Assessing the relationship between the rumen microbiota and feed efficiency in Nellore steers.

BACKGROUND: Ruminants rely upon a complex community of microbes in their rumen to convert host-indigestible feed into nutrients. However, little is known about the association between the rumen microbiota and feed efficiency traits in Nellore (Bos indicus) cattle, a breed of major economic importance to the global beef market. Here, we compare the composition of the bacterial, archaeal and fungal communities in the rumen of Nellore steers with high and low feed efficiency (FE) phenotypes, as measured by residual feed intake (RFI). RESULTS: The Firmicutes to Bacteroidetes ratio was significantly higher (P < 0.05) in positive-RFI steers (p-RFI, low feed efficiency) than in negative-RFI (n-RFI, high feed efficiency) steers. The differences in bacterial composition from steers with high and low FE were mainly associated with members of the families Lachnospiraceae, Ruminococcaceae and Christensenellaceae, as well as the genus Prevotella. Archaeal community richness was lower (P < 0.05) in p-RFI than in n-RFI steers and the genus Methanobrevibacter was either increased or exclusive of p-RFI steers. The fungal genus Buwchfawromyces was more abundant in the rumen solid fraction of n-RFI steers (P < 0.05) and a highly abundant OTU belonging to the genus Piromyces was also increased in the rumen microbiota of high-efficiency steers. However, analysis of rumen fermentation variables and functional predictions indicated similar metabolic outputs for the microbiota of distinct FE groups. CONCLUSIONS: Our results demonstrate that differences in the ruminal microbiota of high and low FE Nellore steers comprise specific taxa from the bacterial, archaeal and fungal communities. Biomarker OTUs belonging to the genus Piromyces were identified in animals showing high feed efficiency, whereas among archaea, Methanobrevibacter was associated with steers classified as p-RFI. The identification of specific RFI-associated microorganisms in Nellore steers could guide further studies targeting the isolation and functional characterization of rumen microbes potentially important for the energy-harvesting efficiency of ruminants.

The Bacterial and Fungal Microbiota of Nelore Steers Is Dynamic Across the Gastrointestinal Tract and Its Fecal-Associated Microbiota Is Correlated to Feed Efficiency.

The ruminant gastrointestinal tract (GIT) microbiome plays a major role in the health, physiology and production traits of the host. In this work, we characterized the bacterial and fungal microbiota of the rumen, small intestine (SI), cecum and feces of 27 Nelore steers using next-generation sequencing and evaluated biochemical parameters within the GIT segments. We found that only the bacterial microbiota clustered according to each GIT segment. Bacterial diversity and richness as well as volatile fatty acid concentration was lowest in the SI. Taxonomic grouping of bacterial operational taxonomic units (OTUs) revealed that Lachnospiraceae (24.61 ± SD 6.58%) and Ruminococcaceae (20.87 ± SD 4.22%) were the two most abundant taxa across the GIT. For the fungi, the family Neocallismastigaceae dominated in all GIT segments, with the genus Orpinomyces being the most abundant. Twenty-eight bacterial and six fungal OTUs were shared across all GIT segments in at least 50% of the steers. We also evaluated if the fecal-associated microbiota of steers showing negative and positive residual feed intake (n-RFI and p-RFI, respectively) was associated with their feed efficiency phenotype. Diversity indices for both bacterial and fungal fecal microbiota did not vary between the two feed efficiency groups. Differences in the fecal bacterial composition between high and low feed efficiency steers were primarily assigned to OTUs belonging to the families Lachnospiraceae and Ruminococcaceae and to the genus Prevotella. The fungal OTUs shared across the GIT did not vary between feed efficiency groups, but 7 and 3 OTUs were found only in steers with positive and negative RFI, respectively. These results provide further insights into the composition of the Nelore GIT microbiota, which could have implications for improving animal health and productivity. Our findings also reveal differences in fecal-associated bacterial OTUs between steers from different feed efficiency groups, suggesting that fecal sampling may represent a non-invasive strategy to link the bovine microbiota with productivity phenotypes.

