Host and Environmental Factors Affecting the Intestinal Microbiota in Chickens - PubMed (original) (raw)

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Host and Environmental Factors Affecting the Intestinal Microbiota in Chickens

Jannigje G Kers et al. Front Microbiol. 2018.

Abstract

The initial development of intestinal microbiota in poultry plays an important role in production performance, overall health and resistance against microbial infections. Multiplexed sequencing of 16S ribosomal RNA gene amplicons is often used in studies, such as feed intervention or antimicrobial drug trials, to determine corresponding effects on the composition of intestinal microbiota. However, considerable variation of intestinal microbiota composition has been observed both within and across studies. Such variation may in part be attributed to technical factors, such as sampling procedures, sample storage, DNA extraction, the choice of PCR primers and corresponding region to be sequenced, and the sequencing platforms used. Furthermore, part of this variation in microbiota composition may also be explained by different host characteristics and environmental factors. To facilitate the improvement of design, reproducibility and interpretation of poultry microbiota studies, we have reviewed the literature on confounding factors influencing the observed intestinal microbiota in chickens. First, it has been identified that host-related factors, such as age, sex, and breed, have a large effect on intestinal microbiota. The diversity of chicken intestinal microbiota tends to increase most during the first weeks of life, and corresponding colonization patterns seem to differ between layer- and meat-type chickens. Second, it has been found that environmental factors, such as biosecurity level, housing, litter, feed access and climate also have an effect on the composition of the intestinal microbiota. As microbiota studies have to deal with many of these unknown or hidden host and environmental variables, the choice of study designs can have a great impact on study outcomes and interpretation of the data. Providing details on a broad range of host and environmental factors in articles and sequence data repositories is highly recommended. This creates opportunities to combine data from different studies for meta-analysis, which will facilitate scientific breakthroughs toward nutritional and husbandry associated strategies to improve animal health and performance.

Keywords: 16S rRNA; confounding factors; gut health; gut microbiota; microbiome; poultry.

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Figures

FIGURE 1

FIGURE 1

Factors that affect the intestinal microbiota composition of chickens. Factors found in the literature that determine the development of the intestinal microbiota in broiler chickens. Solid line indicates host characteristics, dashed line indicates environmental factors. The gut regions comprise the crop, proventriculus, gizzard, duodenum, jejunum, ileum, caeca, large intestine and cloaca. Maternal factors include horizontal transmission, vertical transmission and maternal antibodies.

FIGURE 2

FIGURE 2

The composition of the cecal microbiota in Cobb broilers at phylum level. General composition of the cecal microbiota in Cobb broilers across different ages, from control groups, not exposed to specific treatments. The data is from four different studies, based on 16S rRNA 454 pyrosequencing (PS), n = 3 and MiSeq sequencing n = 1. Pedroso et al. (2016), Figure 7, stacked bar chart A was used. Mohd Shaufi et al. (2015), Figure 4, the last four bars were used. Singh et al. (2013), the data from Figure 1 was used. Stanley et al. (2013), the data from MG-RAST was used to combine the data from Figure 6.

FIGURE 3

FIGURE 3

The composition of the cecal microbiota in Ross broilers at phylum level. General composition of the cecal microbiota in Ross broilers across different ages, from control groups, not exposed to specific treatments. The data is from eight different studies, based on 16S rRNA 454 pyrosequencing (PS), n = 6 and MiSeq sequencing n = 2. Danzeisen et al. (2011), the data from the supporting information Supplementary Table S1 was used. Han et al. (2016b), the data from Figure 6, the first bar of the histogram was used. Han et al. (2016c), the data from Figure 7, pie chart A and C was used. Pourabedin et al. (2015), the data from the supplementary data, Supplementary Figure S1A was used. Witzig et al. (2015), the data from the Supplementary Data, Supplementary Table S4 was used. Choi et al. (2014), data from Figure 1 was used. Sergeant et al. (2014), the data from the Supplementary Data 1 was used. Sohail et al. (2015), the data from Supplementary Table 2 was used.

FIGURE 4

FIGURE 4

The composition of the cecal microbiota in layer-type chickens at phylum level. General composition of the cecal microbiota in laying hens across different ages, from control groups, not exposed to specific treatments. The data is from four different studies, based on 16S rRNA 454 pyrosequencing (PS), n = 1 and MiSeq sequencing n = 4. Ballou et al. (2016), data from Figure 2B was used. Videnska et al. (2014b), data from the Supplementary Data S1 for ages 7, 14, 21, 28, and 56, data from the Supplementary Data S2 for ages 4, 7, 13, 16, and 19, and data from the Supplementary S3 data for age 21 was used. Polansky et al. (2016), data from Figure 1, bar 1 and 3 from the histogram was used. Han et al. (2016b) the data from Figure 6, the second bar of the histogram was used.

FIGURE 5

FIGURE 5

Known and potential factors that affect the intestinal microbiota composition of chickens during life. These factors can have short- and long-term effects and may even originate from the hatching stage or a previous generation. Grandparent flocks and the rearing period of the parent flock are not included in the figure. Layer- (white arrow) and broiler-type (gray arrow) have different production systems and are therefore displayed separately.

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