Identification of Uncultured Bacterial Species from Firmicutes, Bacteroidetes and CANDIDATUS Saccharibacteria as Candidate Cellulose Utilizers from the Rumen of Beef Cows

In-Silico and in vitro Studies Revealed that Rosmarinic Acid Inhibited Methanogenesis via Regulating Composition and Function of Rumen Microbiota

Inhibition of methyl-coenzyme M reductase can suppress the activity of ruminal methanogens, thereby reducing enteric methane emissions of ruminants. However, developing specific and environmentally friendly inhibitors is a challenging endeavor. To identify a natural and effective methane inhibitor that specifically targets methyl-coenzyme M reductase, molecular docking technology was employed to screen a library of phytogenic compounds. A total of 52 candidate compounds were obtained through molecular docking technique. Rosmarinic acid (RA) was one of the compounds that could traverse a narrow channel and bind to the active sites of methyl-coenzyme M reductase, with a calculated binding free energy of -9.355 kcal/mol. Furthermore, the effects of rosmarinic acid supplementation on methane production, rumen fermentation, and the microorganism's community in dairy cows were investigated through in vitro rumen fermentation simulations according to a random design. Supplementation of RA resulted in a 15% decrease in methane production compared with the control. In addition, RA increased the molar proportion of acetate and propionate, whereas the sum of acetate and butyrate divided by propionate was decreased. At the bacterial level, the relative abundance of Rikenellaceae RC9 gut group, Christensenellaceae R7 group, Candidatus Saccharimonas, Desulfovibrio, and Lachnospiraceae FE2018 group decreased with RA supplementation. Conversely, the addition of RA significantly increased the relative abundance of DNF00809 (a genus from Eggerthellaceae), Denitrobacterium, an unclassified genus from Eggerthellaceae, an unclassified genus from Bacteroidales, and an unclassified genus from Atopobiaceae. At the archaeal level, the relative abundance of Methanobrevibacter decreased, while that of Methanosphaera increased with the RA supplementation. These findings suggested that RA has the potential to be used as a novel natural additive for inhibiting ruminal methane production.

Effects of Palm Oil Deodorizer Distillate on the Ruminal Environment of Sheep

This study aimed to assess the impact of palm oil deodorizer distillate (POD) on the ruminal environment, including (i) microbial community, (ii) ruminal degradability, and (iii) apparent digestibility in sheep. The data used were derived from twenty rumen-cannulated sheep fed five isoproteic and isofiber diets based on elephant grass (Pennisetum purpureum Schum. cv. Roxo) silage supplemented with 0, 25, 50, 75, or 100 g kg-1 POD on a dry matter (DM) basis. Rumen fluid samples were collected three hours after feeding directly from the ventral sac of the rumen via a cannula and then subjected to DNA extraction, which was subsequently used for 16S rDNA amplification, followed by sequencing and diversity analysis. In this study, the microbial diversity was dominated by Bacteroidetes and Firmicutes, followed by Euryarchaetoa, Actinobacteria, and Tenericutes, in the ruminal environment, and was slightly modified when supplemented with the POD up to 100 g/kg (10%), leading to only a slight decrease in the diversity index. The ruminal degradability, ruminal fermentation parameters, and apparent digestibility were slightly compromised by the inclusion of up to 25 g of POD per kg of DM, and larger inclusions interfered with the ruminal degradability of fibrous fractions and the apparent digestibility of dry matter. This lipid supplement showed good results for feeding sheep and is an inexpensive and abundant alternative in the regional market.

Effects of adding bile acids to dietary storage japonica brown rice on growth performance, meat quality, and intestinal microbiota of growing-finishing Min pigs

Introduction

This study investigated the effects of storage japonica brown rice (SJBR) and bile acids (BA) on the growth performance, meat quality, and intestinal microbiota of growing-finishing Min pigs.

Methods

A total of 24 healthy Min pigs with a similar body weight of 42.25 ± 2.13 kg were randomly divided into three groups with eight replicates of one pig each. The groups were as follows: CON (50% corn), SJBR (25% corn +25% SJBR), and SJBR + BA (25% corn +25% SJBR +0.025% hyodeoxycholic acid). The experimental period lasted from day 90 (the end of the nursery phase) to day 210 (the end of the finishing phase).

Results

The results showed the following: (1) Compared with the CON group, there was no significant difference in the average daily gain (ADG) and average daily feed intake (ADFI) of the SJBR and SJBR + BA groups, and the feed conversion ratio (FCR) was significantly decreased (p < 0.05). (2) Compared with the CON group, the total protein (TP) content in the serum was significantly increased, and the blood urea nitrogen (BUN) content was significantly decreased (p < 0.05) in the SJBR and SJBR + BA groups; moreover, HDL-C was significantly higher by 35% (p < 0.05) in the SJBR + BA group. (3) There were no significant differences in carcass weight, carcass length, pH, drip loss, cooking loss, and shear force among the groups; the eye muscle area was significantly increased in the SJBR group compared with the CON group (p < 0.05); back fat thickness was significantly decreased in the SJBR + BA group compared with the SJBR group (p < 0.05); and the addition of SJBR significantly increased the mRNA expression of MyHC I in the longissimus dorsi (LD) muscle of growing-finishing Min pigs (p < 0.05). (4) The cecal bacteria were detected using 16S rDNA, and the proportion of Lactobacillus was increased gradually at the genus level, but there was no significant difference among the different groups.

Conclusion

In conclusion, 25% SJBR can improve the growth performance and increase the abundance of intestinal beneficial bacteria, and based on this, adding bile acids can reduce the back fat thickness of growing-finishing Min pigs.

Tracking the extracellular and intracellular antibiotic resistance genes across whole year in wastewater of intensive dairy farm

Monitoring the annual variation of antibiotic resistance genes (ARGs) in livestock wastewater is important for determining the high-risk period of transfer and spread of animal-derived antibiotic resistance into the environment. However, the knowledge regarding the variation patterns of ARGs, especially intracellular ARGs (iARGs) and extracellular ARGs (eARGs), over time in livestock wastewater is still unclear. Herein, we conducted a year-round study to trace the profiles of ARGs at a Chinese-intensive dairy farm, focusing on the shifts observed in different months. The results showed significant differences in the composition and variation between iARGs and eARGs. Tetracycline, sulfonamide, and macrolide resistance genes were the major types of iARGs, while cfr was the major type of eARG. The environmental adaptations of the host bacteria determine whether ARGs appear as intracellular or extracellular forms. The total abundance of ARGs was higher from April to September, which can be attributed to the favorable climatic conditions for bacterial colonization and increased antibiotic administration during this period. Integron was found to be highly correlated with most iARGs, potentially playing a role in the presence of these genes within cells and their similar transmission patterns in wastewater. The intracellular and extracellular bacterial communities were significantly different, primarily because of variations in bacterial adaptability to the high salt and anaerobic environment. The intracellular co-occurrence network indicated that some dominant genera in wastewater, such as Turicibacter, Clostridium IV, Cloacibacillus, Subdivision5_genera_incertae_sedis, Saccharibacteria_genera_incertae_sedis and Halomonas, were potential hosts for many ARGs. To the best of our knowledge, this study demonstrates, for the first time, the annual variation of ARGs at critical points in the reuse of dairy farm wastewater. It also offers valuable insights into the prevention and control of ARGs derived from animals.

