The chicken microbiota is often analyzed to address questions about the effects of diet or disease on poultry health. To analyze the microbiota, bioinformatic platforms such as QIIME 2 and mothur are used, which incorporate public taxonomic databases such as Greengenes, the ribosomal database project (RDP), and SILVA to assign taxonomies to bacterial sequences. Many chicken microbiota studies continue to incorporate the Greengenes database, which has not been updated since 2013. To determine whether a choice of database could affect results, this study compared the results of bioinformatic analyses obtained using the Greengenes, RDP, and SILVA databases on a cecal luminal microbiome dataset. The QIIME 2 platform was used to process 16S bacterial sequences and assign taxonomies with Greengenes, RDP, and SILVA. Linear discriminant analysis effect size (LEfSe) was performed, allowing for the comparison of taxonomies considered significantly differentially abundant between the three databases. Some notable differences between databases were observed in results, in particular the ability of SILVA database to classify members of the family Lachnospiraceae into separate genera, while these members remained in one group of unclassified Lachnospiraceae through Greengenes and RDP. LEfSe analyses showed that the SILVA database produced more differentially abundant genera, in large part due to the classification of these separate Lachnospiraceae genera. Additionally, the relative abundance of unclassified Lachnospiraceae in SILVA results was significantly lower than in RDP results. Our results show the choice of taxonomic database can influence the results of a microbiota study at the genus level, potentially affecting the interpretation of the results. The use of the SILVA database is recommended over Greengenes in chicken microbiota studies, as more specific classifications at the genus level may provide more accurate interpretations of changes in the microbiota.

Chronic heat stress (HS) is known to depress feed intake (FI) and growth in broiler chickens, and may alter the gut microbiota and health, however, the amplitude and duration of each (HS and depressed FI) effect on gut microbiota is still unclear. This study aimed to determine the effects of chronic and acute HS on the cecal and ileal microbiota profiles. Broilers were subjected to thermoneutral (TN, 23°C) or chronic cyclic HS (CHS, 8 h/d, 35°C) condition from d29-42, and one group to acute HS (AHS, 2 h, 35°C) at d42. To distinguish between the effect of HS and FI, one pair-fed (PF) group (maintained at TN condition but had similar FI as CHS birds) was used from d29-42. Chronic HS decreased richness in the cecal microbiota compared to TN, while PF did not, and AHS led to higher richness compared to CHS. Acute HS and PF altered cecal microbiota profiles similarly to CHS under weighted UniFrac. In the ileum, PF altered microbiota under unweighted UniFrac, and CHS further altered microbiota. Decreased Lactobacillus and increased Ligilactobacillus were observed with CHS, AHS, and PF in the cecum. Chronic HS may influence different predicted metabolic pathways compared to PF, while AHS shared some similarities with CHS. Understanding both the direct effects of CHS and indirect effects through depressed FI, along with the short-term effects from AHS, will be of importance in devising nutritional strategies to maintain gut microbial balance and limit negative effects to broiler chickens' performance and health.

Coccidiosis in broiler chickens continues to be a major disease of the gastrointestinal tract, causing economic losses to the poultry industry worldwide. The goal of this study was to generate a symptomatic Eimeria maxima (1000 oocysts) infection to determine its effect on the luminal and mucosal microbiota populations (L and M) in the jejunum and ileum (J and IL). Samples were taken from day 0 to 14 post-infection, and sequencing of 16S rRNA was performed using Illumina technology. Infected birds had significantly (p < 0.0001) lower body weight gain (BWG), higher feed conversion ratio (FCR) (p = 0.0015), increased crypt depth, and decreased villus height (p < 0.05). The significant differences in alpha and beta diversity were observed primarily at height of infection (D7). Analysis of taxonomy indicated that J-L and M were dominated by Lactobacillus, and in IL-M, changeover from Candidatus Arthromitus to Lactobacillus as the major taxon was observed, which occurred quicky in infected animals. LEfSe analysis found that in the J-M of infected chickens, Lactobacillus was significantly more abundant in infected (IF) chickens. These findings show that E. maxima infection affects the microbiota of the small intestine in a time-dependent manner, with different effects on the luminal and mucosal populations.

