Search Results (321)

The interaction between bacteria and fungi is one of the key interactions of microbial ecology, including mutualism, antagonism, and competition, which profoundly affects the balance and functions of animal microbial ecosystems. This article reviews the interactive dynamics of bacteria and fungi in more concerned microenvironments in animals, such as gut, rumen, and skin. Moreover, we summarize the molecular mechanisms and ecological functions of the interaction between bacteria and fungi. Three major bacterial–fungal interactions (mutualism, antagonism, and competition) are deeply discussed. Understanding of the interactions between bacteria and fungi allows us to understand, modulate, and maintain the community structure and functions. Furthermore, this summarization will provide a comprehensive perspective on animal production and veterinary medicine, as well as guide future research directions. Full article

Optimizing the metabolizable protein level in ruminant diets represents a promising strategy to increase nitrogen use efficiency and mitigate environmental pollution. This study explored the impacts of varying metabolizable protein (MP) levels on amino acid (AA) balance, nitrogen (N) utilization, and the ruminal microbiota in Hu lambs. Fifty-four female Hu lambs of 60 d old, with an average body weight (BW) of 18.7 ± 2.37 kg, were randomly allocated to three dietary MP groups: (1) low MP (LMP, 7.38% of DM), (2) moderate MP (MMP, 8.66% of DM), and (3) high MP (HMP, 9.93% of DM). Three lambs with similar BW within each group were housed together in a single pen, serving as one experimental replicate (n = 6). The feeding trial lasted for 60 days with 10 days for adaptation. The final BW of lambs in the MMP and HMP groups increased (p < 0.05) by 5.64% and 5.26%, respectively, compared to the LMP group. Additionally, lambs fed the MMP diet exhibited an 11.6% higher (p < 0.05) average daily gain than those in the LMP group. Increasing dietary MP levels enhanced (p < 0.05) N intake, urinary N, retained N, and percent N retained, but decreased apparent N digestibility (p < 0.05). Urinary uric acid, total purine derivatives, intestinally absorbable dietary protein, microbial crude protein, intestinally absorbable microbial crude protein, and actual MP supply all increased (p < 0.05) with higher MP values in the diet. The plasma concentrations of arginine, lysine, methionine, phenylalanine, threonine, aspartic acid, proline, total essential AAs, and total nonessential AAs were the lowest (p < 0.05) in the LMP group. In the rumen, elevated MP levels led to a significant increase (p < 0.05) in the ammonia N content. The relative abundances of Candidatus_Saccharimonas, Ruminococcus, and Oscillospira were the lowest (p < 0.05), whereas the relative abundances of Terrisporobacter and the Christensenellaceae_R-7_group were the highest (p < 0.05) in the MMP group. In conclusion, the moderate dietary metabolizable protein level could enhance growth performance, balance the plasma amino acid profiles, and increase nitrogen utilization efficiency in Hu lambs, while also altering the rumen bacterial community by increasing beneficial probiotics like the Christensenellaceae_R-7_group. Full article

Animal feed made from fermented agricultural residues using Lactobacillus sp. and Bacillus sp. has received significant attention. However, interactions between differentially expressed genes (DEGs) in adipose, liver, and muscle tissues and bacteria or fungi in the rumen remain largely unknown. This study determined effects of normal diet feed (NF) and alternative diet feed made by Lactobacillus sp. and Bacillus sp. (AF) on gene expression in major metabolic organs and on microbial populations in the rumen of Bos-Taurus using high-throughput sequencing methods. Rumen bacteria/fungi interaction with DEGs in key metabolic organs was also investigated. According to our findings, 34, 36, and 28 genes were differentially expressed in adipose, liver, and muscle tissues, respectively. Most DEGs were associated with osteoclast differentiation and immune functions. Microbial dynamics analysis showed that the AF diet significantly (p < 0.05) increased Firmicutes but reduced Bacterioidetes abundances. At the genus level, Faecalicatena, Intestinimonas, Lachnoclostridium, Faecalicatena, and Intestinimonas were significantly higher (p < 0.05) in animals fed with the AF diet. Regarding fungal populations, Neocallimastigomycota accounted for 98.2% in the NF diet and 86.88% in the AF diet. AF feeding increased Orpinomyces and Piromyces but decreased Neocallimastix abundances. These findings highlight the potential of fermented feeds to improve metabolic responses and rumen microbial balance, contributing to enhanced animal performance. Full article

