scholarly journals Transition of microbiota in chicken cecal droppings from commercial broiler farms

2021 ◽  
Vol 17 (1) ◽  
Author(s):  
Nachiko Takeshita ◽  
Takayasu Watanabe ◽  
Kasumi Ishida-Kuroki ◽  
Tsutomu Sekizaki
Keyword(s):  
Broiler Chickens ◽  
Competitive Exclusion ◽  
Amplicon Sequencing ◽  
Growth Stages ◽  
Climate Conditions ◽  
16S Rrna Amplicon Sequencing ◽  
Fundamental Information ◽  
Commercial Broiler ◽  
Commercial Farms ◽  
Chicken Cecum

Abstract Background Chickens are major sources of human nutrition worldwide, but the chicken intestinal microbiota can be a source of bacterial infection. The microbiota has potential to regulate the colonization of pathogens by competitive exclusion, production of antimicrobial compounds, and stimulation of the mucosal immune system. But information on the microbiota in commercial broiler chickens is limited because of the difficulty of conducting studies at commercial farms. To obtain fundamental information that can be used to control pathogens in chickens, we determined the 6-week dynamics of microbiota in chicken cecal droppings from commercial broiler farms. Results Cecal droppings from four chickens were collected once a week from 1 to 6 weeks of age at three commercial broiler farms. A total of 168 samples were collected from 7 flocks and subjected to 16S rRNA amplicon sequencing. Despite the farms have distinctly different climate conditions, the microbiota in the same growth stages were similar among farms. Moreover, as the chickens grew and the feed types were switched, the richness and diversity of the microbiota gradually increased and convergence of the composition of the microbiota was apparent. Notably, minor bacterial taxa (i.e. OTUs with relative abundance < 0.05%) within the microbiota were changed by the chicken age, switching of feed types, and presence of Campylobacter. In particular, the effects of switching of feed types on the microbiota were larger than the effects of age and Campylobacter. Conclusions Irrespective of the locations of the farms, the microbiota of chicken cecum, especially minor bacteria, was successively changed more affected by feed types than by ages. Switching of feed types inducing the alteration of the microbiota may be associated with the colonization of pathogens in the chicken gut. These results will also help with extrapolation of studies in experimental animals to those in the commercial farms.

scholarly journals Compositional and functional analysis of the gut microbiota of Radix auricularia (Linnaeus) via high-throughput Illumina sequencing

2018 ◽  
Author(s):  
Zongfu Hu ◽  
Xi CHEN ◽  
Jie CHANG ◽  
Jianhua YU ◽  
Qing TONG ◽  
...  
Keyword(s):  
16S Rrna ◽  
Bacterial Species ◽  
Intestinal Bacteria ◽  
Amplicon Sequencing ◽  
Freshwater Snail ◽  
Gonadal Development ◽  
Growth Stages ◽  
Rrna Gene ◽  
16S Rrna Amplicon Sequencing ◽  
Radix Auricularia

Widely distributed across the world, the freshwater snail Radix auricularia plays an important role in freshwater systems. In this study, gut bacterial communities of R. auricularia were characterized using 16S rRNA amplicon sequencing, then intestinal bacteria were compared at different growth stages: adult snails (AS) (with complete gonadal development) and juvenile snails (JS) (with incomplete gonadal development). We obtained 251,072 high quality sequences which were clustered into 1,196 operational taxonomic units (OTUs) with 97% sequence identity. The predominant phyla were Proteobacteria and Cyanobacteria, followed by Chloroflexi, Firmicutes, and Actinobacteria. Other bacterial species such as Tenericutes, Bacteroidetes, Fusobacteria and Verrucomicrobia were present to a lesser extent. 52 bacterial families and 55 genera were found in > 1% of each sample. A large number of species could not be successfully identified. 469 core OTUs were found to make up 39.38% of all OTUs and 88.38% of all sequences. Samples obtained from juvenile organisms possessed higher ratios of Ruminococcaceae, Subdoligranulum, and Faecalibacterium than adult species. Furthermore, 16S rRNA gene data was used to predict function, showing that genes related to metabolism and environmental information processing were rich in snail samples.

scholarly journals Compositional and functional analysis of the gut microbiota of Radix auricularia (Linnaeus) via high-throughput Illumina sequencing

