The effect of a diet based on rice straw co-fermented with probiotics and enzymes versus a fresh corn Stover-based diet on the rumen bacterial community and metabolites of beef cattle

The Rumen Microbiome Composition of Raramuri Criollo and European Cattle in an Extensive System

Understanding the relationship between Raramuri Criollo cattle (RC) and their microbial ruminal ecosystem will help identify advantageous characteristics of adapted cattle as alternatives to achieve sustainable beef production systems. Our objective was to characterize the rumen microbiome of RC in comparison to Angus and Hereford breeds (European, E) and the cross between them (E × RC). Ruminal fluid was collected from 63 cows in their second productive cycle after grazing in the same paddock for 45 d, in the dry (n = 28) and rain (n = 35) seasons. DNA from ruminal fluid was isolated for 16s rRNA gene next-generation sequencing. The data were analyzed with QIIME2 and compared against the SILVA 16s rRNA database. Beta diversity was different (p < 0.05) between RC and E in both seasons. A microbial core was represented by the most abundant phyla. Planctomycetes and Spirochaetes represented above 1% in the rain season and below 1% in the dry one, whereas Euryarchaeota was below 1% and around 3%, respectively. LEfSe analysis identified differentiated (p < 0.05) key microbial groups that explain the differences between lineages at different taxonomic levels, reflecting the ability of the rumen ecosystem of RC cattle to adapt to hostile environmental conditions by having microbial groups specialized in the degradation of highly fibrous content.

Survey of the fecal microbiota of indigenous small ruminants living in different areas of Guizhou

Introduction

Gut microbiota are associated with the health and performance of ruminant species, and they are affected by altitude, host genetics, and sex. However, there has been little research on comparing the fecal microbiota of indigenous small ruminants such as sheep and goats in Guizhou province, China. In the present study, we revealed the effect of altitude, genetics, and sex on fecal microbiota profiles and enterotypes in indigenous small ruminants of Guizhou province, China.

Methods

Fecal samples were collected from Hei and Qianbei Ma goats and Weining sheep in the Chinese province of Guizhou. 16S rRNA gene sequencing targeting the V3-V4 region was performed using the Illumina MiSeq platform. Sequences were processed using QIIME2, and the qualified sequences were processed using the plugin DADA2 to generate amplicon sequence variants (ASVs). The statistical analysis was performed using R studio.

Results

The fecal microbial profile was found to vary by herd (influenced by genetics/altitude) and sex. All samples were categorized into two enterotypes. The first enterotype is dominated by UCG-005, and the second enterotype is dominated by the Christensenellaceae_R-7_group, which may be highly driven by the host's genetics (breed). The predicted functional profiles of the fecal microbiota were also assigned to two clusters that corresponded exactly to the enterotypes. Cluster 1 of the functional profiling was characterized by biosynthesis pathways, and cluster 2 was characterized by energy metabolism pathways.

Discussion

Our findings may provide new insights into the fecal microbial community and enterotypes in small ruminants by herds, offering clues for understanding the mechanisms by which the fecal microbiota contribute to divergent host phenotypes in indigenous small ruminants in Guizhou.

Diversity and host interaction of the gut microbiota in specific pathogen-free pigs

Pigs are widely used as animal models in various studies related to humans. The interaction between the gut microbiota and the host has significant effects on the host's health and disease status. However, although there have been many studies investigating the pig gut microbiota, the findings have been inconsistent due to variations in rearing conditions. Interactions between the gut microbiota and host have not been fully explored in pigs. Specific pathogen-free (SPF) pigs are ideal non-primate large animals to study the interactions between the gut microbiota and the host. In this study, we performed high-throughput sequencing analysis of the gut microbiota and the gut tissue transcriptome of six SPF pigs to provide a systematic understanding of the composition, function, and spatial distribution of gut microbiota in SPF pigs. We identified significant differences in microbial diversity and functionality among different gastrointestinal tract sites. Metagenomics data analysis revealed significant differences in alpha diversity and beta diversity of microbiota in different gastrointestinal sites of SPF pigs. Additionally, transcriptomic data indicated significant differences in gene expression as well as KEGG and GO functional enrichment between the small intestine and large intestine. Furthermore, by combining microbial metagenomics and host transcriptomics analyses, specific correlations were found between gut microbiota and host genes. These included a negative correlation between the TCN1 gene and Prevotella dentalis, possibly related to bacterial metabolic pathways involving vitamin B12, and a positive correlation between the BDH1 gene and Roseburia hominis, possibly because both are involved in fatty acid metabolism. These findings lay the groundwork for further exploration of the co-evolution between the microbiota and the host, specifically in relation to nutrition, metabolism, and immunity. In conclusion, we have elucidated the diversity of the gut microbiota in SPF pigs and conducted a detailed investigation into the interactions between the gut microbiota and host gene expression. These results contribute to our understanding of the intricate dynamics between the gut microbiota and the host, offering important references for advancements in life science research, bioproduct production, and sustainable development in animal husbandry.