Understanding the influence of the sheep breed and roughage source on the composition of rumen bacteria and methanogens is essential for optimizing roughage efficiency. The experiment employed a 2 × 2 factorial design. Twenty-four Dumont and Mongolian sheep (initial body weight of 18.94 ± 1.01 kg) were randomly assigned by breed to two dietary treatment groups (AH: alfalfa hay; CS: corn straw); the experiment lasted 90 days. The results showed that sheep fed alfalfa hay diets had a higher feed intake and weight gain, and Dumont sheep had a higher feed intake than Mongolian sheep (p < 0.05). The diversity and composition of ruminal bacteria and methanogens differed between Dumont and Mongolian sheep fed either AH or CS diets. The taxonomic analysis revealed a distinct clustering pattern based on the roughage source, but not on the breed. When fed a corn straw diet, the bacterial Chao1 index of Dumont sheep increased (p < 0.05), while the diversity and richness of methanogens in Mongolian sheep increased (p < 0.05). Additionally, we have identified unique biomarkers for the rumen bacteria and methanogens of Dumont and Mongolian sheep in response to different roughage sources. The results suggest that the differences in the microbiota of the sheep were associated with the roughage source and breed. The higher growth performance of Dumont sheep might be attributed to the increase in bacterial diversity and the decrease in methanogenic bacteria diversity. Full article

Our previous study has shown that supplementation of 0.50% benzoic acid (BA) increased growth performance, promoted rumen fermentation, and improved the composition and function of rumen microbiota. This research was designed to conduct a deeper exploration of the impacts of dietary supplementation with BA on the apparent digestibility of nutrients and the composition of rectal microbiota in weaned Holstein dairy calves. Sixteen Holstein heifer calves with similar body weights (91.2 ± 0.7 kg) were selected and randomly allocated into two groups, each comprising eight calves. Calves in the control group (CON group) were fed with a basal diet, while those in the benzoic acid group (BA group) were fed with the basal diet supplemented with 0.50% benzoic acid (on a dry matter basis). The experimental period started at 60 days of age and ended at 102 days of age, lasting for a total of 42 days. The calves were weaned at 60 days of age, with a transition period of 7 days. Feed samples were collected every two weeks, fecal samples were collected from 99 to 101 days of age, and blood samples were collected at 102 days of age. The results showed that supplementation with BA did not influence the digestibility of dry matter, crude protein, ether extract, neutral detergent fiber, acid detergent fiber, calcium, and phosphorus between the two groups. Compared with the CON group, BA supplementation tended to decrease the total cholesterol (TC) in the serum of the calves (p = 0.067). Supplementation with BA increased the relative abundances of the two beneficial bacteria, Bifidobacterium and Bifidobacterium pseudolongum (p < 0.05, LDA > 2), but decreased that of the harmful bacterium, Clostridium sensu stricto 1, in the rectum of dairy calves. The microbial functional prediction revealed that the fecal microbial metabolism involved in primary bile acid biosynthesis was higher in the calves from the BA group. In conclusion, the present study demonstrated that adding 0.50% BA to the diet did not influence the apparent nutrient digestibility, but improved rectal microbiota health, which finally promoted the growth performance in weaned Holstein dairy calves. Full article

Utilizing straw feed is an effective strategy to optimize straw resource utilization by incorporating microbial degradation agents to expedite lignocellulose breakdown and enhance feed efficiency. Lignocellulose-degrading species and microbial communities are present in various Earth ecosystems, including the rumen of ruminants, insect digestive tracts, forest soil, and microbial populations in papermaking processes. The rumen of ruminants harbors a diverse range of microbial species, making it a promising source of lignocellulose-degrading microorganisms. Exploring alternative systems like insect intestines and forest soil is essential for future research. Current studies primarily rely on traditional microbial isolation techniques to identify lignocellulose-degrading strains, underscoring the necessity to transition to utilizing microbial culturomics and genome-editing technologies for discovering and manipulating cellulose-degrading microbes. This review provides an overview of lignocellulose-degrading microbial communities from diverse environments, encompassing bacterial and fungal populations. It also delves into the use of metagenomic, metatranscriptomic, and metaproteomic approaches to pinpoint highly efficient cellulase genes, along with the application of genome-editing tools for engineering lignocellulose-degrading microorganisms. The primary objective of this review is to offer insights for further exploration of potential lignocellulose-degrading microbial resources and high-performance cellulase genes to enhance roughage utilization in ruminant rumen ecosystems. Full article