High potential for biomass-degrading CAZymes revealed by pine forest soil metagenomics

The undisturbed environment in Netarhat, with its high levels of accumulated lignocellulosic biomass, presents an opportunity to identify microbes for biomass digestion. This study focuses on the bioprospecting of native soil microbes from the Netarhat forest in Jharkhand, India, with the potential for lignocellulosic substrate digestion. These biocatalysts could help overcome the bottleneck of biomass saccharification and reduce the overall cost of biofuel production, replacing harmful fossil fuels. The study used metagenomic analysis of pine forest soil via whole genome shotgun sequencing, revealing that most of the reads matched with the bacterial species, very low percentage of reads (0.1%) belongs to fungal species, with 13% of unclassified reads. Actinobacteria were found to be predominant among the bacterial species. MetaErg annotation identified 11,830 protein family genes and 2 metabolic marker genes in the soil samples. Based on the Carbohydrate Active EnZyme (CAZy) database, 3,996 carbohydrate enzyme families were identified, with family Glycosyl hydrolase (GH) dominating with 1,704 genes. Most observed GH families in the study were GH0, 3, 5, 6. 9, 12. 13, 15, 16, 39, 43, 57, and 97. Modelling analysis of a representative GH 43 gene suggested a strong affinity for cellulose than xylan. This study highlights the lignocellulosic digestion potential of the native microfauna of the lesser-known pine forest of Netarhat.Communicated by Ramaswamy H. Sarma.

Physiological Conditions Leading to Maternal Subclinical Ketosis in Holstein Dairy Cows Can Impair the Offspring's Postnatal Growth and Gut Microbiome Development

Maternal metabolic disruptions, such as ketosis, can have adverse effects on fetal development and influence postnatal factors. Twelve Holstein calves were randomly enrolled in this study at birth and monitored until 8 weeks of age. The study was conducted from fall 2018 until spring 2019. After completing the data collection period, calves were classified according to their respective dams ketotic condition after parturition. This classification was based on dam blood β-hydroxybutyrate < 1.4 mmol/L nonketotic (NONKET; n = 6 calves) or ≥1.4 mmol/L subclinical-ketotic (SK; n = 6 calves). SK calves had greater birth body weight (p = 0.05) but exhibited a slower growth rate compared to NONKET calves from 1 to 8 weeks (p = 0.02). At birth, SK calves had lower (p < 0.01) levels of non-esterified fatty acids and bilirubin compared to NONKET calves. Analysis of feces alpha diversity indicates that by 3 weeks, NONKET calves had greater diversity, richness, and evenness. Butyricicoccus pullicaecorum and Gallibacterium anatis were more abundant in SK calves (p < 0.05) at 3 weeks. In contrast, NONKET calves had a greater (p < 0.05) abundance of Sharpae azabuensis at 3 weeks. These findings suggest that subclinical ketosis in cows can impact the in-utero development, postnatal growth, and maturing gut microbiome of their offspring.

Metagenomics-Based Analysis of Candidate Lactate Utilizers from the Rumen of Beef Cattle

In ruminant livestock production, ruminal acidosis is an unintended consequence of the elevated dietary intake of starch-rich feedstuffs. The transition from a state of subacute acidosis (SARA) to acute acidosis is due in large part to the accumulation of lactate in the rumen, which is a consequence of the inability of lactate utilizers to compensate for the increased production of lactate. In this report, we present the 16S rRNA gene-based identification of two bacterial operational taxonomic units (OTUs), Bt-01708_Bf (89.0% identical to Butyrivibrio fibrisolvens) and Bt-01899_Ap (95.3% identical to Anaerococcus prevotii), that were enriched from rumen fluid cultures in which only lactate was provided as an exogenous substrate. Analyses of in-silico-predicted proteomes from metagenomics-assembled contigs assigned to these candidate ruminal bacterial species (Bt-01708_Bf: 1270 annotated coding sequences, 1365 hypothetical coding sequences; Bt-01899_Ap: 871 annotated coding sequences, 1343 hypothetical coding sequences) revealed genes encoding lactate dehydrogenase, a putative lactate transporter, as well as pathways for the production of short chain fatty acids (formate, acetate and butyrate) and for the synthesis of glycogen. In contrast to these shared functions, each OTU also exhibited distinct features, such as the potential for the utilization of a diversified set of small molecules as substrates (Bt-01708_Bf: malate, quinate, taurine and polyamines) or for the utilization of starch (Bt-01899_Ap: alpha-amylase enzymes). Together, these results will contribute to the continued characterization of ruminal bacterial species that can metabolize lactate into distinct subgroups based on other metabolic capabilities.

Effect of supplementation with ruminal probiotics on growth performance, carcass characteristics, plasma metabolites, methane emissions, and the associated rumen microbiome changes in beef cattle

To evaluate the effect of supplementing beef cattle with a ruminal probiotic consisting of native rumen microbes (NRM; Chordicoccus furentiruminis, Prevotella albensis, and Succinivibrio dextrinosolvens) on methane (CH4) emissions, growth performance, carcass characteristics, and plasma metabolites, Angus × SimAngus-crossbred steers (n = 32; 8 per pen) and heifers (n = 48; 12 per pen) with an initial body weight (BW) of 353 ± 64 kg were used in randomized complete block design. Cattle were blocked by sex and BW and randomly assigned to 1 of 2 treatments (2 pens per treatment). Treatments consisted of diets offered for ad libitum intake with (NRM) or without (CON) the inclusion of the ruminal probiotic. Cattle were fed a growing diet for 49 d followed by a ground corn-based diet for 124 ± 27 d until reaching the targeted final BW (635 kg for steers and 590 kg for heifers). Methane emissions were estimated using the GreenFeed system (n = 12 per treatment) prior to trial commencement (baseline; period 1), and on three (2, 3, and 4), and two (5 and 6) different sampling periods throughout the growing and finishing stage, respectively. All data were analyzed using the PROC MIXED procedure of SAS. For CH4 production (g/d), there was a tendency for an NRM supplementation × period interaction (P = 0.07) where cattle-fed diets with NRM had lower production of methane in periods 3 and 4. Including NRM in the diet decreased CH4 yield (g/kg of dry matter intake (DMI)) by 20%. For CH4 emission intensity (g/kg of average daily gain (ADG)), an interaction (P < 0.01) of NRM supplementation × period occurred. In periods 2 and 3, cattle-fed diets with NRM inclusion had lower CH4 emission intensity than CON cattle. During the 84-d period when all cattle were still on the finishing diet, feeding NRM increased (P = 0.02) ADG and tended to increase (P = 0.10) DMI. At the end of the 84-d period, cattle-fed NRM tended to be heavier (P = 0.06) than CON cattle. Cattle supplemented with NRM required less (P = 0.04) days on feed to reach the targeted final BW. No differences (P ≤ 0.11) were detected for gain-to-feed ratio and carcass characteristics. Cattle-fed NRM had greater abundance of uncultured rumen bacteria that may improve rumen digestion when fed a high grain diet and potentially promote the reduction of enteric CH4 production. Results from this study suggest that daily administration of NRM may be a strategy to mitigate methanogenesis and improve the growth performance of beef cattle.

