Transcriptomics analysis of host liver and meta-transcriptome analysis of rumen epimural microbial community in young calves treated with artificial dosing of rumen content from adult donor cow

Liver microbial community and associated host transcriptome in calves with feed induced acidosis

Introduction

In 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.

Methods

Using 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.

Results

AC 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.

Discussion

By 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.

Long-term effects of early-life rumen microbiota modulation on dairy cow production performance and methane emissions

Rumen microbiota modulation during the pre-weaning period has been suggested as means to affect animal performance later in life. In this follow-up study, we examined the post-weaning rumen microbiota development differences in monozygotic twin-heifers that were inoculated (T-group) or not inoculated (C-group) (n = 4 each) with fresh adult rumen liquid during their pre-weaning period. We also assessed the treatment effect on production parameters and methane emissions of cows during their 1st lactation period. The rumen microbiota was determined by the 16S rRNA gene, 18S rRNA gene, and ITS1 amplicon sequencing. Animal weight gain and rumen fermentation parameters were monitored from 2 to 12 months of age. The weight gain was not affected by treatment, but butyrate proportion was higher in T-group in month 3 (p = 0.04). Apart from archaea (p = 0.084), the richness of bacteria (p < 0.0001) and ciliate protozoa increased until month 7 (p = 0.004) and anaerobic fungi until month 11 (p = 0.005). The microbiota structure, measured as Bray-Curtis distances, continued to develop until months 3, 6, 7, and 10, in archaea, ciliate protozoa, bacteria, and anaerobic fungi, respectively (for all: p = 0.001). Treatment or age × treatment interaction had a significant (p < 0.05) effect on 18 bacterial, 2 archaeal, and 6 ciliate protozoan taxonomic groups, with differences occurring mostly before month 4 in bacteria, and month 3 in archaea and ciliate protozoa. Treatment stimulated earlier maturation of prokaryote community in T-group before month 4 and earlier maturation of ciliate protozoa at month 2 (Random Forest: 0.75 month for bacteria and 1.5 month for protozoa). No treatment effect on the maturity of anaerobic fungi was observed. The milk production and quality, feed efficiency, and methane emissions were monitored during cow's 1st lactation. The T-group had lower variation in energy-corrected milk yield (p < 0.001), tended to differ in pattern of residual energy intake over time (p = 0.069), and had numerically lower somatic cell count throughout their 1st lactation period (p = 0.081), but no differences between the groups in methane emissions (g/d, g/kg DMI, or g/kg milk) were observed. Our results demonstrated that the orally administered microbial inoculant induced transient changes in early rumen microbiome maturation. In addition, the treatment may influence the later production performance, although the mechanisms that mediate these effects need to be further explored.

Regulation of the cecal microbiota community and the fatty liver deposition by the addition of brewers’ spent grain to feed of Landes geese

The effects of brewers’ spent grain (BSG) diets on the fatty liver deposition and the cecal microbial community were investigated in a total of 320 healthy 5-day-old Landes geese. These geese were randomly and evenly divided into 4 groups each containing 8 replicates and 10 geese per replicate. These four groups of geese were fed from the rearing stage (days 5–60) to the overfeeding stage (days 61–90). The Landes geese in group C (control) were fed with basal diet (days 5–90); group B fed first with basal diet in the rearing stage and then basal diet + 4% BSG in the overfeeding stage; group F first with basal diet + 4% BSG during the rearing stage and then basal diet in the overfeeding stage; and group W with basal diet + 4% BSG (days 5–90). The results showed that during the rearing stage, the body weight (BW) and the average daily gain (ADG) of Landes geese were significantly increased in groups F and W, while during the overfeeding stage, the liver weights of groups W and B were significantly higher than that of group C. The taxonomic structure of the intestinal microbiota revealed that during the overfeeding period, the relative abundance of Bacteroides in group W was increased compared to group C, while the relative abundances of Escherichia–Shigella and prevotellaceae_Ga6A1_group were decreased. Results of the transcriptomics analysis showed that addition of BSG to Landes geese diets altered the expression of genes involved in PI3K-Akt signaling pathway and sphingolipid metabolism in the liver. Our study provided novel experimental evidence based on the cecal microbiota to support the application of BSG in the regulation of fatty liver deposition by modulating the gut microbiota in Landes geese.

Effects of dietary supplementation with multispecies probiotics on intestinal epithelial development and growth performance of neonatal calves challenged with Escherichia coli K99

BACKGROUND

Probiotics exhibit antibiotic properties and are capable of treating certain bacterial infections, including diarrhea. Therefore, the aim of this study is to investigate the effects of dietary supplementation with multispecies probiotic (MSP) on diarrhea, average daily gain (ADG) and intestinal development of neonatal calves challenged with Escherichia coli K99.

