Chicken Caecal Microbiome Modifications Induced by Campylobacter jejuni Colonization and by a Non-Antibiotic Feed Additive

Abstract

Campylobacter jejuni is an important zoonotic foodborne pathogen causing acute gastroenteritis in humans. Chickens are often colonized at very high numbers by C. jejuni, up to 10(9) CFU per gram of caecal content, with no detrimental effects on their health. Farm control strategies are being developed to lower the C. jejuni contamination of chicken food products in an effort to reduce human campylobacteriosis incidence. It is believed that intestinal microbiome composition may affect gut colonization by such undesirable bacteria but, although the chicken microbiome is being increasingly characterized, information is lacking on the factors affecting its modulation, especially by foodborne pathogens. This study monitored the effects of C. jejuni chicken caecal colonization on the chicken microbiome in healthy chickens. It also evaluated the capacity of a feed additive to affect caecal bacterial populations and to lower C. jejuni colonization. From day-0, chickens received or not a microencapsulated feed additive and were inoculated or not with C. jejuni at 14 days of age. Fresh caecal content was harvested at 35 days of age. The caecal microbiome was characterized by real time quantitative PCR and Ion Torrent sequencing. We observed that the feed additive lowered C. jejuni caecal count by 0.7 log (p<0.05). Alpha-diversity of the caecal microbiome was not affected by C. jejuni colonization or by the feed additive. C. jejuni colonization modified the caecal beta-diversity while the feed additive did not. We observed that C. jejuni colonization was associated with an increase of Bifidobacterium and affected Clostridia and Mollicutes relative abundances. The feed additive was associated with a lower Streptococcus relative abundance. The caecal microbiome remained relatively unchanged despite high C. jejuni colonization. The feed additive was efficient in lowering C. jejuni colonization while not disturbing the caecal microbiome.

Fig 1. Campylobacter caecal counts in chickens at 35 days of age.

No Campylobacter could be detected for the Campy- groups; each point represents the caecal content of a single chicken; horizontal bars illustrate the mean for each group; insufficient caecal matter was recovered from some chicken to allow the enumeration of C. jejuni; ** indicates p<0.01.

Fig 2. Bifidobacterium 16S copies in caecal content at 35 days of age across all chicken groups; * indicates p<0.05.

Each point represents the caecal content of a single chicken; horizontal bars illustrate the mean for each group.

Fig 3. NMDS plot illustrating the chicken microbiome beta-diversity according to C. jejuni status.

Each point represents a single chicken caecal microbiome; based on a subsample of 898 OTU.

Fig 4. NMDS plot illustrating the chicken microbiome beta-diversity according to feed additive use.

Each point represents a single chicken caecal microbiome; based on a subsample of 898 OTU.