Coccidiosis is a gastrointestinal disease caused by Eimeria parasites which leads to major economic losses in the poultry industry worldwide. Eimeria infection may alter the gut microbiota, which has been associated with chicken health and performance. This study aimed to determine the effects of Eimeria maxima infection on the luminal and mucosal microbiota of the cecum (CeL and CeM) at multiple time points post-infection (days 3, 5, 7, 10, and 14). Infection decreased Shannon diversity at d 3 (P = 0.03), increased observed features (ASVs) at d 5 (P < 0.01), and increased Shannon diversity at d 10 (P = 0.04) in the CeL microbiota compared to the control. In CeM microbiota, infection increased observed features at d 5 (P = 0.03), but later decreased observed features at d 14 (P = 0.01). Relative abundance of potential butyrate-producing bacteria such as [Ruminococcus] torques group in CeL and Butyricicoccus in CeM were decreased in infected birds, and some metabolic pathways related to butyrate production were predicted to be decreased. These findings show E. maxima may affect cecal microbiota alpha diversity in a time-dependent manner and reduce abundance of bacteria potentially important to gut health.

Climatic change and increased use of alternative sources of feed ingredients could influence poultry production. Mycotoxin and oxidized oil are two contaminations that may occur in chicken feed as a result of climate change and use of alternative feed ingredients, and these factors may have differential and potentially additive effects on birds’ intestinal microbiota. The study objective was to determine the main effects of corn, oil quality, and their interaction on ileal content, ileal scrapings, cecal content, and whole cecum (content and tissue) microbiota in broiler chickens. Broiler chickens were raised for 21 days post-hatch and fed diet made with regular or mycotoxin-contaminated corn (7,959 ppb of deoxynivalenol, 2.1 ppm of aflatoxin, 23,200 ppb of fumonisin, and 1,403 ppb of zearalenone), and regular or oxidized (148 meq/kg) oil. Bacterial genomic DNA was extracted and sequenced targeting the variable (V3-V4) region of the 16S gene. The bioinformatic and statistical analysis of the microbiota data showed mycotoxin and mycotoxin by oxidized oil interaction increased the richness and evenness in the ileal content and only evenness in the cecal content. Mycotoxin and mycotoxin by oxidized oil interaction also increased beta diversity based on the variability in microbial community in the ileal content while increasing the abundance of bacterial taxa, including Streptomyces and Escherichia-Shigella, and predicted pathways related to RNA and DNA synthesis (Mycothiol and pyrimidine deoxyribonucleotides synthesis) and redox regulation (ergothioneine biosynthesis) in ileal content and pathways related to glycol metabolism and degradation and amino acids degradation were increased in the cecal content. Streptomyces has been associated with mycotoxin detoxication, and its increase could reduce the negative effects of mycotoxins contrary to Escherichia-Shigella, which has been negatively correlated with weight gain in chickens. These results show that mycotoxin alone and its combination with oxidized oil affect bacterial diversity and abundance mostly in the ileum content and predicted metabolic pathways across intestinal sections.

The gastrointestinal tract and its microbiota are researched for their impact on the health and performance of broiler chickens, which have been selected for rapid growth rate to meet demand. Untargeted metabolomics is one method that can potentially link changes in the gut microbiota to changes in metabolites and assist in revealing mechanisms affecting health outcomes. In this study, untargeted metabolomics via Ultra Performance Liquid Chromatography-Mass Spectrometry (UPLC-MS) was performed to characterize changes in ceca and plasma metabolite profiles during early development (d 1, 3, and 10 post-hatch), a time period known for rapid changes in the cecal microbiota. PCA, PLS-DA, OPLS-DA, and fold change analyses revealed shifts in metabolite profiles and individual metabolites over time. The results suggested that shifts in cecal metabolites occurred mostly from d 1 to d 3, while plasma metabolites shifted more gradually from d 1 to d 10. Metabolites linked to KEGG pathway enrichment and potentially influential to growth, such as 5-Glutamyl-taurine and stachyose, greatly increased in concentration in the ceca. These findings show promise in utilization of metabolomics for time-dependent studies on broiler chicken gut health and integration with gut microbiota analysis.