2018 ◽  
Author(s):  
Zongfu Hu ◽  
Xi CHEN ◽  
Jie CHANG ◽  
Jianhua YU ◽  
Qing TONG ◽  
...  
Keyword(s):  
16S Rrna ◽  
Bacterial Species ◽  
Intestinal Bacteria ◽  
Amplicon Sequencing ◽  
Freshwater Snail ◽  
Gonadal Development ◽  
Growth Stages ◽  
Rrna Gene ◽  
16S Rrna Amplicon Sequencing ◽  
Radix Auricularia

Widely distributed across the world, the freshwater snail Radix auricularia plays an important role in freshwater systems. In this study, gut bacterial communities of R. auricularia were characterized using 16S rRNA amplicon sequencing, then intestinal bacteria were compared at different growth stages: adult snails (AS) (with complete gonadal development) and juvenile snails (JS) (with incomplete gonadal development). We obtained 251,072 high quality sequences which were clustered into 1,196 operational taxonomic units (OTUs) with 97% sequence identity. The predominant phyla were Proteobacteria and Cyanobacteria, followed by Chloroflexi, Firmicutes, and Actinobacteria. Other bacterial species such as Tenericutes, Bacteroidetes, Fusobacteria and Verrucomicrobia were present to a lesser extent. 52 bacterial families and 55 genera were found in > 1% of each sample. A large number of species could not be successfully identified. 469 core OTUs were found to make up 39.38% of all OTUs and 88.38% of all sequences. Samples obtained from juvenile organisms possessed higher ratios of Ruminococcaceae, Subdoligranulum, and Faecalibacterium than adult species. Furthermore, 16S rRNA gene data was used to predict function, showing that genes related to metabolism and environmental information processing were rich in snail samples.

scholarly journals Investigation into the effect of divergent feed efficiency phenotype on the bovine rumen microbiota across diet and breed

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Emily McGovern ◽  
Mark McGee ◽  
Colin J. Byrne ◽  
David A. Kenny ◽  
Alan K. Kelly ◽  
...  
Keyword(s):  
Feed Efficiency ◽  
Production Systems ◽  
Rumen Fluid ◽  
Average Daily Gain ◽  
Amplicon Sequencing ◽  
Growth Stages ◽  
Rumen Microbiota ◽  
Grass Silage ◽  
16S Rrna Amplicon Sequencing ◽  
P 75

Abstract The relationship between rumen microbiota and host feed efficiency phenotype, for genetically divergent beef cattle breeds is unclear. This is further exacerbated when different growth stages, chemically diverse diets and production systems are considered. Residual feed intake (RFI), a measure of feed efficiency, was calculated for individually fed Charolais (CH) and Holstein–Friesian (HF) steers during each of four 70-day (excluding adaptation) successive dietary phases: namely, high-concentrate, grass silage, fresh zero-grazed grass and high-concentrate again. Rumen fluid from the ten highest- (HRFI) and ten lowest-ranking (LRFI) animals for RFI, within breed, during each dietary phase was collected using a trans-oesophageal sampler and subjected to 16S rRNA amplicon sequencing and metabolic profiling. The datasets were analysed to identify microbial and rumen fermentation markers associated with RFI status. Age, dietary phase and breed were included in the statistical model. Within breed, for each dietary phase, mid-test metabolic weight and average daily gain did not differ (P > 0.05) between HRFI and LRFI steers; however, for the initial high-concentrate, grass silage, fresh grass herbage and final high-concentrate dietary phases, HRFI HF steers consumed 19, 23, 18 and 27% more (P < 0.001) than their LRFI counterparts. Corresponding percentages for CH HRFI compared to CH LRFI steers were 18, 23, 13 and 22%. Ten OTUs were associated with RFI (q < 0.05) independent of the other factors investigated. Of these Methanomassiliicoccaceae, Mogibacteriaceae and the genus p-75-a5 of Erysipelotrichaceae and were negatively associated (q < 0.05) with RFI. The results gave evidence that microbial species could potentially be an indicator of RFI in ruminants rather than broader microbiome metrics; however, further research is required to elucidate this association.

scholarly journals Regulatory Effects of Combined Dietary Supplementation With Essential Oils and Organic Acids on Microbial Communities of Cobb Broilers

2022 ◽  
Vol 12 ◽  
Author(s):  
Jiayun Qiao ◽  
Zhiyuan Shang ◽  
Xuejiao Liu ◽  
Kewei Wang ◽  
Zhiwei Wu ◽  
...  
Keyword(s):  
Organic Acids ◽  
Essential Oils ◽  
Microbial Communities ◽  
Broiler Chickens ◽  
Animal Feed ◽  
Antibiotic Resistance Genes ◽  
Dietary Supplementation ◽  
Amplicon Sequencing ◽  
Growth Stages ◽  
Growth Promoters