Distribution of bacteria in different regions of the small intestine with Zanthoxylum bungeanum essential oil supplement in small-tailed Han sheep

Zanthoxylum bungeanum essential oil (EOZB) as an extract of Zanthoxylum bungeanum has a range of pharmacological effects such as antibacterial, anti-inflammatory, and antioxidant. However, there were no relevant studies on the regulation of gut microbes by EOZB in ruminants. In this study, the effects of different doses of EOZB on the structure and distribution of microorganisms in the small intestine of small-tailed Han sheep (STH) were investigated by 16s rRNA gene sequencing technique. We found that with the intervention of EOZB. The differential bacteria of duodenal at the phylum level were Firmicutes, Bacteroidetes, Tenericutes and Proteobacteria, and genus level differential bacteria were Prevotella 1, Ruminococcus 2 and Eubacterium coprostanoligenes group. The differential bacteria of jejunal at the phylum level were Firmicutes, Bacteroidetes, Tenericutes and Proteobacteria, and genus level differential bacteria were Prevotella 1, Rikenellaceae RC9 gut group, Christensenellaceae R-7 group, Ruminococcaceae UCG-014, Saccharofermentans, Ruminococcaceae NK4A214 group and Prevotellaceae UCG-001. The differential bacteria of ileal at the phylum level were Firmicutes, Bacteroidetes and Tenericutes, and genus level differential bacteria were Prevotella 1, Christensenellaceae R-7 group, Romboutsia and Ruminococcaceae UCG-014. In addition, at the same dose of EOZB, the five most abundant genera of bacteria varied in different regions of the small intestine. Among them, the abundance of Prevotella 1, Christensenellacea R-7 group and Ruminococcus 2 in ALW group was the highest in jejunum, duodenum and ileum, respectively. The abundance of Prevotella 1, Christensenellacea R-7 group and Rikenellacea RC9 gut group in BLW group was the highest in duodenum, jejunum and ileum, respectively. The abundance of Prevotella 1, Christensenellacea R-7 group and Ruminococcaeae NK4A214 group in CLW group was the highest in jejunum, duodenum and ileum, respectively. The abundance of Prevotella 1, Ruminococcus 2 and Ruminococcus NK4A214 groups in DLW group was the highest in jejunum, duodenum and ileum, respectively. Differential bacteria formed under the regulation of EOZB are associated with the digestion and absorption of nutrients and the state of intestinal health in the host. This study is the first to investigate the effect of EOZB on the distribution and structure of bacteria in the small intestine of STH. The results of the study enriched the structure and distribution of bacteria in the small intestine of ruminants and provided new insights into the future application of herbal medicine in ruminant production. Additionally, it provides a theoretical basis for the selection of probiotic bacteria for ruminants and the development and application of microecological preparations.

Degradation of Cellulose and Hemicellulose by Ruminal Microorganisms

As major structural components of plant cell walls, cellulose and hemicellulose are degraded and fermented by anaerobic microbes in the rumen to produce volatile fatty acids, the main nutrient source for the host. Cellulose degradation is carried out primarily by specialist bacteria, with additional contributions from protists and fungi, via a variety of mechanisms. Hemicelluloses are hydrolyzed by cellulolytic bacteria and by generalist, non-cellulolytic microbes, largely via extracellular enzymes. Cellulose hydrolysis follows first-order kinetics and its rate is limited by available substrate surface area. Nevertheless, its rate is at least an order of magnitude more rapid than in anaerobic digesters, due to near-obligatory adherence of microbial cells to the cellulose surface, and a lack of downstream inhibitory effects; in the host animal, fiber degradation rate is also enhanced by the unique process of rumination. Cellulolytic and hemicellulolytic microbes exhibit intense competition and amensalism, but they also display mutualistic interactions with microbes at other trophic levels. Collectively, the fiber-degrading community of the rumen displays functional redundancy, partial niche overlap, and convergence of catabolic pathways that all contribute to stability of the ruminal fermentation. The superior hydrolytic and fermentative capabilities of ruminal fiber degraders make them promising candidates for several fermentation technologies.

Red seaweed extracts reduce methane production by altering rumen fermentation and microbial composition in vitro

A series of in vitro batch culture incubations were carried out to investigate changes in rumen fermentation characteristics, methane (CH4) production, and microbial composition in response to supplementation with five different red seaweed species (Amphiroa anceps, AANC; Asparagopsis taxiformis, ATAX; Chondracanthus tenellus, CTEN; Grateloupia elliptica, GELL; and Gracilaria parvispora, GPAR). Prior to the incubations, the total flavonoid and polyphenol content of the red seaweed extracts was quantified. The incubated substrate consisted of timothy hay and corn grain [60:40 dry matter (DM) basis]. Treatments were substrate mixtures without seaweed extract (CON) or substrate mixtures supplemented with 0.25 mg/mL of red seaweed extract. Samples were incubated for 6, 12, 24, 36, and 48 h. Each sample was incubated in triplicates in three separate runs. In vitro DM degradability, fermentation parameters (i.e., pH, volatile fatty acids, and ammonia nitrogen), total gas production, and CH4 production were analyzed for all time points. Microbial composition was analyzed using 16S rRNA amplicon sequencing after 24 h of incubation. The highest CH4 reduction (mL/g DM, mL/g digested DM, and % of total gas production) was observed in ATAX (51.3, 50.1, and 51.5%, respectively, compared to CON; P < 0.001) after 12 h of incubation. The other red seaweed extracts reduced the CH4 production (mL/g DM; P < 0.001) in the range of 4.6-35.0% compared to CON after 24 h of incubation. After 24 h of incubation, supplementation with red seaweed extracts tended to increase the molar proportion of propionate (P = 0.057) and decreased the acetate to propionate ratio (P = 0.033) compared to the CON. Abundances of the genus Methanobrevibacter and total methanogens were reduced (P = 0.050 and P = 0.016) by red seaweed extract supplementation. The linear discriminant analysis effect size (P < 0.05, LDA ≥ 2.0) showed that UG Succinivibrionaceae, Anaeroplasma, and UG Ruminococcaceae, which are associated with higher propionate production, starch degradation, and amylase activity were relatively more abundant in red seaweed extracts than in the CON. Our results suggest that supplementation with red seaweed extracts altered the microbiota, leading to the acceleration of propionate production and reduction in CH4 production.

The gastrointestinal microbiome of browsing goats (Capra hircus)

Despite the growing interest in the ruminants' gastrointestinal tract (GIT) microbiomes' ability to degrade plant materials by animal husbandry and industrial sectors, only a few studies addressed browsing ruminants. The present work describes the taxonomic and functional profile of the bacterial and archaeal communities from five different gastrointestinal sections (rumen, omasum-abomasum, jejunum, cecum and colon) of browsing Capra hircus, by metabarcoding using 16S rRNA genes hypervariable regions. The bacterial communities across the GITs are mainly composed of Bacillota and Bacteroidota. Prevotella was the leading bacterial group found in the stomachs, Romboutsia in the jejuna, and Rikenellaceae_RC9_gut_group, Bacteroides, UCG-010_ge, UCG-005, and Alistipes in large intestines. The archaeal communities in the stomachs and jejuna revealed to be mainly composed of Methanobrevibacter, while in the large intestines its dominance is shared with Methanocorpusculum. Across the GITs, the main metabolic functions were related to carbohydrate, amino acid, and energy metabolisms. Significant differences in the composition and potential biological functions of the bacterial communities were observed among stomachs, jejuna and large intestines. In contrast, significant differences were observed among stomachs and jejuna verse large intestines for archaeal communities. Overall different regions of the GIT are occupied by different microbial communities performing distinct biological functions. A high variety of glycoside hydrolases (GHs) indispensable for degrading plant cell wall materials were predicted to be present in all the GIT sections.

