Week-Old Chicks with High Bacteroides Abundance Have Increased Short-Chain Fatty Acids and Reduced Markers of Gut Inflammation

Fan Y, Ju T, Bhardwaj T, Korver DR, Willing BP. Week-Old Chicks with High Bacteroides Abundance Have Increased Short-Chain Fatty Acids and Reduced Markers of Gut Inflammation. Microbiol Spectr. 2023 Jan 31;11(2):e0361622. doi: 10.1128/spectrum.03616-22


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Firmicutes and Bacteroidetes represent more than 90% of the total cecal microbiota in the ceca of matured chickens but have relatively low abundance in the ceca of newly hatched chicks. Limited information is available regarding how differential abundance of this taxa affects gut immune state or functional capacity of the gut microbiota in broiler chickens. The aim of this study was to understand how high and low Bacteroides abundances are associated with early life chicken gut microbial functional capacity, and immune response. This was achieved by sampling and characterizing week-old broiler chickens from commercial production flocks with distinct cecal Bacteroides abundance.


A total of 14 broiler flocks reared under the same condition in similarly engineered broiler production houses were sampled. For each flock, 14,000 Ross 308 broiler chicks were placed at 1 day of age, and fed ad libitum until the end of the production cycle. At day 7, five chicks from each flock were euthanized for sampling. Approximately 300 mg of cecal contents and cecal tonsil tissue were collected for further analyses. Total DNA was extracted from cecal contents. The mean value and standard deviation of Bacteroides relative abundance was calculated. The extracted genomic DNA was also used to measure the abundance of the Bacteroides-Prevotella group in the cecal content using qPCR, targeting the 16s rRNA gene. To examine host response to different Bacteroides relative abundance, cecal tonsils were subjected to RNA extraction, followed by cDNA synthesis and qPCR assay.

Analysis of Results

The 3 most abundant phyla on the early life chicken cecal microbiome made up over 98% of the population, and included Firmicutes (76.16 ± 15.72%), Bacteroidetes (17.54 ± 16.59%), and Proteobacteria (5.07 ± 6.83%). Low Bacteroides samples were defined as samples with Bacteroides relative abundance lower than 0.7% (mean − SD); whereas high Bacteroides samples were defined as samples with Bacteroides relative abundance higher than 31.9% (mean + SD). As a result, chickens from 11 different flocks were assigned to either the LB or HB group. Specifically, 18 birds with low Bacteroides levels from 6 flocks and 15 birds with high Bacteroides from 6 flocks were identified. Chickens that were not assigned to either group were marked as not assigned (n/a). The average 32-day flock bodyweight (P = 0.91) and mortality rate (P = 0.93) were similar between flocks that had the majority of birds identified as LB, HB, or n/a. It was observed that HB individuals had higher short-chain fatty acid concentrations in cecal contents. The gut microbiota of the HB group harbored more abundant pathways, than the LB microbiota.


Results revealed that elevated level of cecal Bacteroides in young chickens had altered the gut microbiome’s microbial functional capacity, which promoted the production of SCFA. Coinciding with that, compared to the LB group, chickens from the HB group had lower expression of pro-inflammatory cytokines and higher expressions of anti-inflammatory cytokine and tight-junction protein gene. Consequently, it indicated that elevated cecal Bacteroides may be beneficial to commercial broiler chickens in suppressing gut inflammation through the increment of short-chain fatty acid production.


As important commensals in the chicken intestine, Bacteroides are essential complex carbohydrate degraders, and short-chain fatty acid (SCFA) producers that are highly adapted to the distal gut. Previous studies have shown large variation in Bacteroides abundance in young chickens. However, limited information is available regarding how this variation affects the gut microbiome and host immunity. To investigate how elevated or depleted Bacteroides levels affect gut microbial functional capacity and impact host response, we sampled 7-day-old broiler chickens from 14 commercial production flocks. Week-old broiler chickens were screened and birds with low Bacteroides (LB) and high Bacteroides (HB) abundance were identified via 16S rRNA gene amplicon sequencing and quantitative PCR (qPCR) assays. Cecal microbial functionality and SCFA concentration of chickens with distinct cecal Bacteroides abundance were profiled by shotgun metagenomic sequencing and gas chromatography, respectively. The intestinal immune responses of LB and HB chickens were assessed via reverse transcription qPCR. Results showed that the gut microbiota of the LB group had increased abundance of lactic acid bacteria pyruvate fermentation pathway, whereas complex polysaccharide degradation and SCFA production pathways were enriched in the HB group (P < 0.05), which was supported by increased SCFA concentrations in the ceca of HB chickens (P < 0.05). HB chickens also showed decreased expression of interleukin-1β and increased expression of interleukin-10 and tight-junction protein claudin-1 (P < 0.05). Overall, the results indicated that elevated Bacteroides may benefit the 7-day broiler gut and that further work should be done to confirm the causal role of Bacteroides in the observed positive outcomes.