The emergence and spread of antibiotic resistance genes in pathogenic microorganisms have resulted in many countries restricting the use of antibiotics as growth promoters in animal feed. The combined use of essential oils and organic acids can help maintain intestinal health, improve animal growth performance, and alleviate the negative effects of banned antibiotics for certain economically important animals. Although the modes of action for the combined dietary supplementation of essential oils and organic acids such as thymol-citric acid (EOA1) and thymol-butyric acid (EOA2) remain unclear, it is speculated that their activities are achieved through beneficial modulation of gastrointestinal microbial communities and inhibition of pathogen growth. In this study, 16S rDNA amplicon sequencing was used to analyze the effects of treatment with EOA1 and EOA2 on the jejunal, cecal, and fecal microbial communities of Cobb broilers while also evaluating effects over different broiler ages. The intestinal microbial communities of broilers developed with increasing age, and Lactobacillus gradually came to dominate the intestinal communities of treated broilers. Further, the microbial communities of feces were more complex than those of the jejuna and ceca. We systematically elucidate that the longitudinal changes in the intestinal microbial communities of Cobb broiler chickens at different ages. Meanwhile, we found that the addition of EOA1 or EOA2 to the diet: (1) inhibited the proliferation of Ralstonia pickettii and Alcaligenaceae in the jejuna on day 28, (2) promoted the colonization and growth of beneficial bacteria such as Lactobacillus, Clostridia, and Bacteroidia at various growth stages, and (3) enriched the abundance of certain microbiota functions, including biological pathways related to metabolism (e.g., enzyme families). Taken together, the results of this study demonstrate that EOA1 and EOA2 dietary supplementation can affect various microbial metabolic pathways related to the metabolism and absorption of nutrients via regulation of the intestinal microbial community structures of Cobb broilers.

scholarly journals Two-Step Mucosal Competitive Exclusion Flora Treatment to Diminish Salmonellae in Commercial Broiler Chickens

1993 ◽  
Vol 72 (9) ◽  
pp. 1667-1672 ◽  
Author(s):  
L.C. BLANKENSHIP ◽  
J.S. BAILEY ◽  
N.A. COX ◽  
N.J. STERN ◽  
R. BREWER ◽  
...  
Keyword(s):  
Broiler Chickens ◽  
Competitive Exclusion ◽  
Commercial Broiler

Pathogenicity of local identified NDV strain related to genotype VII to 28 day old commercial broiler chickens

2018 ◽  
Vol 5 (4) ◽  
Author(s):  
Mohamed M Amer ◽  
Hagar M Ahmed ◽  
Khaled M Elbayoumi ◽  
Mohamed A Kutkat
Keyword(s):  
Broiler Chickens ◽  
Commercial Broiler ◽  
Genotype Vii

scholarly journals Bacterial Diversity of Breast Milk in Healthy Spanish Women: Evolution from Birth to Five Years Postpartum

Nutrients ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 2414
Author(s):  
Laura Sanjulián ◽  
Alexandre Lamas ◽  
Rocío Barreiro ◽  
Alberto Cepeda ◽  
Cristina A. Fente ◽  
...  
Keyword(s):  
Breast Milk ◽  
16S Rrna ◽  
Human Milk ◽  
Alpha Diversity ◽  
Amplicon Sequencing ◽  
Maternal Body Mass Index ◽  
16S Rrna Amplicon Sequencing ◽  
Spanish Women ◽  
Calcium Magnesium ◽  
Abundant Genus

The objective of this work was to characterize the microbiota of breast milk in healthy Spanish mothers and to investigate the effects of lactation time on its diversity. A total of ninety-nine human milk samples were collected from healthy Spanish women and were assessed by means of next-generation sequencing of 16S rRNA amplicons and by qPCR. Firmicutes was the most abundant phylum, followed by Bacteroidetes, Actinobacteria, and Proteobacteria. Accordingly, Streptococcus was the most abundant genus. Lactation time showed a strong influence in milk microbiota, positively correlating with Actinobacteria and Bacteroidetes, while Firmicutes was relatively constant over lactation. 16S rRNA amplicon sequencing showed that the highest alpha-diversity was found in samples of prolonged lactation, along with wider differences between individuals. As for milk nutrients, calcium, magnesium, and selenium levels were potentially associated with Streptococcus and Staphylococcus abundance. Additionally, Proteobacteria was positively correlated with docosahexaenoic acid (DHA) levels in breast milk, and Staphylococcus with conjugated linoleic acid. Conversely, Streptococcus and trans-palmitoleic acid showed a negative association. Other factors such as maternal body mass index or diet also showed an influence on the structure of these microbial communities. Overall, human milk in Spanish mothers appeared to be a complex niche shaped by host factors and by its own nutrients, increasing in diversity over time.