Effects of replacing hybrid giant napier with sugarcane bagasse and fermented sugarcane bagasse on growth performance, nutrient digestibility, rumen fermentation characteristics, and rumen microorganisms of Simmental crossbred cattle

This study investigated the effects of replacing hybrid giant napiers with sugarcane bagasse and fermented sugarcane bagasse on the growth performance, apparent nutrient digestibility, rumen fermentation characteristics, and rumen microorganisms of Simmental crossbred cattle. Twenty-one Simmental crossbred cattle with similar initial body weight (363.42 ± 8.67 kg) were randomly divided into three groups: Group CON (20% hybrid giant napier +45% distillers grains +35% concentrate mixture), Group SB (20% sugarcane bagasse +45% distillers grains +35% concentrate mixture), and Group FSB (20% fermented sugarcane bagasse +45% distillers grains +35% concentrate mixture). The average daily weight gain in the SB group was lower than in the CON group, no significant difference was found between the CON and FSB groups. The feed conversion ratio of the CON and FSB groups was lower compared to the SB group. The apparent digestibility of neutral detergent fiber and acid detergent fiber in the SB group was lower than in the CON group, no significant difference was found between the CON and FSB groups. The levels of NH3-N, microbial protein, acetate, propionate, butyrate, isobutyrate, and total volatile fatty acids were higher in the CON and FSB groups than in the SB group, no significant difference was found between the CON and FSB groups. The relative abundances of Christensenellaceae_R-7_group, Rikenellaceae_RC9_gut_group, Prevotellaceae_UCG-003, Saccharofermentans, and Eubacteriumcoprostanoligenes_group were lower in the CON and FSB groups compared to the SB group. The relative abundance of Succiniclasticum was highest in the FSB group, followed by the CON group and then the SB group. Correlation analysis showed that the relative abundance of Succiniclasticum was positively correlated with propionate and NH3-N content, while the relative abundance of Rikenellaceae_RC9_gut_group was inversely correlated with NH3-N content. Gene function prediction indicated that fermented sugarcane bagasse promoted rumen microbial amino acid metabolism. In conclusion, replacing hybrid giant napiers with 20% sugarcane bagasse negatively affected the growth performance of Simmental crossbred cattle, while the addition of 20% fermented sugarcane bagasse had no adverse effects on growth performance and rumen fermentation characteristics, and did not alter the abundance of the rumen core flora in Simmental crossbred cattle.

Comparative analysis of rumen metagenome, metatranscriptome, fermentation and methane yield in cattle and buffaloes fed on the same diet