This study aimed to evaluate the effects of studying the effects of the alkali metal ion complexes (AMIC) on the rumen of lambs. Eighteen 3-month-old male Hu lambs (30 ± 2.5 kg) were randomly assigned to three groups (n = 6). Dietary treatments were: control group (CG, base diet), group C1 (base diet + 0.15% AMIC), and group C2 (base diet + 0.30% AMIC). After 60 days of feeding, samples were collected for analysis. Compared with CG, rumen weight significantly increased in both C1 and C2 (p < 0.05). In C2, average daily gain (ADG), bacterial crude protein (BCP), propionic acid concentration, and rumen papillary length were significantly higher than in CG (p < 0.05). Rumen microbiota analysis showed that AMIC supplementation changed the microbial community composition, increasing the relative abundance of fiber-degrading bacteria (e.g., Prevotellaceae_UCG-001) and decreasing pathogenic Proteobacteria. In particular, rumen papillary length positively correlated with Unclassified Oscillospiraceae, Candidatus Saccharimonas, and Unclassified Clostridia vadinBB60 group. Metabolomic analysis revealed that quercetin 3-O-glucuronide levels increased in a dose-dependent manner with higher AMIC. This metabolite positively correlated with Prevotellaceae_UCG-001 abundance and ADG. At 0.30% AMIC, phospholipids PC(18:0/18:4(6Z,9Z,12Z,15Z)) and PE(18:0/16:1(9Z)) were significantly upregulated, and both positively correlated with Candidatus Saccharimonas, Unclassified Clostridia vadinBB60 group, and papillary morphology. In summary, AMIC supplementation affected metabolism by modulating the rumen microbiota, thereby promoting energy absorption and growth. The 0.30% AMIC inclusion significantly enhanced rumen papilla growth, increased the absorption area, promoted propionic acid production, reduced the acetic acid to propionic acid ratio, and ultimately improved the growth rate of Hu lambs. Thus, adding 0.30% AMIC was associated with improved growth performance. Full article

Ferulic acid esterase (FAE) plays an important role in plant fiber degradation by catalyzing the hydrolysis of lignocellulosic structures. FAE-producing lactic acid bacteria (LAB), as potential probiotics, can improve ruminant digestion and gut health. In this study, two LAB strains (Q2 and Q6) with FAE activity were isolated from sheep rumen. Based on 16S rDNA sequencing, they were identified as Lactobacillus mucosae and Streptococcus equinus, respectively. Compared to Q2, Q6 demonstrated higher enzyme production, lactic acid yield, broader carbohydrate utilization, and stronger antimicrobial activity. The whole genome sequencing revealed Q2 and Q6 possess genomes of 2.14 Mbp and 1.95 Mbp, with GC contents of 46.81% and 37.30%, respectively. Q2 and Q6 exhibited the highest average nucleotide identity (ANI) with L. mucosae DSM 13345 (97.30%) and S. equinus ATCC 33317 (97.92%), respectively. The strains harbored 2101 and 1928 predicted genes, including 1984 and 1837 coding sequences (CDSs), respectively. GO enrichment analysis showed the CDSs predominantly associated with membranes (or cells), catalytic activity, and metabolic processes. KEGG analysis revealed both strains enriched in metabolic pathways, with Q6 showing a notably higher number of proteins in the ABC transporters and quorum sensing than Q2. Carbohydrate-active enzymes database (CAZy) profiling identified 75 CAZymes in Q2 and 93 CAZymes in Q6, with each strain containing one novel fae gene. Safety assessment identified 1 and 33 pathogenic genes, along with 2 and 4 putative antimicrobial peptide genes, in Q2 and Q6, respectively. Notably, Q6 carried 12 virulence factor genes. These findings suggest Q2 exhibits a superior safety profile compared to Q6, indicating a higher probability of Q2 being an effective probiotic strain. In conclusion, both LAB strains produce FAE. L. mucosae Q2 demonstrates suitability as a direct-fed probiotic for livestock, while Q6 exhibits potential as a silage inoculant, though comprehensive safety evaluations are required prior to its application. Full article

