Effects of antibacterial peptides on rumen fermentation function and rumen microorganisms in goats

Novel primers to identify a wider diversity of butyrate-producing bacteria

Butyrate-producing bacteria are a functionally important part of the intestinal tract flora, and the resulting butyric acid is essential for maintaining host intestinal health, regulating the immune system, and influencing energy metabolism. However, butyrate-producing bacteria have not been defined as a coherent phylogenetic group. They are primarily identified using primers for key genes in the butyrate-producing pathway, and their use has been limited to the Bacillota and Bacteroidetes phyla. To overcome this limitation, we developed functional gene primers able to identify butyrate-producing bacteria through the butyrate kinase gene, which encodes the enzyme involved in the final step of the butyrate-producing pathway. Genomes extracted from human and rat feces were used to amplify the target genes through PCR. The obtained sequences were analyzed using BLASTX to construct a developmental tree using the MEGA software. The newly designed butyrate kinase gene primers allowed to recognize a wider diversity of butyrate-producing bacteria than that recognized using currently available primers. Specifically, butyrate-producing bacteria from the Synergistota and Spirochaetota phyla were identified for the first time using these primers. Thus, the developed primers provide a more accurate method for researchers and doctors to identify potential butyrate-producing bacteria and deepen our understanding of butyrate-producing bacterial species.

Astragalus additive in feed improved serum immune function, rumen fermentation and the microbiota structure of early-weaned lambs

AIM

The purpose of this study was to determine the mechanism of Astragalus activity on the immune function, rumen microbiota structure, and rumen fermentation of early-weaned lambs.

METHODS AND RESULTS

Thirty healthy early-weaned lambs with similar body weights (17.42 ± 2.02 kg) were selected for the feeding experiment. The control group (KB) was fed a basal diet, and the Astragalus group (HQ) was fed 0.3% Astragalus additive on the basis of a basic diet. The formal trial period was 60 days. The results showed that the concentrations of blood immunoglobulin A (IgA) and immunoglobulin M (IgM) in the HQ group were significantly higher than those in the KB group (P < 0.05). Compared with the KB group, the concentrations of acetic acid, butyric acid, and total volatile fatty acids (VFAs) in the HQ group were higher (P < 0.01). The expression levels of the rumen epithelial-related genes MCT1, MCT4, NHE2, and ZO1 in the Astragalus group were significantly higher than those in the KB group (P < 0.05). 16S rRNA analysis showed that at the phylum level, Bacteroidetes in the HQ group significantly increased (P < 0.01); at the genus level, Prevotella (P < 0.01) and Succiniclasticum (P < 0.01) in the HQ group were found at significantly higher abundances than those in the KB group, and the results of microbiota gene and function prediction showed that "energy metabolism," "glycan biosynthesis and metabolic" pathways were significantly enriched in the HQ group (P < 0.05).

CONCLUSION

As a feed additive, Astragalus can improve the immunity of early-weaned lambs, the structure of the rumen microbiota of lambs, and the fermentation capacity of the rumen.

Dietary protein levels modulate the gut microbiome composition through fecal samples derived from lactating ewes

In ruminants, the digestion and utilization of dietary proteins are closely linked to the bacterial populations that are present in the gastrointestinal tract. In the present study, 16S rDNA sequencing, together with a metagenomic strategy was used to characterize the fecal bacteria of ewes in the early lactation stage after feeding with three levels of dietary proteins 8.58%, 10.34%, and 13.93%, in three different groups (H_1), (H_m) and (H_h), respectively. A total of 376,278,516 clean data-points were obtained by metagenomic sequencing. Firmicutes and Bacteroidetes were the dominant phyla, regardless of the dietary protein levels. In the H_h group, the phyla Proteobacteria, Caldiserica, and Candidatus_Cryosericota were less abundant than those in the H_I group. In contrast, Lentisphaerae, Chlamydiae, and Planctomycetes were significantly more abundant in the H_h group. Some genera, such as Prevotella, Roseburia, and Firmicutes_unclassified, were less abundant in the H_h group than those in the H_I group. In contrast, Ruminococcus, Ruminococcaceae_noname, Anaerotruncus, Thermotalae, Lentisphaerae_noname, and Paraprevotella were enriched in the H_h group. The acquired microbial genes were mainly clustered into biological processes; molecular functions; cytosol; cellular components; cytoplasm; structural constituents of ribosomes; plasma membranes; translation; and catalytic activities. 205987 genes were significantly enriched in the H_h group. In contrast, 108129 genes were more abundant in the H_I group. Our findings reveal that dynamic changes in fecal bacteria and their genes are strongly influenced by the levels of dietary proteins. We discovered that differentially expressed genes mainly regulate metabolic activity and KEGG demonstrated the primary involvement of these genes in the metabolism of carbohydrates, amino acids, nucleotides, and vitamins. Additionally, genes responsible for metabolism were more abundant in the H_h group. Investigating fecal bacterial characteristics may help researchers develop a dietary formula for lactating ewes to optimize the growth and health of ewes and lambs.