RESULTS

Thirty-six neonatal Holstein calves were randomly assigned to three treatment groups. After E. coli K99 challenge, calves in the control (C) and MSP treatment groups had significantly higher ADG and feed efficiency, and significantly lower fecal scores than those of calves in the diarrhea (D) group. The mean time of diarrhea resolution was 4.5 and 3.1 days for calves in the D and MSP treatment groups, respectively. Furthermore, the structures of the various segments (duodenum, jejunum and ileum) of the small intestine of the calves, activities of several small intestinal enzymes, and expression of several energy metabolism-related genes in the small intestine segments were significantly affected by MSP treatments.

CONCLUSION

Dietary supplementation of MSP had a positive effect in treating calf diarrhea; it improved ADG and feed efficiency and promoted development of the small intestine. © 2022 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Transcriptome Analysis of Bovine Rumen Tissue in Three Developmental Stages

Rumen development is a crucial physiological challenge for ruminants. However, the molecular mechanism regulating rumen development has not been clearly elucidated. In this study, we investigated genes involved in rumen development in 13 rumen tissues from three developmental stages (birth, youth, and adult) using RNA sequencing. We identified that 6,048 genes were differentially expressed among three developmental stages. Using weighted correlation network analysis, we found that 12 modules were significantly associated with developmental stages. Functional annotation and protein–protein interaction (PPI) network analysis revealed that CCNB1, CCNB2, IGF1, IGF2, HMGCL, BDH1, ACAT1, HMGCS2, and CREBBP involved in rumen development. Integrated transcriptome with GWAS information of carcass weight (CW), stomach weight (SW), marbling score (MS), backfat thickness (BFT), ribeye area (REA), and lean meat weight (LMW), we found that upregulated DEGs (fold change 0∼1) in birth–youth comparison were significantly enriched with GWAS signals of MS, downregulated DEGs (fold change >3) were significantly enriched with GWAS signals of SW, and fold change 0∼1 up/downregulated DEGs in birth–adult comparison were significantly enriched with GWAS signals of CW, LMW, REA, and BFT. Furthermore, we found that GWAS signals for CW, LMW, and REA were enriched in turquoise module, and GWAS signals for CW was enriched in lightgreen module. Our study provides novel insights into the molecular mechanism underlying rumen development in cattle and highlights an integrative analysis for illustrating the genetic architecture of beef complex traits.

The rumen liquid metatranscriptome of post-weaned dairy calves differed by pre-weaning ruminal administration of differentially-enriched, rumen-derived inocula

Background

Targeted modification of the dairy calf ruminal microbiome has been attempted through rumen fluid inoculation to alter productive phenotypes later in life. However, sustainable effects of the early life interventions have not been well studied, particularly on the metabolically active rumen microbiota and its functions. This study investigated the sustained effects of adult-derived rumen fluid inoculations in pre-weaning dairy calves on the active ruminal microbiome of post-weaned dairy calves analyzed via RNA-sequencing.

Results

Two different adult-derived microbial inocula (bacterial- or protozoal-enriched rumen fluid; BE or PE, respectively) were administered in pre-weaned calves (3–6 weeks) followed by analyzing active rumen microbiome of post-weaned calves (9 weeks). The shared bacterial community at the genus level of 16S amplicon-seq and RNA-seq datasets was significantly different (P = 0.024), 21 out of 31 shared major bacterial genera differed in their relative abundance between the two analytic pipelines. No significant differences were found in any of the prokaryotic alpha- and beta-diversity measurements (P > 0.05), except the archaeota that differed for BE based on the Bray–Curtis dissimilarity matrix (P = 0.009). Even though the relative abundances of potentially transferred microbial and functional features from the inocula were minor, differentially abundant prokaryotic genera significantly correlated to various fermentation and animal measurements including butyrate proportion, body weight, and papillae length and counts. The overall microbial functions were affected quantitatively by BE and qualitatively by PE (P < 0.05), and this might be supported by the individual KEGG module and CAZymes profile differences. Exclusive networks between major active microbial (bacterial and archaeal genera) and functional features (KEGG modules) were determined which were differed by microbial inoculations.

Conclusions

This study demonstrated that actively transcribed microbial and functional features showed reliable connections with different fermentations and animal development responses through adult rumen fluid inoculations compared to our previous 16S amplicon sequencing results. Exclusive microbial and functional networks of the active rumen microbiome of dairy calves created by BE and PE might also be responsible for the different ruminal and animal characteristics. Further understanding of the other parts of the gastrointestinal tract (e.g., abomasum, omasum, and small intestine) using metatranscriptomics will be necessary to elucidate undetermined biological factors affected by microbial inoculations.

Supplementary Information

The online version contains supplementary material available at 10.1186/s42523-021-00142-z.