A study to compare the rumen microbial community composition, functional potential of the microbiota, methane (CH4) yield, and rumen fermentation was conducted in adult male cattle and buffaloes fed on the same diet. A total of 41 phyla, 169 orders, 374 families, and 1,376 microbial genera were identified in the study. Bacteroidetes and Firmicutes were the two most dominant bacterial phyla in both cattle and buffaloes. However, there was no difference in the abundance of Bacteroidetes and Firmicutes in the rumen metagenome of cattle and buffaloes. Based on the abundance, the Proteobacteria was the 3rd largest phylum in the metagenome, constituting 18-20% in both host species. Euryarchaeota was the most abundant phylum of the methanogens, whereas Methanobacteriales and Methanobrevibacter were the most abundant orders and genera in both species. The methanogen abundances were not different between the two host species. Like the metagenome, the difference between the compositional and functional abundances (metagenome vs. metatranscriptome) of the Bacteroidetes and Firmicutes was not significant, whereas the proteobacteria were functionally less active than their metagenomic composition. Contrary to the metagenome, the Euryarchaeota was the 3rd most functional phylum in the rumen and constituted ~15% of the metatranscriptome. Methanobacteriales were the most functional methanogens, accounting for more than 2/3rd of the total archaeal functionality. These results indicated that the methanogens from Euryarchaeota were functionally more active as compared to their compositional abundance. The CH4 yield (g/kg DMI), CH4 emission (g/kg DDM), dry matter (DM) intake, and rumen fermentation did not vary between the two host species. Overall, the study established a substantial difference between the compositional abundances and metabolic functionality of the rumen microbiota; however, feeding cattle and buffaloes on the same diet resulted in similar microbiota composition, metabolic functionality, and CH4 yield. Further studies are warranted to investigate the effect of different diets and environments on the composition and metabolic functionality of the rumen microbiota.

In vitro ruminal fermentation and cow-to-mouse fecal transplantations verify the inter-relationship of microbiome and metabolome biomarkers: potential to promote health in dairy cows

Introduction

There are differences in the gut microbiome and metabolome when the host undergoes different physical or pathological conditions. However, the inter-relationship of microbiome and metabolome biomarkers to potentially promote the health of dairy cows needs to be studied. Further, the development of next-generation probiotics for dairy cattle health promotion has not been demonstrated.

Objective

In the present study, we identified the microbiome and metabolome biomarkers associated with healthy cows.

Methods

We analyzed the relationships of the ruminal microorganism profile and metabolites between healthy and mastitis lactating dairy cows. The roles of bacterial biomarker were further verified by in vitro fermentation and cow-to-mouse fecal microbiota transplantation (FMT).

Results

Two species, Ruminococcus flavefaciens and Bifidobacterium longum subsp. longum, and six rumen metabolites were positively correlated with healthy cows by Spearman's correlation analysis. Through in vitro ruminal fermentation, inoculating R. flavefaciens and B. longum subsp. longum showed the upregulation of the levels of putrescine, xanthurenic acid, and pyridoxal in the mastitis ruminal fluid, which confirmed the inter-relationships between these microbiota and metabolites associated with healthy cows. Further, we verified the role of R. flavefaciens and B. longum subsp. longum in promoting health by FMT. The administration of R. flavefaciens and B. longum subsp. longum reduced the death rate and recovered the bodyweight loss of germ-free mice caused by FMT mastitis feces.

Discussion

We provided evidence that the bacterial biomarkers alter downstream metabolites. This could indirectly indicate that the two bacterial biomarkers have the potential to be used as next-generation probiotics for dairy cattle, although it needs more evidence to support our hypothesis. Two species, R. flavefaciens and B. longum subsp. longum, with three metabolites, putrescine, xanthurenic acid, and pyridoxal, identified in the ruminal fluid, may point to a new health-promoting and disease-preventing approach for dairy cattle.

Effects of Lactic Acid Bacteria-Inoculated Corn Silage on Bacterial Communities and Metabolites of Digestive Tract of Sheep

Silage is widely used as ruminant feed all over the world. Lactic acid bacteria inoculants are commonly applied in silage production to improve preservation efficiency. To investigate the effects of lactic acid bacteria-inoculated silage on the bacterial communities and metabolites of the digestive tract, twenty-four local hybrid rams (a hybrid of Small Tail Han sheep and Mongolian sheep with an average initial BW 27.8 ± 3.05 kg) were randomly divided into four groups fed with corn stalk (S), corn stalk silage, corn stalk silage treated with Lentilactobacillusplantarum (P), or corn stalk silage treated with L. buchneri (B). The results showed that compared with the control and B groups, the inoculant with P significantly increased silage dry matter (DM) content, while the pH value was significantly higher than that in group B, and the aerobic stability was significantly lower than that in group B. Firmicutes and Bacteroidetes were the two dominant phyla of digestive tract microbiota in sheep. Compared with corn stalk, sheep fed with corn stalk silage showed a higher relative abundance of Prevotella. P-treated silage decreased the relative abundance of Firmicutes at the phylum level in rumen fluid. Silage treated with P or B increased the relative abundance of Prevotella, Ruminococcus, and Fibrobacter at the genus level in the rumen. A total of 498 differential metabolites in the rumen were detected when comparing the corn stalk and corn stalk silage groups. A total of 257 and 141 differential metabolites were detected when comparing the untreated silage and silages treated with P and B, respectively. These metabolites in the sheep rumen were correlated with bacterial communities, especially Butyrivibrio, Fibrobacter, and Prevotella. In conclusion, the addition of P and B during ensiling could change the fermentation and metabolites in the rumen by influencing the bacterial community. The change induced by these inoculants might be beneficial for animals’ performance and the health of ruminants.