Effects of graded levels of dietary protein supplementation on milk yield, body weight gain, blood biochemical parameters, and gut microbiota in lactating ewes

Diet-associated characteristics such as dietary protein levels can modulate the composition and diversity of the gut microbiota, leading to effects on the productive performance and overall health of animals. The objective of this study was to see how changes in dietary protein levels affect milk yield, body weight gain, blood biochemical parameters, and gut microbiota in lactating ewes. In a completely randomized design, eighteen ewes were randomly assigned to three groups (n = 6 ewes/group), and each group was assigned to one of three dietary treatments with different protein contents. The ewes' groups were fed on 8.38% (S-I), 10.42% (S-m), and 13.93% (S-h) dietary protein levels on a dry basis. The body weight gain and milk yield were greater (p < 0.05) in ewes fed the S-h dietary treatment than in those fed the S-m and S-1 diets, respectively. However, milk protein contents were similar (p > 0.05) across the treatments. The blood glucose, total protein, cholesterol, triglycerides, high-density lipoprotein, low-density lipoprotein, lactate, creatinine, and C-reactive protein contents of lactating ewes were not influenced (p > 0.05) by different dietary protein levels. The alanine transaminase, aminotransferase, and lactate dehydrogenase activities were also not changed (p > 0.05) across the groups. However, blood urea nitrogen and albumin contents of lactating ewes were changed (p < 0.05) with increasing levels of dietary protein, and these metabolite concentrations were higher (p < 0.05) for S-h than the rest of the treatments. In the different treatment groups, Firmicutes and Bacteroidetes were found to be the most dominant phyla. However, the abundance of Lachnospiraceae species decreased as dietary protein levels increased. Within the Bacteroidetes phylum, Rikenellaceae were more abundant, followed by Prevotellaceae, in ewes fed the S-m diet compared to those fed the other diets. Based on the results, feeding at an optimal protein level improved milk yield and body weight gain through modifying the digestive tract's beneficial bacterial communities. The results of blood metabolites suggested that feeding higher-protein diets has no negative impact on health.

Antimicrobial Peptides Relieve Transportation Stress in Ragdoll Cats by Regulating the Gut Microbiota

Transportation is common in cats and often causes stress and intestinal disorders. Antimicrobial peptides (AMPs) exhibit a broad spectrum of antibacterial activity, and they may have the capacity for antioxidant and immune regulation. The objective of this study was to investigate the effects of dietary supplementation with AMPs on stress response, gut microbiota and metabolites of cats that have undergone transport stress. A total of 14 Ragdoll cats were randomly allocated into 2 treatments: basal diet (CON) and a basal diet supplemented with 0.3% AMPs. After a 6-week feeding period, all cats were transported for 3 h and, then, fed for another week. The results show that the diarrhea rate of cats was markedly reduced by supplementation with AMPs throughout the trial period (p < 0.05). In addition, AMPs significantly reduced serum cortisol and serum amyloid A (p < 0.05) and increased apolipoprotein 1 after transportation (p < 0.05). Moreover, AMPs reduced the level of inflammatory factors in the serum caused by transportation stress, including tumor necrosis factor-alpha (TNF-α) and interleukin-1 beta (IL-1β) (p < 0.05). The AMPs enhanced the activities of glutathione peroxidase (p < 0.01) and superoxide dismutase (p < 0.05). Furthermore, cats fed AMPs had higher levels of branched chain fatty acids (BCFAs) and a relative abundance of Blautia and a lower relative abundance of Negativibacillus after transportation (p < 0.05). The serum metabolome analysis further revealed that AMPs markedly regulated lipid metabolism by upregulating cholic acid expression. In conclusion, AMP supplementation alleviated oxidative stress and inflammatory response in transportation by regulating the gut microbiota and metabolites, thereby relieving stress-induced diarrhea and supporting gut and host health in cats.