As high-quality sheep germplasm resources in China, Hu sheep are characterized by fast growth and development, high fecundity, and tolerance to drought and cold. Tibetan sheep, adapted to high-altitude environments, have developed strong environmental adaptability. To explore the differences in the interaction among rumen microbial flora, hepatic gluconeogenesis, and mitochondrial function between Tibetan sheep and Hu sheep in the Qinghai–Tibet Plateau, this study systematically compared and analyzed the rumen flora density, key enzyme activities related to hepatic gluconeogenesis and mitochondrial function, and the expression levels of related genes in Tibetan sheep and Hu sheep under identical feeding management conditions, followed by correlation analysis. The results showed that Hu sheep had significantly higher densities of Ruminobacteramylophilus (Ram) and Fibrobacter succinogenes (Fs) associated with starch and protein degradation (p < 0.01). The expression levels of Forkhead box O1 (FOXO1), pyruvate carboxylase (PC) activity, and adenosine triphosphate (ATP) content were also significantly higher than those in Tibetan sheep (p < 0.01). In contrast, Tibetan sheep had higher densities of Butyrivibrio fibrisolvens (Bf), Ruminococcus albus (Ra), Ruminococcus flavefaciens (Rf), etc., related to cellulose degradation (p < 0.01). The gluconeogenesis-related genes, Glucose-6-phosphatase catalytic subunit 1 (G6PC1) and phosphoenolpyruvate carboxykinase1 (PCK1), and the activities of phosphoenolpyruvate carboxykinase (PEPCK) and fructose-1,6-bisphosphatase (FBPase) were significantly higher in Tibetan sheep than in Hu sheep (p < 0.01). Mitochondrial function-related genes Mitofusin-1 (Mfn1), Mitofusin-2 (Mfn2), subunit 6 of ATP synthase (ATP6), cytochrome b (Cytb), etc., also showed significantly higher expression in Tibetan sheep (p < 0.01). While no significant differences were observed in the contents of citric acid (CA), pyruvic acid (PA), glucose (Glu), etc. (p > 0.05). Correlation analysis indicated that rumen flora was associated with the key enzyme activities and gene expressions of hepatic gluconeogenesis and mitochondrial function to varying degrees. In summary, Tibetan sheep exhibit strong fiber degradation capacity, the efficient utilization of gluconeogenic intermediates, and mitochondrial oxidative phosphorylation (OXPHOS) ability, forming adaptive strategies for high-altitude environments. By contrast, Hu sheep show efficient protein and starch degradation capacity, thereby enhancing the supply of gluconeogenic precursors. It is indicated that when introducing Hu sheep to high-altitude areas, dietary intervention can be used to regulate rumen microorganisms, such as increasing fiber-decomposing bacteria or enhancing mitochondrial oxidative capacity, to counteract metabolic limitations induced by hypoxia. Full article

This study aimed to determine the optimal supplementation level of sodium humate (SH) for improving rumen fermentation efficiency in vitro. Using rumen fluid from four donor ewes with three experimental replicates per treatment, we evaluated a basal diet supplemented with SH at 0 (control), 0.5 (SH0.5), 1 (SH1), and 2 (SH2) g/kg dry matter. The results of this study revealed that after 12 h of incubation, compared to the control group, the SH0.5 group significantly decreased gas production (GP) by −11.66% (p < 0.01). There were no significant differences in pH values, bacterial crude protein (BCP) content, and ammonia nitrogen (NH₃-N) concentration among the groups (p > 0.05). After 24 h of incubation, no significant differences in pH values were observed among the groups (p > 0.05). The SH1 group exhibited significantly higher BCP content compared to other treatments (p < 0.05), concomitant with a marked reduction in NH₃-N concentration (p < 0.01). Compared to the control group, GP in the SH1 group increased significantly by 7.16%, and a significant increase of 5.43% (p < 0.05), while it decreased significantly by −9.96% in the SH0.5 group (p < 0.01). However, no significant differences in volatile fatty acids were observed among the groups after either 12 or 24 h of fermentation. The addition of 1 g/kg SH altered the composition of the rumen bacterial community, which was indicated by the increased relative abundances of Prevotella, Anaerovibrio, and Saccharofermentans and the decreased relative abundances of Actinobacteriota, Lachnospiraceae_NK3A20_group, and [Ruminococcus]_gauvreauii_group (p < 0.05). Furthermore, Anaerovibrio was negatively correlated with NH₃-N and positively correlated with gas production, while [Ruminococcus]_gauvreauii_group was negatively correlated with gas production. The study indicates that the addition of 1 g/kg SH optimizes rumen fermentation efficiency and improves nutrient utilization by modulating the structure and composition of the bacterial community, thus serving as an effective additive for enhancing rumen fermentation and feed utilization in ruminants. Full article