Effects of Concentrate Supplementation on Growth Performance, Rumen Fermentation, and Bacterial Community Composition in Grazing Yaks during the Warm Season

This study aimed to evaluate the effects of concentrate supplementation on the growth performance, serum biochemical parameters, rumen fermentation, and bacterial community composition of grazing yaks during the warm season. Eight male yaks (body weight, 123.96 ± 7.43 kg; 3-years) were randomly allocated to two treatments groups: grazing (n = 4, GY) and concentrate supplement group (n = 4, GYS). Concentrate supplementation increased the average daily gain (ADG) (p < 0.05). Glucose (GLU), total protein (TP), and aspartate aminotransferase (AST) serum concentrations were significantly higher in the GYS group than in the GY group (p < 0.05). Ammonia-N, MCP: microbial protein, and total volatile fatty acid concentrations were significantly higher in the GYS group than in the GY group (p < 0.01), whereas the pH and acetate: propionate values were significantly decreased (p < 0.01). The relative abundance of Firmicutes in the rumen fluid was significantly higher in the GYS group than in the GY group (p < 0.01). At the genus level, the relative abundances of Succiniclasticum, Prevotellaceae_UCG_003, Prevotellaceae_UCG_005, and Ruminococcus_1 were significantly greater in the GY group than in the GYS group (p < 0.01). In conclusion, concentrate supplementation improved yaks’ growth potential during the warm season, improved ruminal fermentation, and altered core bacteria abundance.

Contribution of Ruminal Bacteriome to the Individual Variation of Nitrogen Utilization Efficiency of Dairy Cows

High nitrogen utilization efficiency (NUE) is important for increasing milk protein production and decreasing the feed nitrogen cost and nitrogen emission to the environment. Currently, there is a limited whole picture of the relationship between ruminal bacteriome and the NUE of dairy cows, even though some information has been revealed about the bacteriome and milk or milk protein production of dairy cows. The purpose of this study was to compare the rumen bacterial community in dairy cows with different nitrogen utilization efficiency under the same diet. The natural abundance of 15N between the animal proteins and diet (Δ15N) was used as a simple, non-invasive, and accurate biomarker for NUE in ruminants to mark the individual variation. Dairy cows with high NUE (HE_HP, n = 7), medium NUE (ME_MP, n = 7), and low NUE (LE_LP, n = 7) were selected from 284 Holstein dairy cows with the same diet. Measurement of the rumen fermentation indices showed that the proportion of propionate was higher in HE_HP cows and ME_MP cows than in LE_LP cows (P < 0.05). The diversity of rumen bacterial community was higher in LE_LP cows than in ME_MP cows and HE_HP cows by 16S rRNA sequencing analysis (P < 0.05). Moreover, at the genus level, the relative abundances of Succinivibrionaceae_UCG_001, uncultured_Selenomonadaceae, and Acidaminococcus were higher in HE_HP cows than in LE_LP cows (P < 0.05). Interestingly, we found that these bacteria were positively correlated with milk protein yield and negatively correlated with Δ15N (P < 0.05). However, Clostridia_UCG_014, Saccharofermentans, Bacilli_RF39, and Desulfovibrio were lower in HE_HP cows and ME_MP cows than in LE_LP cows (P < 0.05), which were negatively correlated with milk protein yield and positively correlated with Δ15N (P < 0.05). In conclusion, the study showed that the diversity and relative abundances of rumen bacteria differed among different NUE cows, indicating that rumen bacteriome contributes to nitrogen metabolism in dairy cows.

The structure and functional profile of ruminal microbiota in young and adult reindeers (Rangifer tarandus) consuming natural winter-spring and summer-autumn seasonal diets

Background

The key natural area of Russian reindeer (Rangifer tarandus, Nenets breed) is arctic zones, with severe climatic conditions and scarce feed resources, especially in the cold winter season. The adaptation of reindeer to these conditions is associated not only with the genetic potential of the animal itself. The rumen microbiome provides significant assistance in adapting animals to difficult conditions by participating in the fiber digestion. The aim of our study is to investigate the taxonomy and predicted metabolic pathways of the ruminal microbiota (RM) during the winter–spring (WS) and summer–autumn (SA) seasons, in calves and adult reindeer inhabiting the natural pastures of the Yamalo-Nenetsky Autonomous District of the Russian Federation.

Methods

The RM in reindeer was studied using the Next Generation Sequencing method with the MiSeq (Illumina, San Diego, CA, USA) platform. Reconstruction and prediction of functional profiles of the metagenome, gene families, and enzymes were performed using the software package PICRUSt2 (v.2.3.0).

Results

The nutritional value of WS and SA diets significantly differed. Crude fiber content in the WS diet was higher by 22.4% (p < 0.05), compared to SA, indicating possibly poorer digestibility and necessity of the adaptation of the RM to this seasonal change. A total of 22 bacterial superphyla and phyla were found in the rumen, superphylum Bacteroidota and phylum Firmicutes being the dominating taxa (up to 48.1% ± 4.30% and 46.1% ± 4.80%, respectively); while only two archaeal phyla presented as minor communities (no more then 0.54% ± 0.14% totally). The percentages of the dominating taxa were not affected by age or season. However, significant changes in certain minor communities were found, with seasonal changes being more significant than age-related ones. The percentage of phylum Actinobacteriota significantly increased (19.3-fold) in SA, compared to WS (p = 0.02) in adults, and the percentage of phylum Cyanobacteria increased up to seven-fold (p = 0.002) in adults and calves. Seasonal changes in RM can improve the ability of reindeer to withstand the seasons characterized by a low availability of nutrients. The PICRUSt2 results revealed 257 predicted metabolic pathways in RM: 41 pathways were significantly (p < 0.05) influenced by season and/or age, including the processes of synthesis of vitamins, volatile fatty acids, and pigments; metabolism of protein, lipids, and energy; pathogenesis, methanogenesis, butanediol to pyruvate biosynthesis, cell wall biosynthesis, degradation of neurotransmitters, lactic acid fermentation, and biosynthesis of nucleic acids. A large part of these changeable pathways (13 of 41) was related to the synthesis of vitamin K homologues.

Conclusion

The results obtained improve our knowledge on the structure and possible metabolic pathways of the RM in reindeer, in relation to seasonal changes.

Effects of mulberry leaf silage on antioxidant and immunomodulatory activity and rumen bacterial community of lambs

Background

Rumen is a natural fermentation system and the microorganisms inside can effectively utilize plant bioresource and interact with host metabolism. Here, analysis of rumen microbiome, together with animal performance and serum metabolism in a lamb model were performed to identify the potential use of mulberry leaf silage (MS) to replace alfalfa silage (AS) as a new functional feed resource and to mining the novel specific mulberry leaf associated rumen bacteria interact with host metabolism.

Results

The lambs fed with MS diet showed improved antioxidant capacity and immune function compared to those fed AS diet. The MS diet significantly altered rumen microbiota α- and β-diversity and taxonomic composition. Microbial analysis revealed that Bifidobacterium, Lactobacillus and Schwartzia were enhanced, and Ruminococcaceae UCG-010 and Lachnospiraceae_XPB1014_group were down-regulated in the rumen of MS group. A strong association was also found between these rumen microbial taxa and host antioxidant and immunomodulatory capacity.