Effect of Energy Provision Strategy on Rumen Fermentation Characteristics, Bacterial Diversity and Community Composition

This study was conducted to explore the rumen fermentation characteristics, bacterial diversity, and community composition of Hu sheep under four energy provision strategies. Ninety-six Hu sheep (body weight: 17.78 ± 1.24 kg) were equally assigned to four energy provision strategies: (1) low-energy diet for the whole finishing stage (LL); (2) high-energy diet for the whole finishing stage (HH); (3) low-energy diet in the early finishing stage and high-energy diet in the late finishing stage (LH); (4) high-energy diet in the early finishing stage and low-energy diet in the late finishing stage (HL). The results showed that the proportion of acetate was lower in the HH group than that in the HL group, whereas the opposite result was observed for the butyrate proportion (p < 0.05). The Chao 1, observed species, PD whole tree, and Shannon index of the rumen bacteria were higher in the LL group than that in the HH group (p < 0.05). The taxonomic annotations revealed that the Patescibacteria, Rikenellaceae RC9 gut group, Christensenellaceae R-7 group, and Anaeroplasma abundances were higher in the HL group than that in the HH group, and the opposite results were observed regarding the relative abundances of Selenomonas and Anaerovibrio (p < 0.05). The relative abundances of Spirochaetota and Treponema were higher in the LH group than that in the HH group (p < 0.05). Moreover, the analysis of similarity (ANOSIM) showed significant differences between groups (R = 0.6792 and p = 0.001). This study indicates that the energy provision strategy had little impact on the rumen fermentation characteristics, while it heavily affected the rumen bacterial diversity and community composition. This study may provide insight into the rumen fermentation characteristics and bacterial community under routine finishing models and contribute to the optimization of energy provision strategies of Hu sheep.

Effects of Replacing Alfalfa Hay with Oat Hay in Fermented Total Mixed Ration on Growth Performance and Rumen Microbiota in Lambs

The use of the fermented total mixed ration (FTMR) is a promising approach for the preservation of feedstuff, but the effect of FTMR on the between growth performance and ruminal microflora of lambs are still limited. This study aimed to assess the effects of different roughage types in the FTMR on growth performance and rumen microbiota of lambs. Forty-five six-month-old Small tail Han sheep × Ujumqin male lambs were randomly allocated into three groups (three pens per treatment and five lambs per pen) with the initial body weight (BW) of 28.50 ± 1.50 kg. The three treatments were as follows: the low oat percentages group (LO) contained 200 g/kg oat hay + 400 g/kg alfalfa hay, the medium oat percentages group (MO) contained 300 g/kg oat hay + 300 g/kg alfalfa hay, and the high oat percentages group (HO) contained 400 g/kg oat hay + 200 g/kg alfalfa hay. The result revealed that the dry matter intake and average daily gain were markedly (p < 0.05) higher in the MO treatment than in the LO and HO treatments, whereas no significant difference (p > 0.05) was found in the final body weight. There were no significant (p > 0.05) differences on the Shannon and Simpson index among the three treatments. The PCoA score plot illustrated the individual separation in the LO, MO, and HO treatments. At the phylum level, the presence of Bacteroidetes and Firmicutes belonging to the dominant phyla is widely described in rumen communities among the three treatments. The relative abundances of Prevotella, Fibrobacter, and Succinivibrio in the level of the genes were remarkably higher (p < 0.05) in MO treatment than that in LO and HO treatments, while the relative abundance of Sediminispirochaeta was remarkably higher (p < 0.05) in LO treatment than that in MO and HO treatments. These results indicated that the MO treatments could more effectively improve growth performance than the LO and HO treatments, and also revealed that the different forage types in diets reshaped the compositions and function of the rumen microbiota. Consequently, the findings presented in this study provide a reference for the application of FTMR in animal production and the understanding of the interaction between diet, animal performance, and ruminal microbiota.