Sorghum silage supplemented with crambe meal improves dry matter intake and milk production in crossbred Holstein cows.

We studied the feed intake and milk production of Holstein × Zebu crossbred cows fed sorghum silage diets and concentrates, with and without the addition of crambe meal. Using a change-over design for a total of 120 days, eight cows were fed two diets (concentrates + silages with and without crambe meal) in four 30-day periods, with four replications (animals). The crambe meal diet increased (P < 0.05) the dry matter intake (DMI), crude protein intake (CPI), and non-fibrous carbohydrates intake (NFCI) as well as milk production (4.3%). No difference was noted (P > 0.05) for the milk composition between the treatments. Crambe meal as an additive in sorghum silage (100 g/kg in natural matter) showed a great potential for introduction in dairy farming as it substantially increases CP intake, does not reduce food intake, raises animal productivity, and does not affect milk composition.

Acyl homoserine lactone changes the abundance of proteins and the levels of organic acids associated with stationary phase in Salmonella Enteritidis.

Quorum sensing (QS) is cell-cell communication mechanism mediated by signaling molecules known as autoinducers (AIs) that lead to differential gene expression. Salmonella is unable to synthesize the AI-1 acyl homoserine lactone (AHL), but is able to recognize AHLs produced by other microorganisms through SdiA protein. Our study aimed to evaluate the influence of AI-1 on the abundance of proteins and the levels of organic acids of Salmonella Enteritidis. The presence of N-dodecyl-homoserine lactone (C12-HSL) did not interfere on the growth or the total amount of extracted proteins of Salmonella. However, the abundance of the proteins PheT, HtpG, PtsI, Adi, TalB, PmgI (or GpmI), Eno, and PykF enhanced while the abundance of the proteins RplB, RplE, RpsB, Tsf, OmpA, OmpC, OmpD, and GapA decreased when Salmonella Enteritidis was anaerobically cultivated in the presence of C12-HSL. Additionally, the bacterium produced less succinic, lactic, and acetic acids in the presence of C12-HSL. However, the concentration of extracellular formic acid reached 20.46 mM after 24 h and was not detected when the growth was in the absence of AI-1. Considering the cultivation period for protein extraction, their abundance, process and function, as well as the levels of organic acids, we observed in cells cultivated in presence of C12-HSL a correlation with what is described in the literature as entry into the stationary phase of growth, mainly related to nitrogen and amino acid starvation and acid stress. Further studies are needed in order to determine the specific role of the differentially abundant proteins and extracellular organic acids secreted by Salmonella in the presence of quorum sensing signaling molecules.

Tithonia diversifolia as a Supplementary Feed for Dairy Cows.

The objective of this study was to examine the effects of Tithonia diversifolia as a supplementary forage on dairy cow performance and methane production. Nine lactating Holstein × Zebu dairy cows (519 ± 53.3 kg of body weight and 66 ± 13.3 d in milk) were paired by milk yield (21.3 ± 2.34 kg/d) and body weight and randomly assigned to three dietary treatments in a Latin square design with 21-d experimental periods (14 d for diet adaptation and 7 d for measurements and sample collection). The dietary treatments included the control diet consisting of fresh sugar cane plus concentrate (44:56, % of diet DM), and two treatment diets containing different levels of fresh T. diversifolia (6.5 and 15.4%, DM basis) which partially replaced both sugarcane and concentrates. Methane production was measured using the sulphur hexafluoride (SF6) technique from d 16 to d 21 of each experimental period. Analysis of the gas samples was performed by gas chromatography. The inclusion of T. diversifolia at 15.4% DM had no effects on DM intake, milk production, nitrogen balance or methane production. There was no effect on the concentrations of total saturated fatty acids (SFA), monounsaturated fatty acids (MUFA), and polyunsaturated fatty acids (PUFA) in milk fat (P ≥ 0.28), though individual milk fatty acids were affected. Serum concentrations of glucose, urea nitrogen (BUN), triglycerides, ß-hydroxybutyrate (BHBA), and cholesterol were unaffected by the dietary treatments (P ≥ 0.13). There was a time (2 and 6 h post-feeding) and dietary treatment effect (P < 0.01) on the acetate to propionate ratio in the rumen. A denaturing gradient gel electrophoresis analysis of the archaeal community showed distinct clustering of the archaea populations for control and treatment diets. Taken together, our results indicate the potential of T. diversifolia as a supplementary forage for dairy cattle in the tropics.