Conclusion

These findings indicated that mulberry leaf silage can be a high-quality feed source or bioactive pharmaceutical that is responsible for ruminant’s health benefits. The modified rumen microbial community by mulberry leaf silage were associated with the enhanced antioxidant capacity and immunomodulatory of lambs.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02311-1.

Early Life Fecal Microbiota Transplantation in Neonatal Dairy Calves Promotes Growth Performance and Alleviates Inflammation and Oxidative Stress during Weaning

This study aimed to evaluate the effects of early life fecal microbiota transplantation (FMT) on the health and performance of neonatal dairy calves. The donor was selected based on health and production records and fecal material testing negative for infectious pathogens. Sixteen healthy newborn Holstein calves were randomized to either a baseline nutritional program (CON) or 1×/d inoculations with 25 g of fecal donor material (FMT) mixed in the milk replacer (n = 8/TRT) from 8 to 12 days of age. Blood and fecal samples were collected weekly, and calves were weaned at 7 weeks of age. A TRT × Week interaction was observed in haptoglobin, which was reflected in a positive quadratic effect in FMT calves but not in CON. A trend for a TRT × Week interaction was observed in the liver function biomarker paraoxonase, which resulted in greater paraoxonase in FMT calves than CON at three weeks of age. Fecal microbial community analysis revealed a significant increase in the alpha-diversity between week 1 and week 5 for the FMT calves. These results suggest that early life FMT in neonatal calves has positive effects in mediating the inflammatory response and gut microbial maturation.

Comparative study of growth performance, nutrient digestibility, and ruminal and fecal bacterial community between yaks and cattle-yaks raised by stall-feeding

The experiment was conducted to compare the growth performance, rumen fermentation, nutrient digestibility, and ruminal and fecal bacterial community between yaks and cattle-yaks. Ten male yaks (36-month-old) were used as the yak (YAK) group and 10 male cattle-yaks with similar age were selected as the cattle-yak (CAY) group. All the animals were fed same ration and the experiment lasted for 60 days. The results showed that the average daily gain and dry matter intake of CAY group were higher (P < 0.05) than those of YAK group. The ruminal concentrations of total volatile fatty acids, acetate, and butyrate were higher (P < 0.05) in CAY group than those in YAK group. However, the neutral detergent fiber and acid detergent fiber digestibility exhibited an opposite between two groups. In the rumen, the relative abundances of Prevotella 1 and Prevotellaceae UCG-001 were higher (P < 0.05) and Succiniclasticum and Butyrivibrio 2 were lower (P < 0.05) in YAK group compared to CAY group. In the feces, the unclassified Lachnospiraceae, Lachnospiraceae NK4A136 group, and Lachnospiraceae AC2044 group were significantly enriched (P < 0.05) in YAK group, whereas the Ruminococcaceae UCG-010, Ruminococcaceae UCG-013, and Succiniclasticum were significantly enriched (P < 0.05) in CAY group. Overall, under the same diet, the yaks have higher fiber utilization and cattle-yaks have higher energy utilization.

Inter and intraspecies comparison of the level of selected bacterial phyla in in cattle and sheep based on feces

Background

The microbiome of the digestive tract of ruminants contains microbial ecosystem that is affected by both environmental and genetic factors. The subject of this study concerns the influence of selected genetic factors, such as species of animals and “host” individual differences on the digestive tract microbiome composition. The results show the core microbiological composition (Firmicutes and Bacteroidetes) of ruminants digestive tract (based on feces) depending on breed and “host”. The Bacteroidetes and Firmicutes phyla are the most abundant in ruminants digestive tract. The aim of the study was to determine the differences prevalence level of Bacteroidetes and Firmicutes phyla in feces of Charolaise cattle and Polish Olkuska Sheep with respect to intra- and inter-species variability.

Results

The research group in the experiment consisted of animals at the age of 3 months kept in the same environmental conditions – rams of Polish Olkuska Sheep (n = 10) and Charolaise bulls (n = 10). Feces were collected individually from each animal (animals without disease symptoms were selected), living on the same environmental conditions. The analysis of the results in terms of species showed differences in the Firmicutes phylum level and Lactobacillaceae family between rams and bulls. Subsequently, the analysis performed for the “host effect” showed differentiation in the levels of the Bacteroidetes and Firmicutes phyla between individuals in a group and also between the groups.

Conclusion

The obtained results suggest that, apart from the diet and the environment, the species and the individual host are equally important factors influencing the microbiological composition of the digestive system of ruminants.

Characterization of the bacterial microbiota across the different intestinal segments of the Qinghai semi-fine wool sheep on the Qinghai-Tibetan Plateau

Objective

The intestinal microbiota enhances nutrient absorption in the host and thus promotes heath. Qinghai semi-fine wool sheep is an important livestock raised in the Qinghai-Tibetan Plateau; however, little is known about the bacterial microbiota of its intestinal tract. The aim of this study was to detect the microbial characterization in the intestinal tract of the Qinghai semi-fine wool sheep.

Methods

The bacterial profiles of the six different intestinal segments (duodenum, jejunum, ileum, cecum, colon and rectum) of Qinghai semi-fine wool sheep were studied using 16S rRNA V3-V4 hypervariable amplicon sequencing.

Results

A total of 2,623,323 effective sequences were obtained, and 441 OTUs shared all six intestinal segments. The bacterial diversity was significantly different among the different intestinal segments, and the large intestine exhibited higher bacterial diversity than the small intestine. Firmicutes, Bacteroidetes, and Patescibacteria were the dominant phyla in these bacterial communities. Additionally, at the genus level, Prevotella_1, Candidatus_Saccharimonas, and Ruminococcaceae_UCG-005 were the most predominant genus in duodenal segment, jejunal and ileal segments, and cecal, colonic, and rectal segments, respectively. We predicted that the microbial functions and the relative abundance of the genes involved in carbohydrate metabolism were overrepresented in the intestinal segments of Qinghai semi-fine wool sheep.

Conclusion

The bacterial communities and functions differed among different intestinal segments. Our study is the first to provide insights into the composition and biological functions of the intestinal microbiota of Qinghai semi-fine wool sheep. Our results also provide useful information for the nutritional regulation and production development in Qinghai semi-fine wool sheep.

Effects of a Bioprocessed Soybean Meal Ingredient on the Intestinal Microbiota of Hybrid Striped Bass, Morone chrysops x M. saxatilis

The hybrid striped bass (Morone chrysops x M. saxatilis) is a carnivorous species and a major product of US aquaculture. To reduce costs and improve resource sustainability, traditional ingredients used in fish diets are becoming more broadly replaced by plant-based products; however, plant meals can be problematic for carnivorous fish. Bioprocessing has improved nutritional quality and allowed higher inclusions in fish diets, but these could potentially affect other systems such as the gut microbiome. In this context, the effects of bioprocessed soybean meal on the intestinal bacterial composition in hybrid striped bass were investigated. Using high-throughput sequencing of amplicons targeting the V1-V3 region of the 16S rRNA gene, no significant difference in bacterial composition was observed between fish fed a control diet, and fish fed a diet with the base bioprocessed soybean meal. The prominent Operational Taxonomic Unit (OTU) in these samples was predicted to be a novel species affiliated to Peptostreptococcaceae. In contrast, the intestinal bacterial communities of fish fed bioprocessed soybean meal that had been further modified after fermentation exhibited lower alpha diversity (p < 0.05), as well as distinct and more varied composition patterns, with OTUs predicted to be strains of Lactococcus lactis, Plesiomonas shigelloides, or Ralstonia pickettii being the most dominant. Together, these results suggest that compounds in bioprocessed soybean meal can affect intestinal bacterial communities in hybrid striped bass.