The dual antimicrobial and immunomodulatory roles of host defense peptides and their applications in animal production

Host defense peptides (HDPs) are small molecules with broad-spectrum antimicrobial activities against infectious bacteria, viruses, and fungi. Increasing evidence suggests that HDPs can also indirectly protect hosts by modulating their immune responses. Due to these dual roles, HDPs have been considered one of the most promising antibiotic substitutes to improve growth performance, intestinal health, and immunity in farm animals. This review describes the antimicrobial and immunomodulatory roles of host defense peptides and their recent applications in animal production.

Gut Microbiome Studies in Livestock: Achievements, Challenges, and Perspectives

The variety and makeup of the gut microbiome are frequently regarded as the primary determinants of health and production performances in domestic animals. High-throughput DNA/RNA sequencing techniques (NGS) have recently gained popularity and permitted previously unheard-of advancements in the study of gut microbiota, particularly for determining the taxonomic composition of such complex communities. Here, we summarize the existing body of knowledge on livestock gut microbiome, discuss the state-of-the-art in sequencing techniques, and offer predictions for next research. We found that the enormous volumes of available data are biased toward a small number of globally distributed and carefully chosen varieties, while local breeds (or populations) are frequently overlooked despite their demonstrated resistance to harsh environmental circumstances. Furthermore, the bulk of this research has mostly focused on bacteria, whereas other microbial components such as protists, fungi, and viruses have received far less attention. The majority of these data were gathered utilizing traditional metabarcoding techniques that taxonomically identify the gut microbiota by analyzing small portions of their genome (less than 1000 base pairs). However, to extend the coverage of microbial genomes for a more precise and thorough characterization of microbial communities, a variety of increasingly practical and economical shotgun techniques are currently available.

A buffalo rumen-derived probiotic (SN-6) could effectively increase simmental growth performance by regulating fecal microbiota and metabolism

Microorganisms play a key role in ruminal digestion, some of which can be used as probiotics to promote growth in ruminants. However, which potential bacteria are responsible for ruminant growth and how they potentiate the basic mechanism is unclear. In this study, three bacterial strains, Bacillus pumilus (SN-3), Bacillus paralicheniformis (SN-6), and Bacillus altitudinis (SN-20) with multiple digestive enzymes were isolated from the rumen of healthy buffaloes. Among these strains, SN-6 secreted cellulase, laccase, and amylase, and significantly inhibited Staphylococcus aureus ATCC25923 and Escherichia coli K99 in vitro. In addition, SN-6 exhibited strong tolerance to artificial gastric juice, intestinal juice, and high temperature. Antibiotic resistance test, virulence gene test, and mouse toxicity test confirmed the safety of SN-6. Further, SN-6 significantly increased the body weight (p < 0.01), affects the intestinal microbiota structure, and alters the metabolomic patterns of Simmental. There was a remarkable difference in the β diversity of fecal microflora between SN-6 and control groups (p < 0.05). Furthermore, SN-6 significantly increased the abundance of Clostridium_sensu_stricto_1, Bifidobacterium, Blautia, and Cellulolyticum, decreased the relative abundance of Monoglobus and norank_f_Ruminococcacea. Moreover, SN-6 feeding significantly enriched intestinal metabolites (i.e., 3-indoleacrylic acid, kynurenic acid) to maintain intestinal homeostasis. Finally, the microbial and metabolic functional analysis indicated that SN-6 could enhance amino acid metabolism (mainly tryptophan metabolism) and lipid metabolism pathways. Overall, these findings indicated that SN-6 could be used as a probiotic in ruminants.