Diversity of endophytic fungi in Glycine max.

Endophytic fungi are microorganisms that live within plant tissues without causing disease during part of their life cycle. With the isolation and identification of these fungi, new species are being discovered, and ecological relationships with their hosts have also been studied. In Glycine max, limited studies have investigated the isolation and distribution of endophytic fungi throughout leaves and roots. The distribution of these fungi in various plant organs differs in diversity and abundance, even when analyzed using molecular techniques that can evaluate fungal communities in different parts of the plants, such as denaturing gradient gel electrophoresis (DGGE). Our results show there is greater species richness of culturable endophytic filamentous fungi in the leaves G. max as compared to roots. Additionally, the leaves had high values for diversity indices, i.e. Simpsons, Shannon and Equitability. Conversely, dominance index was higher in roots as compared to leaves. The fungi Ampelomyces sp., Cladosporium cladosporioides, Colletotrichum gloeosporioides, Diaporthe helianthi, Guignardia mangiferae and Phoma sp. were more frequently isolated from the leaves, whereas the fungi Fusarium oxysporum, Fusarium solani and Fusarium sp. were prevalent in the roots. However, by evaluating the two communities by DGGE, we concluded that the species richness was higher in the roots than in the leaves. UPGMA analysis showed consistent clustering of isolates; however, the fungus Leptospora rubella, which belongs to the order Dothideales, was grouped among species of the order Pleosporales. The presence of endophytic Fusarium species in G. max roots is unsurprising, since Fusarium spp. isolates have been previously described as endophyte in other reports. However, it remains to be determined whether the G. max Fusarium endophytes are latent pathogens or non-pathogenic forms that benefit the plant. This study provides a broader knowledge of the distribution of the fungal community in G. max leaves and roots, and identifies the genetic relationships among the isolated species.

Biochemical and genetic diversity of carbohydrate-fermenting and obligate amino acid-fermenting hyper-ammonia-producing bacteria from Nellore steers fed tropical forages and supplemented with casein.

BACKGROUND: Dietary protein plays a major role in ruminant nutrition, and protein supplementation is a widespread practice among farmers in the tropics. Ruminal bacteria are the main agents of dietary protein and amino acid degradation, yet few studies have focused on the isolation and characterization of hyper-ammonia-producing bacteria in animals fed tropical diets or supplemented with rumen-degradable proteins. This work investigated the bacterial community diversity of the rumen of Nellore steers fed tropical forages, with or without casein supplementation. We also isolated and characterized ruminal bacteria showing high levels of ammonia production. RESULTS: Polymerase chain reaction-denaturing gradient gel electrophoresis analysis indicated no differences in the ruminal bacterial community composition between the control and supplemented animals. Amino acid-fermenting bacteria (n = 250) were isolated from crossbred Nellore steers fed Tifton 85 (Cynodon sp.) using trypticase as the sole carbon and organic nitrogen source in the enrichment and isolation media. The deamination rates in isolates obtained from steers supplemented with casein showed a higher incidence of deamination rates >350 nmol NH3 mg protein(-1) min(-1) (P < 0.05), whereas isolates obtained from steers without supplementation showed deamination rates <200 nmol NH3 mg protein(-1) min(-1). Although most isolates (84%) could ferment carbohydrates, none could hydrolyze proteins or use urea to sustain growth. All isolates were sensitive to lasalocid and monensin (1 µmol l(-1)), and similarity analysis of the 16S rRNA sequences indicated a predominance of bacteria from the order Clostridiales, with variable homology (73-99%) to known bacterial species. CONCLUSIONS: These results expand what is known about the biochemical and genetic diversity of hyper-ammonia-producing bacteria, and emphasize the role of carbohydrate-fermenting bacteria in ammonia production in the rumen.