Effects of Bovine Pichia kudriavzevii T7, Candida glabrata B14, and Lactobacillus plantarum Y9 on Milk Production, Quality and Digestive Tract Microbiome in Dairy Cows

Microbial administration has been used successfully to improve host health. However, the positive effects of endogenous microbials are still underexplored. This study investigated the effects of bovine Lactic acid bacteria and yeast on the milk production, quality and digestive tract microbiome of dairy cows. Lactobacillus plantarum Y9, Pichia kudriavzevii T7 and Candida glabrata B14 isolated from high-yielding dairy cows were selected to feed low-yielding Holstein cows. Pichia kudriavzevii T7 could significantly increase milk yield, meanwhile, Pichia kudriavzevii T7 and Candida glabrata B14 could obviously reduce the number of somatic cell counts (SCC). However, slight differences were found in milk fat, protein, lactose and SNF (solids not fat) percentage. High throughput sequencing showed that the dominant bacteria were Prevotella and Ruminococcaceae in rumen and feces, respectively, and the dominant fungi were Penicillium, Aspergillus and Trichoderma in both samples, before and after feeding the microbial addition. Nonetheless, microbial addition changed the abundance and structure of the microbiome in the digestive tract. Our data showed bovine yeast and LAB were beneficial for improving performance and regulating the microbial structure of dairy cows. This study was expected to enrich the knowledge of the digestive tract microbiome in dairy cows and provide a feasible strategy for the further utilization of bovine microorganisms.

Construction of a fungal consortium for effective degradation of rice straw lignin and potential application in bio-pulping

To improve the lignin degradation efficiency, we established a co-culture consortium (LDFC) consisting of Trametes hirsuta BYL-3, Trametes versicolor BYL-7 and Trametes hirsuta BYL-8. The testing results showed that the constructed consortium showed improved the lignin degradation rate by fungi. The optimal cultivation conditions were mixture at 1:1:1 vol ratio of each fungus, 7% (w/v) of inoculum amount, culture temperature at 26 °C, pH was 6.9 and 10 days of culturing time. Under these conditions, the degradation rate of lignin was 39.7%, which was 9.3% higher than those before optimization (30.4%). Using rice straw for treatment by LDFC to papermaking, the paper tensile strength was 8 N, and the ring pressure index was 2.46 N·m/g, which meets the standards for the production of corrugated paper for packaging. These results indicate that LDFC has potential application value to convert rice straw resources for bio-pulping to make papers.

Distribution patterns of functional microbial community in anaerobic digesters under different operational circumstances: A review

Anaerobic digestion (AD) processes are promising to effectively recover resources from organic wastes or wastewater. As a microbial-driven process, the functional anaerobic species played critical roles in AD. However, the lack of effective understanding of the correlations of varying microbial communities with different operational factors hinders the microbial regulation to improve the AD performance. In this paper, the main anaerobic functional microorganisms involved in different stages of AD processes were first demonstrated. Then, the response of anaerobic microbial community to different operating parameters, exogenous interfering substances and digestion substrates, as well as the digestion efficiency, were discussed. Finally, the research gaps and future directions on the understanding of functional microorganisms in AD were proposed. This review provides insightful knowledge of distribution patterns of functional microbial community in anaerobic digesters, and gives critical guidance to regulate and enrich specific functional microorganisms to accumulate certain AD products.

