Data_Sheet_2_Liver microbial community and associated host transcriptome in calves with feed induced acidosis.CSV

IntroductionIn the dairy industry, calves are typically fed diets rich in highly fermentable carbohydrates and low in fibrous feeds to maximize ruminal papillae and tissue development. Calves on such diets are vulnerable at developing ruminal acidosis. Prevalent in cattle, liver abscess (LA) is considered a sequela to ruminal acidosis. LAs can cause significant liver function condemnation and decreased growth and production. Currently, we know little about the liver microbiome in calves with feed-induced acidosis.
MethodsUsing our established model of ruminal acidosis, where young calves were fed an acidosis-inducing (AC) or -blunting (control) diet starting at birth until 17-week of age, we investigated microbial community changes in the liver resultant from ruminal acidosis. Eight calves were randomly assigned to each diet, with four animals per treatment. Rumen epithelium and liver tissues were collected at 17 weeks of age right after euthanasia. Total RNAs were extracted and followed by whole transcriptome sequencing. Microbial RNA reads were enriched bioinformatically and used for microbial taxonomy classification using Kraken2.
ResultsAC Calves showed significantly less weight gain over the course of the experiment, in addition to significantly lower ruminal pH, and rumen degradation comparison to the control group (p < 0.05). In the liver, a total of 29 genera showed a significant (p < 0.05) abundance change (> 2-fold) between the treatments at 17-week of age. Among these, Fibrobacter, Treponema, Lactobacillus, and Olsenella have been reported in abscessed liver in cattle. Concurrent abundance changes in 9 of the genera were observed in both the liver and rumen tissues collected at 17-week of age, indicating potential crosstalk between the liver and rumen epithelial microbial communities. Significant association was identified between host liver gene and its embedded microbial taxa. Aside from identifying previously reported microbial taxa in cattle abscessed liver, new repertoire of actively transcribed microbial taxa was identified in this study.
DiscussionBy employing metatranscriptome sequencing, our study painted a picture of liver microbiome in young calves with or without feed induced acidosis. Our study suggested that liver microbiome may have a critical impact on host liver physiology. Novel findings of this study emphasize the need for further in-depth analysis to uncover the functional roles of liver resident microbiome in liver metabolic acidosis resultant from feed-related ruminal acidosis.

引言：在乳制品养殖行业中，为最大化促进犊牛的瘤胃乳头与组织发育，通常会为其饲喂高发酵碳水化合物含量高、粗纤维含量低的饲粮。采用此类饲粮的犊牛易罹患瘤胃酸中毒（ruminal acidosis）。肝脓肿（liver abscess, LA）在牛群中较为普遍，被认为是瘤胃酸中毒的继发后遗症。肝脓肿可导致肝脏功能废弃率显著上升，同时降低犊牛的生长性能与生产效率。目前，学界对饲粮诱导酸中毒犊牛的肝脏微生物组仍知之甚少。
材料与方法：本研究依托已建立的瘤胃酸中毒模型，将新生犊牛随机分为两组，自出生至17周龄分别饲喂诱导酸中毒（acidosis-inducing, AC）饲粮与缓减酸中毒（对照组）饲粮，以此探究瘤胃酸中毒引发的肝脏微生物群落变化。每组各随机纳入8头犊牛，每处理组设4个生物学重复。于17周龄对犊牛实施安乐死后，采集瘤胃上皮与肝脏组织，提取总RNA后开展全转录组测序（whole transcriptome sequencing）。通过生物信息学方法富集微生物RNA测序读段（reads），并利用Kraken2工具进行微生物分类学注释。
结果：试验全程中，AC组犊牛的体重增长显著低于对照组，瘤胃pH值与瘤胃降解能力也显著低于对照组（p < 0.05）。17周龄时，两组肝脏组织中共计29个菌属的丰度发生显著变化（p < 0.05）且变化幅度超过2倍。其中，纤维杆菌属（Fibrobacter）、密螺旋体属（Treponema）、乳杆菌属（Lactobacillus）与奥尔森菌属（Olsenella）已在牛脓肿肝脏样本中被报道过。同时，在17周龄采集的肝脏与瘤胃组织中，共有9个菌属的丰度发生同向变化，提示肝脏与瘤胃上皮微生物群落间存在潜在互作。研究还发现宿主肝脏基因与其定植的微生物分类群间存在显著关联。本研究除鉴定出此前已在牛脓肿肝脏中报道过的微生物分类群外，还发现了一批新的活跃转录微生物类群。
讨论：本研究通过宏转录组测序（metatranscriptome sequencing），清晰描绘了有无饲粮诱导酸中毒犊牛的肝脏微生物组特征。研究结果表明，肝脏微生物组可能对宿主肝脏生理功能具有关键调控作用。本研究的新颖发现强调，需开展进一步深入分析，以阐明肝脏定植微生物组在饲粮相关瘤胃酸中毒引发的肝脏代谢性酸中毒中的功能角色。