In the mid-twentieth century, the solid waste generated was mostly made of biodegradable materials. However, the invention of plastic and its widespread use have led to a staggering accumulation of plastic in the environment, posing a severe threat to the biosphere. The environmental degradation of plastic can take thousands of years and poses a significant concern for environmental and human health. Until recently, it was thought that some plastics were non-biodegradable; however, there are microorganisms capable of degrading both plastics derived from fossil resources and those from biomass or renewable resources. This review aims to highlight the impact of plastic waste on the environment and the biosphere, as well as the great taxonomic diversity of microorganisms potentially linked to plastic degradation. Research in plastic biodegradability includes the identification of bacteria, fungi, archaea, and algae from virtually any environment: soil, atmosphere, landfills, freshwater, seawater, marine sediments, rumen, and waxworm guts. Identifying microbial consortia that degrade plastic and improving their degrading activity could shorten the plastic degradation time and reduce its uncontrolled accumulation around the globe. Research in this field is vital for advancing biodegradable plastics and elucidating the potential and limitations of microbial degradation as a large-scale approach to plastic pollution. Full article

The aim of the present study was to evaluate the effect of grazing the low deciduous forest (LDF) vegetation on the diversity of the rumen microbiome in growing lambs and its relationship with volatile fatty acid (VFA) profiles. After a 35-day indoor acclimatization (stabilization period), the lambs were assigned to two groups: housed (CG, n = 4) and grazing (EG, n = 4). The grazing lambs had a 14-day habituation period in the LDF (4 h/day) and a further 30 grazing days when fodder intake was observed. Ruminal samples were collected at the end of the stabilization, on day 14 post-stabilization (14DPS), and on day 44 post-stabilization (44DPS). The ruminal butyrate concentration showed a progressive decrease of approximately 23% over the time (p = 0.0130). The qualitative composition (p = 0.001) and relative proportions of bacteria (p = 0.004) in EG-44DPS exhibited a greater diversity, with 107 total genera and 19 unique, significant abundances in 13 genera with a higher presence of Bacteroidales_RF16_group, Lachnospiraceae_ND3007_group, and WCHB1-41. Moreover, significant functional profiles are associated with key metabolic pathways in bacteria and are interconnected by the need to generate energy and biosynthetic precursors and to manage available nitrogen and carbon. Finally, eight bacterial genera were identified as biomarkers correlated with the increase in VFA in EG-44DPS. Full article

The purpose of this research was to investigate the impact of chestnut tannins (CHTs) on nutrient digestibility, nitrogen balance, in situ crude protein (CP) digestibility, protease enzymes, and microbial community composition in sheep. Eighteen 1.5-year-old sheep (43.0 ± 2.0 kg initial BW) fitted with permanent ruminal cannula were selected and randomly divided into three groups, which were fed with CHTs added at 0, 2, and 6%/kg DM. The pre-feeding period lasted for 12 days, and the actual trial period was 18 days. Rumen fluid was collected to assess in situ crude protein (CP) degradability, while rumen digesta was analyzed for total and ruminal proteolytic bacterial populations. Using one-way ANOVA in SAS to analyze data, the results indicated that 2% CHT reduced in situ degradability by 26.23%, while 6% reduced it by 58.01% in the rumen of the sheep. The CP apparent digestibility, nitrogen metabolism, and population of proteolytic bacteria of sheep were decreased in the 6% CHT group (p < 0.05), while the above indices of the 2% CHT group were not affected. Furthermore, CHT supplementation significantly altered the ruminal microbial community structure. Particularly in the 2% CHT group, the relative abundances of Bacteroidota and Prevotella increased. LEfSe analysis revealed that Bacteroidale replaced U29-B03 as the dominant microbiota at 2% CHT. Doses of 2% CHT can be incorporated into sheep diets without impairing digestion. These findings support the inclusion of CHT doses of less than 2% for enhancing protein digestion and increasing the types of beneficial bacteria in the rumen, while doses above 6% should be avoided. Full article