Genome-Wide Identification of Reference Genes for Reverse-Transcription Quantitative PCR in Goat Rumen

Simple Summary

The rumen plays an essential role as a digestive organ and serves as the primary site of energy substrate absorption for the productive ruminants. Understanding gene expression profiles is necessary to explore the intrinsic regulatory mechanisms of rumen development in goats. The selection of suitable reference genes (RGs) was the primary assay before the real-time quantitative PCR (RT-qPCR). We identified sixteen genome-wide candidate RGs for normalization of gene expression assessments in goat rumen tissues. We demonstrate that the RGs selected (RPS4X and RPS6) were more stably expressed than the commonly used HKGs (ACTB and GAPDH) in goat rumen tissues, suggesting that the ribosomal protein gene family may be another source for the RG pool.

Abstract

As the largest chamber of the ruminant stomach, the rumen not only serves as the principal absorptive surface and nutrient transport pathway from the lumen into the animal, but also plays an important short-chain fatty acid (SCFA) metabolic role in addition to protective functions. Accurate characterization of the gene expression profiles of genes of interest is essential to the exploration of the intrinsic regulatory mechanisms of rumen development in goats. Thus, the selection of suitable reference genes (RGs) is an important prerequisite for real-time quantitative PCR (RT-qPCR). In the present study, 16 candidate RGs were identified from our previous transcriptome sequencing of caprine rumen tissues. The quantitative expressions of the candidate RGs were measured using the RT-qPCR method, and the expression stability of the RGs was assessed using the geNorm, NormFinder, and BestKeeper programs. GeNorm analysis showed that the M values were less than 0.5 for all the RGs except GAPT4, indicating that they were stably expressed in the rumen tissues throughout development. RPS4X and RPS6 were the two most stable RGs. Furthermore, the expressions of two randomly selected target genes (IGF1 and TOP2A), normalized by the selected most stable RGs (RPS4X and RPS6), were consistent with the results of RNA sequencing, while the use of GAPDH and ACTB as RGs resulted in altered profiles. Overall, RPS4X and RPS6 showed the highest expression stability and the lowest coefficients of variation, and could be used as the optimal reference combination for quantifying gene expression in rumen tissues via RT-qPCR analysis.

Analysis of Cow-Calf Microbiome Transfer Routes and Microbiome Diversity in the Newborn Holstein Dairy Calf Hindgut

Hindgut microorganisms in newborn calves play an important role in the development of immunity and metabolism, and optimization of performance. However, knowledge of the extent to which microbiome colonization of the calf intestine is dependent on maternal characteristics is limited. In this study, placenta, umbilical cord, amniotic fluid, colostrum, cow feces, and calf meconium samples were collected from 6 Holstein cow-calf pairs. Microbial composition was analyzed by 16S rRNA gene high-throughput sequencing, and maternal transfer characteristics assessed using SourceTracker based on Gibbs sampling to fit the joint distribution using the mean proportions of each sample with meconium as the "sink" and other sample types as different "sources." Alpha and beta diversity analyses revealed sample type-specific microbiome features: microbial composition of the placenta, umbilical cord, amniotic fluid, colostrum, and calf feces were similar, but differed from cow feces (p < 0.05). Compared with profiles of meconium vs. placenta, meconium vs. umbilical cord, and meconium vs. colostrum, differences between the meconium and amniotic fluid were most obvious. SourceTracker analysis revealed that 23.8 ± 2.21% of the meconium OTUs matched those of umbilical cord samples, followed by the meconium-placenta pair (15.57 ± 2.2%), meconium-colostrum pair (14.4 ± 1.9%), and meconium-amniotic fluid pair (11.2 ± 1.7%). The matching ratio between meconium and cow feces was the smallest (10.5 ± 1%). Overall, our data indicated that the composition of the meconium microflora was similar compared with multiple maternal sites including umbilical cord, placenta, colostrum, and amniotic fluid. The umbilical cord microflora seemed to contribute the most to colonization of the fecal microflora of calves. Bacteria with digestive functions such as cellulose decomposition and rumen fermentation were mainly transmitted during the maternal transfer process.