Response of Ruminal Microbiota-Host Gene Interaction to High-Altitude Environments in Tibetan Sheep

Altitude is the main external environmental pressure affecting the production performance of Tibetan sheep, and the adaptive evolution of many years has formed a certain response mechanism. However, there are few reports on the response of ruminal microbiota and host genomes of Tibetan sheep to high-altitude environments. Here, we conducted an integrated analysis of volatile fatty acids (VFAs), microbial diversity (16S rRNA), epithelial morphology, and epithelial transcriptome in the rumen of Tibetan sheep at different altitudes to understand the changes in ruminal microbiota−host interaction in response to high altitude. The differences in the nutritional quality of forage at different altitudes, especially the differences in fiber content (ADF/NDF), led to changes in rumen VFAs of Tibetan sheep, in which the A/P value (acetic acid/propionic acid) was significantly decreased (p < 0.05). In addition, the concentrations of IgA and IgG in Middle-altitude (MA) and High-altitude Tibetan sheep (HA) were significantly increased (p < 0.05), while the concentrations of IgM were significantly increased in MA (p < 0.05). Morphological results showed that the width of the rumen papilla and the thickness of the basal layer increased significantly in HA Tibetan sheep (p < 0.05). The 16S rRNA analysis found that the rumen microbial diversity of Tibetan sheep gradually decreased with increasing altitude, and there were some differences in phylum- and genus-level microbes at the three altitudes. RDA analysis found that the abundance of the Rikenellaceae RC9 gut group and the Ruminococcaceae NK4A214 group increased with altitudes. Furthermore, a functional analysis of the KEGG microbial database found the “lipid metabolism” function of HA Tibetan sheep to be significantly enriched. WGCNA revealed that five gene modules were enriched in “energy production and conversion”, “lipid transport and metabolism”, and “defense mechanisms”, and cooperated with microbiota to regulate rumen fermentation and epithelial immune barrier function, so as to improve the metabolism and immune level of Tibetan sheep at high altitude.

Ruminal background of predisposed milk urea (MU) concentration in Holsteins

Efforts to reduce nitrogen (N) emissions are currently based on the optimization of dietary- N supply at average herd N requirements. The implementation of the considerable individual differences and predispositions in N- use efficiency and N- excretion in breeding programs is hampered by the difficulty of data collection. Cow individual milk urea (MU) concentration has been proposed as an easy-to-measure surrogate trait, but recent studies questioned its predictive power. Therefore, a deeper understanding of the biological mechanisms underlying predisposed higher (HMUg) or lower (LMUg) MU concentration in dairy cows is needed. Considering the complex N- metabolism in ruminants, the distinction between HMUg and LMUg could be based on differences in (i) the rumen microbial community, (ii) the host-specific transcription processes in the rumen villi, and (iii) the host-microbe interaction in the rumen. Therefore, rumen fluid and rumen epithelial samples from 10 HMUg and 10 LMUg cows were analyzed by 16S sequencing and HiSeq sequencing. In addition, the effect of dietary-N reduction on ruminal shifts was investigated in a second step. In total, 10 differentially abundant genera (DAG) were identified between HMUg and LMUg cows, elucidating greater abundances of ureolytic Succinivibrionaceae_UCG-002 and Ruminococcaceae_unclassified in LMUg animals and enhanced occurrences of Butyvibrio in HMUg cows. Differential expression analysis revealed genes of the bovine Major Histocompatibility Complex (BOLA genes) as well as MX1, ISG15, and PRSS2 displaying candidates of MU predisposition that further attributed to enhanced immune system activities in LMUg cows. A number of significant correlations between microbial genera and host transcript abundances were uncovered, including strikingly positive correlations of BOLA-DRA transcripts with Roseburia and Lachnospiraceae family abundances that might constitute particularly prominent microbial-host interplays of MU predisposition. The reduction of feed-N was followed by 18 DAG in HMUg and 19 DAG in LMUg, depicting pronounced interest on Shuttleworthia, which displayed controversial adaption in HMUg and LMUg cows. Lowering feed-N further elicited massive downregulation of immune response and energy metabolism pathways in LMUg. Considering breeding selection strategies, this study attributed information content to MU about predisposed ruminal N-utilization in Holstein-Friesians.