High Potential for Biomass-Degrading Enzymes Revealed by Hot Spring Metagenomics

Enzyme stability and activity at elevated temperatures are important aspects in biotechnological industries, such as the conversion of plant biomass into biofuels. In order to reduce the costs and increase the efficiency of biomass conversion, better enzymatic processing must be developed. Hot springs represent a treasure trove of underexplored microbiological and protein chemistry diversity. Herein, we conduct an exploratory study into the diversity of hot spring biomass-degrading potential. We describe the taxonomic diversity and carbohydrate active enzyme (CAZyme) coding potential in 71 publicly available metagenomic datasets from 58 globally distributed terrestrial geothermal features. Through taxonomic profiling, we detected a wide diversity of microbes unique to varying temperature and pH ranges. Biomass-degrading enzyme potential included all five classes of CAZymes and we described the presence or absence of genes encoding 19 glycosyl hydrolases hypothesized to be involved with cellulose, hemicellulose, and oligosaccharide degradation. Our results highlight hot springs as a promising system for the further discovery and development of thermo-stable biomass-degrading enzymes that can be applied toward generation of renewable biofuels. This study lays a foundation for future research to further investigate the functional diversity of hot spring biomass-degrading enzymes and their potential utility in biotechnological processing.

Effect of substrate load on anaerobic fermentation of rice straw with rumen liquid as inoculum: Hydrolysis and acidogenesis efficiency, enzymatic activities and rumen bacterial community structure

Rumen liquid is excellent to effectively degrade lignocellulose. In this study, the suitable rice straw load during anaerobic fermentation of rice straw with rumen liquid as inoculum was explored to improve volatile fatty acid (VFA) production. At 10.0% rice straw load, the highest VFA concentration reached 10821.4 mg/L, and acetic acid and propionic acid were the main components. In 10.0% rice straw load system, high concentration of soluble chemical oxygen demand (SCOD) was also observed, and the enzymatic activities at 48 h were higher than those at other rice straw loads. At 10.0% rice straw load, lower diversity and richness of rumen bacteria were found than those at other rice straw loads. Bacteroides, Prevotella, and Ruminococcus were the main rumen bacteria during rice straw degradation, and the rumen bacteria might secret effective lignocellulolytic enzymes to enhance the hydrolysis and acidogenesis of rice straw. The determination of suitable rice straw load will be beneficial to the application of rumen liquid as inoculum in actual production.

Comparing the Bacterial Community in the Gastrointestinal Tracts Between Growth-Retarded and Normal Yaks on the Qinghai-Tibetan Plateau

In ruminants, the bacterial community in the gastrointestinal tract (GIT) has an essential role in healthy growth. Examining the bacterial composition in the GIT between growth-retarded and normal yaks could improve our understanding of the role of microorganisms in yaks with growth retardation. In this study, eight male yaks with growth retardation were used as the growth-retarded yak (GRY) group, and another eight male growth normal yaks (GNYs) with the same breed and age were used as the GNY group. We compared the bacterial community in the rumen, duodenum, jejunum, ileum, cecum, and colon between GRY and GNY groups based on the 16S ribosomal RNA gene sequencing. Alpha-diversity revealed that the Shannon index in the duodenum and ileum of the GNY group was higher (P < 0.05) than that of the GRY group. However, the opposite trend was found in the jejunum and cecum. The principal coordinates analysis (PCoA) showed that the bacterial structure in all segments of GIT differed from each other between two groups. In the rumen, the relative abundances of Ruminococcaceae NK4A214 group, Ruminococcaceae UCG-014, and Treponema 2 were higher (P < 0.05) in the GNY group as compared with the GRY group. However, the Christensenellaceae R-7 group exhibited an opposite trend. In the jejunum, compared with the GNY group, the unclassified Chitinophagaceae was enriched significantly (P < 0.05) in the GRY group. However, the unclassified Peptostreptococcaceae, Christensenellaceae R-7 group, and Lachnospiraceae NK3A20 group were enriched (P < 0.05) in the GNY group. In the ileum, the relative abundances of the Rikenellaceae RC9 gut group and Prevotellaceae UCG-004 were higher (P < 0.05) in the GNY group than those in the GRY group. In the cecum, the GNY group showed a higher (P < 0.05) relative abundance of Prevotellaceae UCG-003 as compared with the GRY group. In the colon, the relative abundances of Treponema 2 and unclassified Lachnospiraceae were slightly higher (0.05 < P < 0.10) in the GNY group than those in the GRY group. Overall, these results improve our knowledge about the bacterial composition in the GIT of growth-retarded and normal yaks, and regulating the bacterial community may be an effective solution to promote the compensatory growth of GRYs.

Identification of a Candidate Starch Utilizing Strain of Prevotella albensis from Bovine Rumen

The inclusion of starch-rich feedstuffs, a common practice in intensive ruminant livestock production systems, can result in ruminal acidosis, a condition that can severely impact animal performance and health. One of the main causes of acidosis is the rapid accumulation of ruminal short chain fatty acids (SCFAs) resulting from the microbial digestion of starch. A greater understanding of ruminal bacterial amylolytic activities is therefore critical to improving mitigation of acidosis. To this end, our manuscript reports the identification of a candidate starch utilizer (OTU SD_Bt-00010) using batch culturing of bovine rumen fluid supplemented with starch. Based on 16S rRNA gene sequencing and metagenomics analysis, SD_Bt-00010 is predicted to be a currently uncharacterized strain of Prevotella albensis. Annotation of de novo assembled contigs from metagenomic data not only identified sequences encoding for α-amylase enzymes, but also revealed the potential to metabolize xylan as an alternative substrate. Metagenomics also predicted that SCFA end products for SD_Bt-00010 would be acetate and formate, and further suggested that this candidate strain may be a lactate utilizer. Together, these results indicate that SD_Bt-00010 is an amylolytic symbiont with beneficial attributes for its ruminant host.

Recognition of core microbial communities contributing to complex organic components degradation during dry anaerobic digestion of chicken manure

Microbial metabolism of complex organic components can drive different microbial communities, which is significant to the process of dry anaerobic digestion (AD). However, possible mechanisms between organic components and the corresponding microbial communities during the process of dry AD is poorly investigated. Results showed that the microbial species affecting the degradation of organic components were 69 nodes (13.3%) in the hydrolysis stage, hemicellulose was mainly degraded by Methanobacterium (2.3%), with a degradation rate of 35.0%. In the acetogenesis stage, the microbial species were 27 nodes (10.3%), hemicellulose was mainly degraded by LK-44f (0.1%) and Treponema (0.3%), with a degradation rate of 52.2%. In the methanogenesis stage, the microbial species were 10 nodes (4.8%), polysaccharide was mainly degraded by Ureibacillus (0.1%), with a degradation rate of 46.9%. The study provides theoretical support for the rapid degradation of complex components by segment-oriented regulation.