Nanoemulsified corn oil was tested on twenty-one multiparous lactating Barki ewes (mean ± SD: 3 ± 0.4 parity, 44.3 ± 1.9 kg body weight, 30 ± 2.7 months of age, and 402 ± 23 g/d of prior milk production) randomly allocated to the following treatments (n = 7 ewes/group): Control—a basal diet consisting of 50% concentrate mixtures and 50% berseem clover; CO—the Control diet + 3% of corn oil; NCO—the Control diet + 3% of nanoemulsified corn oil. A completely randomized design of 25 days of adaptation and 5 days of sampling was employed with seven ewes per treatment. Despite feeding oil according to the recommended values, CO decreased the dry matter intake by 8.3% and 6.7% compared to the Control and NCO, respectively. The negative impact of CO extended to reducing the concentrations of ammonia and total volatile fatty acids in the rumen. On the other hand, NCO had less effect on the biohydrogenation intermediates profile compared to CO; noticeably, higher proportions of unsaturated fatty acid (UFA) were associated with NCO; these results were also supported by an increase in the rumen microbial population with NCO compared to CO, especially the biohydrogenation bacteria, which showed higher abundance with NCO despite the low presence of biohydrogenation intermediates. In conclusion, the NCO demonstrated the ability to decrease the transformation of unsaturated fatty acids into saturated fatty acids in the biohydrogenation environment. This effect was not associated with decreased dry matter intake, changes in nutrient digestibility, or alterations in fermentation patterns. Full article

Under long-term ecological stress, the Tarim wapiti (Cervus elaphus yarkandensis) has evolved unique adaptations in digestive physiology and energy metabolism. A multi-omics comparison of three Tarim wapiti and five Karakul sheep was used to examine the synergistic mechanism between rumen bacteria, short-chain fatty acids, and host epithelial regulation in order to clarify the mechanism of high roughage digestion efficiency in Tarim wapiti. Metagenomic sequencing (Illumina NovaSeq 6000) and gas chromatography revealed that Tarim wapiti exhibited significantly higher acetate and total VFA (TVFA) concentrations compared to Karakul sheep (p < 0.01), accompanied by lower ruminal pH and propionate levels. Core microbiota analysis identified Bacteroidetes (relative abundance: 52.3% vs. 48.1%), Prevotellaceae (22.7% vs. 19.4%), and Prevotella (18.9% vs. 15.6%) as dominant taxa in both species, with significant enrichment of Bacteroidetes in wapiti (p < 0.01). Functional annotation (PICRUSt2) demonstrated enhanced glycan biosynthesis (KEGG ko00511), DNA replication/repair (ko03430), and glycoside hydrolases (GH20, GH33, GH92, GH97) in wapiti (FDR < 0.05). Transcriptomic profiling (RNA-Seq) of rumen epithelium showed upregulated expression of SCFA transporters (PAT1: 2.1-fold, DRA: 1.8-fold, AE2: 2.3-fold; p < 0.01) and pH regulators (Na⁺/K⁺ ATPase: 1.7-fold; p < 0.05) in wapiti. Integrated analysis revealed coordinated microbial–host interactions through three key modules: (1) Bacteroidetes-driven polysaccharide degradation, (2) GHs-mediated fiber fermentation, and (3) epithelial transporters facilitating short-chain fatty acids absorption. These evolutionary adaptations, particularly the Bacteroidetes–short-chain fatty acids–transporter axis, likely underpin the wapiti’s superior roughage utilization efficiency, providing molecular insights for improving ruminant feeding strategies in an arid environment. Full article