Antimicrobial Peptides Controlling Resistant Bacteria in Animal Production

In the last few decades, antimicrobial resistance (AMR) has been a worldwide concern. The excessive use of antibiotics affects animal and human health. In the last few years, livestock production has used antibiotics as food supplementation. This massive use can be considered a principal factor in the accelerated development of genetic modifications in bacteria. These modifications are responsible for AMR and can be widespread to pathogenic and commensal bacteria. In addition, these antibiotic residues can be dispersed by water and sewer water systems, the contamination of soil and, water and plants, in addition, can be stocked in tissues such as muscle, milk, eggs, fat, and others. These residues can be spread to humans by the consumption of water or contaminated food. In addition, studies have demonstrated that antimicrobial resistance may be developed by vertical and horizontal gene transfer, producing a risk to public health. Hence, the World Health Organization in 2000 forbid the use of antibiotics for feed supplementation in livestock. In this context, to obtain safe food production, one of the potential substitutes for traditional antibiotics is the use of antimicrobial peptides (AMPs). In general, AMPs present anti-infective activity, and in some cases immune response. A limited number of AMP-based drugs are now available for use in animals and humans. This use is still not widespread due to a few problems like in-vivo effectiveness, stability, and high cost of production. This review will elucidate the different AMPs applications in animal diets, in an effort to generate safe food and control AMR.

Amino acids metabolism by rumen microorganisms: Nutrition and ecology strategies to reduce nitrogen emissions from the inside to the outside

For the ruminant animal industry, the emission of nitrogenous substances, such as nitrous oxide (N₂O) and ammonia (NH₃), not only challenges environmental sustainability but also restricts its development. The metabolism of proteins and amino acids by rumen microorganisms is a key factor affecting nitrogen (N) excretion in ruminant animals. Rumen microorganisms that affect N excretion mainly include three types: proteolytic and peptidolytic bacteria (PPB), ureolytic bacteria (UB), and hyper-ammonia-producing bacteria (HAB). Microbes residing in the rumen, however, are influenced by several complex factors, such as diet, which results in fluctuations in the rumen metabolism of proteins and amino acids and ultimately affects N emission. Combining feed nutrition strategies (including ingredient adjustment and feed additives) and ecological mitigation strategies of N₂O and NH₃ in industrial practice can reduce the emission of nitrogenous pollutants from the ruminant breeding industry. In this review, the characteristics of the rumen microbial community related to N metabolism in ruminants were used as the metabolic basis. Furthermore, an effective strategy to increase N utilisation efficiency in combination with nutrition and ecology was reviewed to provide an inside-out approach to reduce N emissions from ruminants.

Effects of Dietary Energy Levels on Rumen Fermentation, Gastrointestinal Tract Histology, and Bacterial Community Diversity in Fattening Male Hu Lambs

This study investigated rumen fermentation and histological and microbial diversity in male Hu lamb fed diets with different metabolizable energy (ME) levels (MEA, 9.17 MJ/kg, MEB, 10.00 MJ/kg, and MEC, 10.82 MJ/kg). Thirty-six male Hu lambs were randomly allotted to three treatments, and the feeding trial lasted for 67 days. Rumen fermentation results suggest that the iso-valerate had a significant effect on dietary energy level. The papillary height (PH) of rumen was the highest in the MEB group, the crypt depth (CD) was significantly increased in the duodenum and jejunum, and the villus height (VH)-to-CD ratio (VH/CD) was significantly decreased in the duodenum by increasing dietary energy levels; the VH, villus width (VW), and VH/CD also had significant differences in the ileum. 16S rRNA sequencing results showed that the operational taxonomic units (OTUs) number, the ACE, and Chao1 indices were linearly decreased by increasing dietary energy level; 24 phyla including 124 genera were identified, and the relative abundance of Papillibacter and Quinella linearly decreased by increasing the dietary energy level. Compared to MEA and MEB groups, the relative abundance of unidentified_Veillonellaceae and Anaerovibrio was significantly increased in the MEC group at the genus level. The relative abundance of the carbohydrate metabolism pathway predicted by Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) was linearly increased by increasing the dietary energy levels. Three metabolic pathways identified in Kyoto Encyclopedia of Genes and Genomes (KEGG) level 3 were significantly influenced as the dietary energy level increased. In summary, these results demonstrated that the dietary energy levels affected the rumen fermentation parameters, morphological structures of the gastrointestinal tract (GIT), and the composition and function of rumen microflora in male Hu sheep.