Resveratrol affects in vitro rumen fermentation, methane production and prokaryotic community composition in a time- and diet-specific manner

This study aimed to investigate the effect of resveratrol on methane production, rumen fermentation and microbial composition under high-concentrate (HC) and high-forage (HF) diets using the in vitro fermentation system. A total of 25 mg of resveratrol was supplemented into 300 mg of either HC or HF diet. Methane production, total volatile fatty acid (VFA) concentration, molar proportion of VFA, metabolites of resveratrol and prokaryotic community composition were measured after 12 and 24 h of in vitro fermentation. Resveratrol reduced methane production (ml per mg of dry matter degraded) by 41% and 60% under both HC and HF diets (P < 0.001), respectively, and this result could be associated with the lower abundance of Methanobrevibacter (P < 0.001) in response to resveratrol. The molar proportion of propionate was significantly higher in the resveratrol group only under the HC diet (P = 0.045). The relative abundance of 10 bacterial genera was affected by the three-way interaction of treatment, diet and time (P < 0.05). Resveratrol was partly converted to dihydroresveratrol after 24 h of fermentation, and its degradation could be associated with microbes belonging to the order Coriobacteriales. Our results suggest that multiple factors (e.g. diet and time) should be considered in animal experiments to test the effect of polyphenol or other plant extracts on rumen fermentation, methane emission and microbial composition.

Effects of Dietary Energy Levels on Rumen Fermentation, Microbial Diversity, and Feed Efficiency of Yaks (Bos grunniens)

The microbial community of the yak (Bos grunniens) rumen plays an important role in surviving the harsh Tibetan environment where seasonal dynamic changes in pasture cause nutrient supply imbalances, resulting in weight loss in yaks during the cold season. A better understanding of rumen microbiota under different feeding regimes is critical for exploiting the microbiota to enhance feed efficiency and growth performance. This study explored the impact of different dietary energy levels on feed efficiency, rumen fermentation, bacterial community, and abundance of volatile fatty acid (VFA) transporter transcripts in the rumen epithelium of yaks. Fifteen healthy castrated male yaks were divided into three groups and fed with low (YL), medium (YM), and high energy (YH) levels diet having different NEg of 5.5, 6.2, and 6.9 MJ/kg, respectively. The increase in feed efficiency was recorded with an increase in dietary energy levels. The increase in dietary energy levels decreased the pH and increased the concentrations of acetate, propionate, butyrate, and valerate in yak rumens. The increase in the mRNA abundance of VFA transporter genes (MCT1, DRA, PAT1, and AE2) in the rumen epithelium of yaks was recorded as dietary energy level increased. High relative abundances of Firmicutes and Bacteroidetes were recorded with the increase in dietary energy levels. Significant population shifts at the genus level were recorded among the three treatments. This study provides new insights into the dietary energy-derived variations in rumen microbial community.

Study of Jianpi Mixture on Intestinal Microbiota of Diarrhea Irritable Bowel Syndrome Mice

To investigate the differences in intestinal microbiota between diarrhea irritable bowel syndrome mice (IBS-D) and healthy mice and to explore the effects of Jianpi mixture on intestinal microbes' changes in IBS-D mice based on 16S rDNA sequencing analysis. 48 young ICR male mice were randomly divided into four groups (n = 12): (1) control group, (2) IBS-D group fed with distilled water, (3) IBS-D group fed with lactic acid bacteria compound, and (4) IBS-D group fed with Jianpi mixture for 14 days. At the end of the treatment period, 5 mice were randomly selected from each group, and then the changes in intestinal microbiota in the mice before and after treatment were analyzed by 16S rDNA high-throughput gene sequencing. Compared with the control group, the species richness and species diversity of intestinal microbiota in feces and intestinal mucosa of IBS-D mice were decreased (P < 0.05); IBS-D mice showed changes in composition of and in ratio of the intestinal microbiota in feces and intestinal mucosa at the level of phylum, class, order, family, genus, and species. Treatment with Jianpi mixture increased the species diversity of intestinal microbiota in IBS-D mice (P < 0.05) and the abundance of beneficial bacteria (P < 0.05) and decreased the abundance of harmful bacteria (P < 0.05) at the level of phylum and genus. Compared with healthy mice, the species richness and species diversity of intestinal microbiota of IBS-D mice are decreased. The intervention with Jianpi mixture can improve its diversity and regulate the equilibrium between beneficial and harmful bacteria.

Effect of Modified Xijiao Dihuang Decoction () on Intestinal Flora and Th17/Treg in Rats with Radiation Enteritis

OBJECTIVE

To observe the effect of Modified Xijiao Dihuang Decoction (, MXDD) on rats with radiation enteritis, and explore its action mechanism.

METHODS

Thirty female Sprague Dawley rats were divided into the control, model, dexamethasone (DXM), golden bifid (GB) and MXDD groups using random number table, 6 rats in each group. Except the control group, the other rats were developed into radiation enteritis model by exposing to a single ⁶⁰Co-γ ray at a dose of 11 Gy. The rats in the DXM, GB and MXDD groups were treated with DXM (1.425 mg/kg), GB (0.8 g/kg) and MXDD (36.0 g/kg) for 3 days, respectively. Body weight and diarrhea condition of rats were evaluated daily. On day 3, the feces of rats were collected for intestinal flora detection and the small intestinal tissues were also collected. Bacterial species annotation, alpha and beta diversities as well as composition of intestinal flora were detected and compared. The protein and mRNA expressions of interleukin 17 (IL-17), retinoid-related orphan nuclear receptor gamma t (ROR-γt) and forkhead/ winged helix transcription factor p3 (FoxP3) were determined by Western blot and polymerase chain reaction, respectively. The abundance and diversity of intestinal flora as well as the proportion at the phylum and genus levels were assayed by 16S rRNA metagenome sequencing. Correlation between intestinal flora and Th17/Treg was analyzed by heatmap method.

RESULTS

On day 1 to 3 after radiation, compared with the control group, the body weight in model group was decreased (P<0.05 or P<0.01). Compared with the model group, MXDD could alleviate weight loss and diarrhea caused by irradiation. At the phylum level, MXDD cause a significant increase in Firmicutes, and a decrease in Proteobacteria (P<0.05 or P<0.01). At the genus level, MXDD reduced the proportion of Escherichia Shigella (P<0.01). In addition, IL-17 and FoxP3 mRNA and protein expression levels were down-regulated and ROR-γt was up-regulated by MXDD treatment (P<0.05). Besides, Firmicutes and Lactobacillus were positively correlated with FoxP3 (r=0.73, 0.79, respectively; P<0.01), negatively correlated with IL-17 (r=0.66, 0.64, respectively; P<0.01 or P<0.05) and ROR-γt (r0.73, 0.81, respectively; P<0.01). Proteobacteria and Escherichia Shigella both had positive correlation with IL-17 (r 0.77, 0.57, respectively; P<0.01 or P<0.05 ) and ROR-γt (r=0.94, 0.79, respectively; P<0.01) and negative correlation with FoxP3 (r0.74, 0.65; P<0.01).

CONCLUSION

MXDD could improve the survival status of irradiated rats by regulating the richness, diversity and composition of intestinal flora, and restoring the balance of Th17/Treg.

