Respiratory and Gut Microbiota in Commercial Turkey Flocks with Disparate Weight Gain Trajectories Display Differential Compositional Dynamics

Abstract

Communities of gut bacteria (microbiota) are known to play roles in resistance to pathogen infection and optimal weight gain in turkey flocks. However, knowledge of turkey respiratory microbiota and its link to gut microbiota is lacking. This study presents a 16S rRNA gene-based census of the turkey respiratory microbiota (nasal cavity and trachea) alongside gut microbiota (cecum and ileum) in two identical commercial Hybrid Converter turkey flocks raised in parallel under typical field commercial conditions. The flocks were housed in adjacent barns during the brood stage and in geographically separated farms during the grow-out stage. Several bacterial taxa, primarily Staphylococcus, that were acquired in the respiratory tract at the beginning of the brood stage persisted throughout the flock cycle. Late-emerging predominant taxa in the respiratory tract included Deinococcus and Corynebacterium. Tracheal and nasal microbiota of turkeys were identifiably distinct from one another and from gut microbiota. Nevertheless, gut and respiratory microbiota changed in parallel over time and appeared to share many taxa. During the brood stage, the two flocks generally acquired similar gut and respiratory microbiota, and their average body weights were comparable. However, there were qualitative and quantitative differences in microbial profiles and body weight gain trajectories after the flocks were transferred to geographically separated grow-out farms. Lower weight gain corresponded to the emergence of Deinococcus and Ornithobacterium in the respiratory tract and Fusobacterium and Parasutterella in gut. This study provides an overview of turkey microbiota under field conditions and suggests several hypotheses concerning the respiratory microbiome. IMPORTANCE Turkey meat is an important source of animal protein, and the industry around its production contributes significantly to the agricultural economy. The microorganisms present in the gut of turkeys are known to impact bird health and flock performance. However, the respiratory microbiota in turkeys is entirely unexplored. This study has elucidated the microbiota of respiratory tracts of turkeys from two commercial flocks raised in parallel throughout a normal flock cycle. Further, the study suggests that bacteria originating in the gut or in poultry house environments influence respiratory communities; consequently, they induce poor performance, either directly or indirectly. Future attempts to develop microbiome-based interventions for turkey health should delimit the contributions of respiratory microbiota and aim to limit disturbances to those communities.

Assessment of two DNA extraction kits for profiling poultry respiratory microbiota from multiple sample types

“…Our optimized methods for pre-sequencing and sequence processing are detailed in our recent reports [16–17] and are stated here in brief. The 16S rRNA V4 hypervariable region was amplified using primer sets 515F (GTGYCAGCMGCCGCGGTAA) and 806R (GGACTACNVGGGTWTCTAAT).…”

Assessment of two DNA extraction kits for profiling poultry respiratory microbiota from multiple sample types

“…Our optimized methods for pre-sequencing and sequence processing are detailed in our recent reports [15][16][17]. Briefly, DNA concentration was quantified using NanoDrop 2000c spectrophotometer (Thermo Fisher Scientific, Waltham, MA) and adjusted to a concentration of 100 ng/μL.…”

“…For example, the variation attributed to different protocols and its effect on biodiversity profiles in human gut and environmental microbiota has been widely reported [6][7][8][9][10][11][12][13][14]. We and others have evaluated the sample collection methods for poultry respiratory and gut microbiota [2,[15][16][17]. However, confounding factors associated with DNA extraction, sequencing strategies, and bioinformatic analysis in poultry microbiota remain to be studied.…”

“…Five different DNA extraction kits were previously used in poultry respiratory microbiota studies, including BiOstic FFPE Tissue DNA Isolation Kit, PowerSoil DNA Isolation Kit, QIAmp DNA Mini Kit, Maxwell RSC PureFood Pathogen Kit, and Qiagen DNeasy Blood and Tissue Kit [2,[15][16][17][25][26][27][28]. These kits typically employ a combination of mechanical, chemical, and enzymatic disruption methods to increase DNA yields.…”

“…These kits typically employ a combination of mechanical, chemical, and enzymatic disruption methods to increase DNA yields. In our previous poultry respiratory microbiota studies [2,[15][16][17], the Qiagen DNeasy Blood and Tissue kit (BT kit), which utilizes chemical and enzymatic lysis, was used. The BT kit uses proteinase K, a broad-spectrum serine protease, that can potentially lyse all types of bacteria, but an optional use of lysozyme can ensure complete lysis of gram-positive bacteria.…”