Antimicrobial peptides in domestic animals and their applications in veterinary medicine

Antimicrobial peptides (AMPs) are molecules with a broad-spectrum activity against bacteria, fungi, protozoa, and viruses. These peptides are widely distributed in insects, amphibians and mammals. Indeed, they are key molecules of the innate immune system with remarkable antimicrobial and immunomodulatory activity. Besides, these peptides have also shown regulatory activity for gut microbiota and have been considered inductors of growth performance. The current review describes the updated findings of antimicrobial peptides in domestic animals, such as bovines, goats, sheep, pigs, horses, canines and felines, analyzing the most relevant aspects of their use as potential therapeutics and their applications in Veterinary medicine.

Modes of genetic adaptations underlying functional innovations in the rumen

The rumen is the hallmark organ of ruminants and hosts a diverse ecosystem of microorganisms that facilitates efficient digestion of plant fibers. We analyzed 897 transcriptomes from three Cetartiodactyla lineages: ruminants, camels and cetaceans, as well as data from ruminant comparative genomics and functional assays to explore the genetic basis of rumen functional innovations. We identified genes with relatively high expression in the rumen, of which many appeared to be recruited from other tissues. These genes show functional enrichment in ketone body metabolism, regulation of microbial community, and epithelium absorption, which are the most prominent biological processes involved in rumen innovations. Several modes of genetic change underlying rumen functional innovations were uncovered, including coding mutations, genes newly evolved, and changes of regulatory elements. We validated that the key ketogenesis rate-limiting gene (HMGCS2) with five ruminant-specific mutations was under positive selection and exhibits higher synthesis activity than those of other mammals. Two newly evolved genes (LYZ1 and DEFB1) are resistant to Gram-positive bacteria and thereby may regulate microbial community equilibrium. Furthermore, we confirmed that the changes of regulatory elements accounted for the majority of rumen gene recruitment. These results greatly improve our understanding of rumen evolution and organ evo-devo in general.

A Preliminary Study on the Characteristics of microRNAs in Ovarian Stroma and Follicles of Chuanzhong Black Goat during Estrus

microRNAs (miRNAs) play a significant role in ovarian follicular maturity, but miRNA expression patterns in ovarian stroma (OS), large follicles (LF), and small follicles (SF) have been rarely explored. We herein aimed to identify miRNAs, their target genes and signaling pathways, as well as their interaction networks in OS, LF, and SF of Chuanzhong black goats at the estrus phase using small RNA-sequencing. We found that the miRNA expression profiles of LF and SF were more similar than those of OS—32, 16, and 29 differentially expressed miRNAs were identified in OS vs. LF, OS vs. SF, and LF vs. SF, respectively. Analyses of functional enrichment and the miRNA-targeted gene interaction network suggested that miR-182 (SMC3), miR-122 (SGO1), and miR-206 (AURKA) were involved in ovarian organogenesis and hormone secretion by oocyte meiosis. Furthermore, miR-202-5p (EREG) and miR-485-3p (FLT3) were involved in follicular maturation through the MAPK signaling pathway, and miR-2404 (BMP7 and CDKN1C) played a key role in follicular development through the TGF-β signaling pathway and cell cycle; nevertheless, further research is warranted. To our knowledge, this is the first study to investigate miRNA expression patterns in OS, LF, and SF of Chuanzhong black goats during estrus. Our findings provide a theoretical basis to elucidate the role of miRNAs in follicular maturation. These key miRNAs might provide candidate biomarkers for the diagnosis of follicular maturation and will assist in developing new therapeutic targets for female goat infertility.