scholarly journals The Interplay between Campylobacter and the Caecal Microbial Community of Commercial Broiler Chickens over Time

2021 ◽  
Vol 9 (2) ◽  
pp. 221
Author(s):  
Ilaria Patuzzi ◽  
Massimiliano Orsini ◽  
Veronica Cibin ◽  
Sara Petrin ◽  
Eleonora Mastrorilli ◽  
...  
Keyword(s):  
Campylobacter Jejuni ◽  
Broiler Chickens ◽  
Control Strategies ◽  
Chicken Meat ◽  
Control Measures ◽  
Microbial Network ◽  
Gut Colonization ◽  
Commercial Broiler ◽  
Zoonotic Bacteria ◽  
Human Infections

Campylobacter is the most frequent foodborne zoonotic bacteria worldwide, with chicken meat being overwhelmingly the most important reservoir for human infections. Control measures implemented at the farm level (i.e., biosecurity or vaccination), which have been successfully applied to limit other pathogens, such as Salmonella, have not been effective in reducing Campylobacter occurrence. Thus, new approaches are needed to fully understand the ecological interactions of Campylobacter with host animals to effectively comprehend its epidemiology. The objective of this study was to analyse longitudinally the gut microbiota composition of Campylobacter-infected and non-infected farms to identify any difference that could potentially be indicative of gut colonization by Campylobacter spp. Differences in the colonization rate and timing were observed at the farms that became positive for Campylobacter jejuni over the investigated time points, even though in positive tests, the occurrence of Campylobacter jejuni gut colonization was not observed before the second week of the life of the birds. Significant differences were observed in the abundances of specific bacterial taxa between the microbiota of individuals belonging to farms that became Campylobacter positive during the study and those who remained negative with particular reference to Bacteroidales and Clostridiales, respectively. Moreover, Campylobacter colonization dramatically influenced the microbiota richness, although to a different extent depending on the infection timing. Finally, a key role of Faecalibacterium and Lactobacillus genera on the Campylobacter microbial network was observed. Understanding the ecology of the Campylobacter interaction with host microbiota during infection could support novel approaches for broiler microbial barrier restoration. Therefore, evidence obtained through this study can be used to identify options to reduce the incidence of infection at a primary production level based on the targeted influence of the intestinal microbiota, thus helping develop new control strategies in order to mitigate the risk of human exposure to Campylobacter by chicken meat consumption.

scholarly journals Investigation of allele specific expression in various tissues of broiler chickens using the detection tool VADT

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
M. Joseph Tomlinson ◽  
Shawn W. Polson ◽  
Jing Qiu ◽  
Juniper A. Lake ◽  
William Lee ◽  
...  
Keyword(s):  
Broiler Chickens ◽  
Nucleotide Polymorphisms ◽  
Rna Seq ◽  
Specific Expression ◽  
Single Nucleotide ◽  
Allele Specific Expression ◽  
Detection Tool ◽  
Commercial Broiler ◽  
Significant Phenomenon ◽  
Allele Specific

AbstractDifferential abundance of allelic transcripts in a diploid organism, commonly referred to as allele specific expression (ASE), is a biologically significant phenomenon and can be examined using single nucleotide polymorphisms (SNPs) from RNA-seq. Quantifying ASE aids in our ability to identify and understand cis-regulatory mechanisms that influence gene expression, and thereby assist in identifying causal mutations. This study examines ASE in breast muscle, abdominal fat, and liver of commercial broiler chickens using variants called from a large sub-set of the samples (n = 68). ASE analysis was performed using a custom software called VCF ASE Detection Tool (VADT), which detects ASE of biallelic SNPs using a binomial test. On average ~ 174,000 SNPs in each tissue passed our filtering criteria and were considered informative, of which ~ 24,000 (~ 14%) showed ASE. Of all ASE SNPs, only 3.7% exhibited ASE in all three tissues, with ~ 83% showing ASE specific to a single tissue. When ASE genes (genes containing ASE SNPs) were compared between tissues, the overlap among all three tissues increased to 20.1%. Our results indicate that ASE genes show tissue-specific enrichment patterns, but all three tissues showed enrichment for pathways involved in translation.

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