Gut microbiome colonization and development in neonatal ruminants: Strategies, prospects, and opportunities

Colonization and development of the gut microbiome is a crucial consideration for optimizing the health and performance of livestock animals. This is mainly attributed to the fact that dietary and management practices greatly influence the gut microbiota, subsequently leading to changes in nutrient utilization and immune response. A favorable microbiome can be implanted through dietary or management interventions of livestock animals, especially during early life. In this review, we explore all the possible factors (for example gestation, colostrum, and milk feeding, drinking water, starter feed, inoculation from healthy animals, prebiotics/probiotics, weaning time, essential oil and transgenesis), which can influence rumen microbiome colonization and development. We discuss the advantages and disadvantages of potential strategies used to manipulate gut development and microbial colonization to improve the production and health of newborn calves at an early age when they are most susceptible to enteric disease. Moreover, we provide insights into possible interventions and their potential effects on rumen development and microbiota establishment. Prospects of latest techniques like transgenesis and host genetics have also been discussed regarding their potential role in modulation of rumen microbiome and subsequent effects on gut development and performance in neonatal ruminants.

Characterizing the microbiota of wooden boards used for cheese ripening

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The phyla Actinobacteria, Firmicutes, and Proteobacteria dominated the microbiota of the boards.

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The boards displayed differences in both diversity and richness.

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We identified 288 total operational taxonomic units (OTU), with 7 OTU forming a core microbiota across all boards.

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The boards appeared to select for salt- and cold-tolerant bacteria.

Wooden boards are commonly used for aging artisan cheeses. Although considered critical to the development of desired flavors and aromas, knowledge about the microbial communities associated with these boards is limited. To begin to address this need, we performed a 16S ribosomal RNA analysis of the bacterial communities present on the surface and within 5 wooden boards used for cheese ripening that were obtained from 3 cheese-processing facilities. The 5 boards were dominated by bacteria in the phyla Actinobacteria, Firmicutes, and Proteobacteria and displayed differences in both diversity and richness. Analysis of these boards also identified significant board-to-board variation. A total of 288 operational taxonomic units were identified across all samples, with 7 operational taxonomic units forming a core microbiota across all boards. Taken together, these data reflect the cheese-ripening environment, which appears to select for salt- and cold-tolerant bacteria.

MAP, Johne's disease and the microbiome; current knowledge and future considerations

Mycobacterium avium subsp. paratuberculosis is the causative agent of Johne's disease in ruminants. As an infectious disease that causes reduced milk yields, effects fertility and, eventually, the loss of the animal, it is a huge financial burden for associated industries. Efforts to control MAP infection and Johne's disease are complicated due to difficulties of diagnosis in the early stages of infection and challenges relating to the specificity and sensitivity of current testing methods. The methods that are available contribute to widely used test and cull strategies, vaccination programmes also in place in some countries. Next generation sequencing technologies have opened up new avenues for the discovery of novel biomarkers for disease prediction within MAP genomes and within ruminant microbiomes. Controlling Johne's disease in herds can lead to improved animal health and welfare, in turn leading to increased productivity. With current climate change bills, such as the European Green Deal, targeting livestock production systems for more sustainable practices, managing animal health is now more important than ever before. This review provides an overview of the current knowledge on genomics and detection of MAP as it pertains to Johne's disease.

The Rumen Epithelial Microbiota: Possible Gatekeepers of the Rumen Epithelium and Its Potential Contributions to Epithelial Barrier Function and Animal Health and Performance

Ruminants are characterized by their unique mode of digesting cellulose-rich plant material in their forestomach, the rumen, which is densely populated by diverse microorganisms that are crucial for the breakdown of plant material. Among ruminal microbial communities, the microorganisms in the rumen fluid or attached to feed particles have attracted considerable research interest. However, comparatively less is known about the microorganisms attached to the rumen epithelium. Generally, the tissue lining the gastrointestinal tract serves the dual role of absorbing nutrients while preventing the infiltration of unwanted compounds and molecules as well as microorganisms. The rumen epithelium fulfills critical physiological functions for the ruminant host in energy absorption, metabolism, and nutrient transport. Essential host metabolites, such as short-chain fatty acids, ammonia, urea, and minerals, are exchanged across the rumen wall, thereby exposing the rumen epithelial microbiota to these nutrients. The integrity of the gastrointestinal barrier is central to animal health and productivity. The integrity of the rumen epithelium can be compromised by high ruminal microbial fermentation activity resulting in decreased rumen pH or by stress conditions such as heat stress or feed restriction. It is important to keep in mind that feeding strategies in cattle have changed over the last decades in favor of energy- and nutrient-rich concentrates instead of fiber-rich forages. These dietary shifts support high milk yields and growth rates but raised concerns regarding a possibly compromised rumen function. This paper will provide an overview of the composition of rumen epithelial microbial communities under physiological and disease conditions and will provide insights into the knowledge about the function and in situ activity of rumen epithelial microorganisms and their relevance for animal health and production. Given that an impaired intestinal barrier will negatively affect economically significant phenotypes, a better understanding of rumen wall microbiota is urgently needed.