The Impact of Host Genotype, Intestinal Sites and Probiotics Supplementation on the Gut Microbiota Composition and Diversity in Sheep

Three sampling strategies with a 16s rRNA high-throughput sequencing and gene expression assay (by RT-PCR) were designed, to better understand the host and probiotics effect on gut microbiota in sheep. Sampling: (1) colon contents and back-fat tissues from small-tailed Han sheep (SHS), big-tailed Hulun Buir sheep (BHBS), and short-tailed Steppe sheep (SHBS) (n = 12, 14, 12); (2) jejunum, cecum and colon contents, and feces from Tan sheep (TS, n = 6); (3) feces from TS at 4 time points (nonfeeding, 30 and 60 feeding days, and stop feeding 30 days) with probiotics supplementation (n = 7). The results indicated SHS had the highest Firmicutes abundance, the thinnest back-fat, and the lowest expression of C/EBPβ, C/EBPδ, ATGL, CFD, and SREBP1. Some bacteria orders and families could be potential biomarkers for sheep breeds with a distinct distribution of bacterial abundance, implying the host genotype is predominant in shaping unique microbiota under a shared environment. The microbiota diversity and Bifidobacterial populations significantly changed after 60 days of feeding but restored to its initial state, with mostly colonies, after 30 days ceased. The microbiota composition was greatly different between the small and large intestines, but somewhat different between the large intestine and feces; feces may be reliable for studying large intestinal microbiota in ruminants.

Effect of additives and filling methods on whole plant corn silage quality, fermentation characteristics and in situ digestibility

OBJECTIVE

This project aimed to evaluate the effects of both different additives and filling methods on nutritive quality, fermentation profile, and in situ digestibility of whole plant corn silage.

METHODS

Whole plant corn forage harvested at 26.72% dry matter (DM) was chopped and treated with two filling methods, i) fill silos at one time (F1), ii) fill silos at three times (F3), packing samples into one/three silo capacity at the first day, another one/three capacity at the second day, then one/three at the third day, three replicates. For each replicate, samples were treated with three additives, i) control (CTRL, no additive), ii) Sila-Max (MAX, Ralco Nutrition Inc., Marshall, MN, USA), and iii) Sila-Mix (MIX, Ralco Nutrition Inc., USA). With three replicates of each secondary treatment, there were nine silos, 54 silos in total. Each silo had a packing density of 137.61 kg of DM/m3. All silos were weighed and stored in lab at ambient temperature.

RESULTS

After 60 d of ensiling, all items showed good silage fermentation under MAX filled one time or three times (p<0.01). Higher silage quality for all additives was obtained at filling one time than that filled three times (p<0.01). The highest DM and lowest DM loss rate (DMLR) occurred to MAX treatment at two filling methods (p<0.01); Digestibility of acid detergent fiber, neutral detergent fiber (NDF), and curde protein had the same results as silage quality (p<0.01). Yield of digestible DM and digestible NDF also showed higher value under MAX especially for filling one time (p<0.05).

CONCLUSION

All corn silages showed good fermentation attributes (pH<4.0). The forage filled one time had higher silage quality than that filled three times (p<0.01). MAX with homofermentative lactic acid bacteria enhanced the lactic acid fermentation, silage quality and nutrient digestibility, and so improved the digestible nutrient yield.

Effect of Lactic Acid Bacteria on the Nutritive Value and In Vitro Ruminal Digestibility of Maize and Rice Straw Silage

A study was conducted to determine the effects of lactic acid bacteria (LAB) on nutritive value and in vitro rumen digestibility of maize and rice straw silages. Two identical experiments were carried out for each of the two silages. A total of five treatments were used for each experiment: (1) negative control (NC); (2) positive control (PC); (3) Lactobacillus plantarum (LPL); (4) L. paracasei (LPA); and (5) L. acidophilus (LA). Each treatment was then divided into four ensiling periods: 3, 7, 20, and 40 days with three replications. The LPL treatment had significantly higher dry matter (DM), lower ammonia-N, and a lower number of fungi on maize silage after 40 days (p < 0.05). On the other hand, the LA treatment increased DM and CP content, reduced NDF and ADF contents compared to NC, and also produced more lactic acid compared to the other LAB-treated rice straw silages. Results of the in vitro rumen fermentation of maize silages showed no significant differences in DMD after LAB inoculation. However, higher DMD and ruminal ammonia-N were shown by rice straw ensiled with L. acidophilus. In conclusion, silage additives, which could improve the ensiling process of maize and rice straw, appeared to be different and substrate specific.