between treatments as well as taxa associated with age were identified using Qiime2 and the R-Project for statistics.ResultsAnalyses of similarities among communities over time allowed us to identify two stages of microbiota development at the last stage of the production cycle. The core microbiome identified some key species in the adaptation of the microbiota at the last stage of the cycle. Among these there are important degraders of complex polysaccharides and producers of short chain fatty acids such as Eisenbergiella and Lachnoclostridium. Additionally, the phage cocktail did not affect the normal development of the microbiota structure while its application contributes to reduce the presence of pathogenic Enterobacteria including Salmonella. The addition of the phage cocktail led to a significant reduction in the abundance of Campylobacter and Helicobacter and increase in Butyricimonas and Rikenellaceae abundance which are common inhabitants of the chicken gut with known negative and positive effects in the health, respectively.ConclusionsOur results suggest that phages can contribute to improve the chicken health and reduce pathogens burden at the end of the production cycle of broilers. Furthermore, it presents for the first time a detailed look of the microbiota composition and changes in broilers in a commercial scenario, information that will valuable towards the implementation of phage therapy technologies in the field.

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“…This is in agreement with other microbiome studies that observed strong individual variation of microbiome communities in C . elegans (Dirksen et al ., ) and other hosts (Turnbaugh et al ., ; Ainsworth et al ., ; Hernandez‐Agreda et al ., ; Ocejo et al ., ). For instance, a sponge study identified the core microbiome on the operational taxonomic unit level (97% sequence identity) by sampling individuals over 36 months (Bjork et al ., ).…”

Section: Discussionmentioning

confidence: 97%

Community assembly of the native C. elegans microbiome is influenced by time, substrate and individual bacterial taxa

Johnke

Dirksen

Schulenburg

2020

Environmental Microbiology

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Summary Microbiome communities are complex assemblages of bacteria. The dissection of their assembly dynamics is challenging because it requires repeated sampling of both host and source communities. We used the nematode Caenorhabditis elegans as a model to study these dynamics. We characterized microbiome variation from natural worm populations and their substrates for two consecutive years using 16S rDNA amplicon sequencing. We found conservation in microbiome composition across time at the genus, but not amplicon sequencing variant (ASV) level. Only three ASVs were consistently present across worm samples (Comamonas ASV10859, Pseudomonas ASV7162 and Cellvibrio ASV9073). ASVs were more diverse in worms from different rather than the same substrates, indicating an influence of the source community on microbiome assembly. Surprisingly, almost 50% of worm‐associated ASVs were absent in corresponding substrates, potentially due to environmental filtering. Ecological network analysis revealed strong effects of bacteria–bacteria interactions on community composition: While a dominant Erwinia strain correlated with decreased alpha‐diversity, predatory bacteria of the Bdellovibrio and like organisms associated with increased alpha‐diversity. High alpha‐diversity was further linked to high worm population growth, especially on species‐poor substrates. Our results highlight that microbiomes are individually shaped and sensitive to dramatic community shifts in response to particular competitive species.

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16S rRNA amplicon sequencing characterization of caecal microbiome composition of broilers and free-range slow-growing chickens throughout their productive lifespan

Cited by 129 publications

References 63 publications

Assembly of hundreds of novel bacterial genomes from the chicken caecum

Assembly of hundreds of novel bacterial genomes from the chicken caecum

Salmonella Phage cocktail, its effects and benefits on the gut of chickens in a commercial farm.

Community assembly of the native C. elegans microbiome is influenced by time, substrate and individual bacterial taxa

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