The Effects of Artificially Dosed Adult Rumen Contents on Abomasum Transcriptome and Associated Microbial Community Structure in Calves

This study aimed to investigate the changes in abomasum transcriptome and the associated microbial community structure in young calves with artificially dosed, adult rumen contents. Eight young bull calves were randomly dosed with freshly extracted rumen contents from an adult cow (high efficiency (HE), n = 4), or sterilized rumen content (Con, n = 4). The dosing was administered within 3 days of birth, then at 2, 4, and 6 weeks following the initial dosing. Abomasum tissues were collected immediately after sacrifice at 8 weeks of age. Five genera (Tannerella, Desulfovibrio, Deinococcus, Leptotrichia, and Eubacterium; p < 0.05) showed significant difference in abundance between the treatments. A total of 975 differentially expressed genes were identified (p < 0.05, fold-change > 1.5, mean read-counts > 5). Pathway analysis indicated that up-regulated genes were involved in immune system process and defense response to virus, while the down-regulated genes involved in ion transport, ATP biosynthetic process, and mitochondrial electron transport. Positive correlation (r > 0.7, p < 0.05) was observed between TRPM4 gene and Desulfovibrio, which was significantly higher in the HE group. TRPM4 had a reported role in the immune system process. In conclusion, the dosing of adult rumen contents to calves can alter not only the composition of active microorganisms in the abomasum but also the molecular mechanisms in the abomasum tissue, including reduced protease secretion and decreased hydrochloric acid secretion.

Pre-weaning Ruminal Administration of Differentially-Enriched, Rumen-Derived Inocula Shaped Rumen Bacterial Communities and Co-occurrence Networks of Post-weaned Dairy Calves

Adult rumen fluid inoculations have been considered to facilitate the establishment of rumen microbiota of pre-weaned dairy calves. However, the sustained effects of the inoculations remain to be explored. In our previous study, 20 pre-weaned dairy calves had been dosed with four types of adult rumen inoculums [autoclaved rumen fluid, bacterial-enriched rumen fluid (BE), protozoal-enriched (PE), and BE + PE] weekly at 3 to 6 weeks of age. To verify the sustained effect of adult rumen inoculation, the rumen bacterial communities, fermentation characteristics, and animal performance measurements were measured after sacrifice from 20 post-weaned dairy bull calves (9 weeks of age). Ruminal pH tended to be lower in BE treated calves (n = 10). All PE treated calves had rumen ciliates (>104 cells per ml of rumen fluid). PE treated calves had greater VFA concentrations (P = 0.052), lower molar proportions of isobutyrate (P = 0.073), and butyrate (P = 0.019) compared to those of control calves. No treatment differences were found in all animal performance measurements. Both PE and BE inocula increased bacterial species richness, Faith's phylogenetic diversity, and Shannon's index in rumen liquid fractions. However, the relative proportion of those bacterial taxa possibly transferred from the donor's rumen was minor. Microbial network analysis showed different co-occurrence and mutually exclusive interactions between treatments of microbial inoculations. Collectively, adult rumen inoculations in pre-weaned dairy calves slightly altered the rumen bacteriome of post-weaned calves without changing fermentation and animal performance.

Changes in the host transcriptome and microbial metatranscriptome of the ileum of dairy calves subjected to artificial dosing of exogenous rumen contents

Development of a properly functioning gastrointestinal tract (GIT) at an early age is critical for the wellbeing and lifetime productivity of dairy cattle. The role of early microbial colonization on GIT development in neonatal cattle and the associated molecular changes remain largely unknown, particularly for the small intestine. In this study, we performed artificial dosing of exogenous rumen fluid during the early life of the calf, starting at birth through the weaning transition at 8 wk. Six calves were included in this study. At 8 wk of age, tissue from the ileum was collected and subjected to host transcriptome and microbial metatranscriptome analysis using RNA sequencing. A total of 333 genes showed significant differential expression (DE) (fold-change ≥2; adjusted P < 0.1, mean read-count ≥10) between the treated and control calves. Gene ontology analysis indicated that these DE genes are predominantly associated with processes related to the host immune response (P < 0.0001). Association analysis between the host gene expression and the microbial genus abundance identified 57 genes as having significant correlation with the ileum microbial genera (P < 0.0001). Of these, three genes showed significant association with six microbial genera: lysozyme 2 (LYZ2), fatty acid binding protein 5 (FABP5), and fucosyltransferase (FUT1). Specifically, the profound increase in expression of LYZ2 in treated calves suggests the initiation of antibacterial activity and innate response from the host. Despite the limitation of a relatively small sample size, this study sheds light on the potential impact of early introduction of microbes on the small intestine of calves.