Bacterial Community Structure of Pinus Thunbergii Naturally Infected by the Nematode Bursaphelenchus Xylophilus

Pine wilt disease (PWD) caused by the nematode Bursaphelenchusxylophilus is a devastating disease in conifer forests in Eurasia. However, information on the effect of PWD on the host microbial community is limited. In this study, the bacterial community structure and potential function in the needles, roots, and soil of diseased pine were studied under field conditions using Illumina MiSeq coupled with Phylogenetic Investigation of Communities by Reconstruction of Unobserved states (PICRUSt) software. The results showed that the community and functional structure of healthy and diseased trees differed only in the roots and needles, respectively (p < 0.05). The needles, roots, and soil formed unique bacterial community and functional structures. The abundant phyla across all samples were Proteobacteria (41.9% of total sequence), Actinobacteria (29.0%), Acidobacteria (12.2%), Bacteroidetes (4.8%), and Planctomycetes (2.1%). The bacterial community in the healthy roots was dominated by Acidobacteria, Planctomycetes, and Rhizobiales, whereas in the diseased roots, Proteobacteria, Firmicutes, and Burkholderiales were dominant. Functionally, groups involved in the cell process and genetic information processing had a higher abundance in the diseased needles, which contributed to the difference in functional structure. The results indicate that PWD can only affect the host bacteria community structure and function in certain anatomical regions of the host tree.

Dietary inclusion of Peptiva, a peptide-based feed additive, can accelerate the maturation of the fecal bacterial microbiome in weaned pigs

Background

Weaning is one of the most critical transition stages of the swine production cycle, as the piglet gut physiology and microbiome need to rapidly adapt to changes in diet and environmental conditions. Based on their potential for producing a vast array of bioactive molecules, peptide formulations represent a largely untapped source of compounds that could be developed into feed additives to benefit animal health and nutrition. In this context, a commercial-scale nursery trial was performed to evaluate the impact of low inclusion of a peptide-based feed additive (Peptiva, Vitech Bio-Chem Corporation) on the performance and fecal microbiome of weaned pigs.

Results

While no significant differences in body weight, daily gain, daily feed intake nor gain:feed were observed between control and treatment animals (P > 0.05), an effect of Peptiva on the fecal bacterial composition of weaned pigs was observed. The first main observation was that the fecal bacterial profiles from pigs fed Control-Phase II and Control Phase III diets were found to be very distinct, suggesting that a transition or succession stage had occurred between the two phases. Lactobacilli, represented by four main OTUs (Ssd-00002, Ssd-00019, Ssd-00025, and Ssd-00053), were more abundant at the end of Phase II (P < 0.05), while Streptococci, mostly represented by OTUs Ssd-00039 and Ssd-00048, were in higher abundance at the end of Phase III (P < 0.05). Secondly, the fecal bacterial composition from pigs fed Peptiva Phase II diets showed similarities to both Control-Phase II and Control Phase III samples, while there was no difference in fecal bacterial composition between Control-Phase III and Peptiva Phase III samples. For instance, OTUs Ssd-00019,and Ssd-00053 were in lower abundance in Peptiva Phase II samples compared to Control Phase II (P < 0.05), but no significant difference was observed in the abundance of these two OTUs when comparing Peptiva Phase II to Control Phase III (P > 0.05).

Conclusions

Together, these results suggest that Peptiva can modulate the composition of the swine microbiome during a specific window of the nursery stage, potentially by accelerating its maturation.

Selectived and Reshaped Early Dominant Microbial Community in the Cecum With Similar Proportions and Better Homogenization and Species Diversity Due to Organic Acids as AGP Alternatives Mediate Their Effects on Broilers Growth

Understanding the differences in microbial communities shaped by different food selective forces, especially during early post-hatch period, is critical to gain insight into how to select, evaluate, and improve antibiotic growth promoters (AGPs) alternatives in food animals. As a model system, commercial diet-administered OAs (DOAs) and water-administered OAs (WOAs) were used separately or in combination as Virginiamycin alternatives for broiler feeding during two growth phases: 1–21 days and 22–42 days. Among these three OA-treated groups, the DOA group was most similar to the AGP group in the composition and the proportion of these dominant bacterial communities at the level of phylum, family, and genus in cecal chyme of broilers. Sub-therapeutic Virginiamycin decreased the richness, homogenization, and species diversity of gut microbiota, especially in the early growth stage from days 1 to 21. Among these three OA supplementation schemes, it was clear that DOA supplementation was more likely to increase or maintain the richness, homogenization, species diversity, and predicted gene functions of cecal microbiota in treated broilers than either no supplementation or AGP supplementation during two experimental stages. The interference of DOA treatment with early colonization of probiotics and pathogens in broiler cecum was the most similar to AGP treatment, and OAs did not cause the occurrence of Virginiamycin-resistant strains of Enterococcus at the end of this trial. In terms of the predicted gene functions of the microbiota, AGP and DOA treatments provided a similar selective force for microbial metabolism functions in the cecum of broiler chickens, especially in the early growth stage. Noticeably, the relative abundance of some microbiome that was modified by Virginiamycin or DOA supplementation was significantly correlated with body weight gain and KEGG pathway analysis-annotated gene functions such as replication and repair, translation, nucleotide metabolism, and so on. With the comprehensive analysis of these results and practical application, shortened DOA supplementation, after optimization of the amount of addition, would be a suitable alternative to sub-therapeutic Virginiamycin. It was suggested that the programed intestinal microecology under such early selection forces and the effective addition time may be the key elements to focus on the designed alternate strategies of AGPs in food animals.

Implications of gut microbiota dysbiosis and metabolic changes in prion disease

Evidence of the gut microbiota influencing neurodegenerative diseases has been reported for several neural diseases. However, there is little insight regarding the relationship between the gut microbiota and prion disease. Here, using fecal samples of 12 prion-infected mice and 25 healthy controls, we analyzed the structure of the gut microbiota and metabolic changes by 16S rRNA sequencing and LC-MS-based metabolomics respectively as multi-omic analyses. Additionally, SCFAs and common amino acids were detected by GC-MS and UPLC respectively. Enteric changes induced by prion disease affected both structure and abundances of the gut microbiota. The gut microbiota of infected mice displayed greater numbers of Proteobacteria and less Saccharibacteria at the phylum level and more Lactobacillaceae and Helicobacteraceae and less Prevotellaceae and Ruminococcaceae at the family level. A total of 145 fecal metabolites were found to be significantly different in prion infection, and most (114) of these were lipid metabolites. Using KEGG pathway enrichment analysis, we found that 3 phosphatidylcholine (PC) compounds significantly decreased and 4 hydrophobic bile acids significantly increased. Decreases of 8 types of short-chain acids (SCFAs) and increases of Cys and Tyr and decreases of His, Trp, and Arg were observed in prion infection. Correlation analysis indicated that the gut microbiota changes observed in our study may have been the shared outcome of prion disease. These findings suggest that prion disease can cause significant shifts in the gut microbiota. Certain bacterial taxa can then respond to the resulting change to the enteric environment by causing dramatic shifts in metabolite levels. Our data highlight the health impact of the gut microbiota and related metabolites in prion disease.

Effects of Dietary Energy on Growth Performance, Rumen Fermentation and Bacterial Community, and Meat Quality of Holstein-Friesians Bulls Slaughtered at Different Ages

Simple Summary

Beef tenderness, flavour and juiciness are quality characteristics of consumer eating satisfaction. Marbling level of beef could determine quality characteristics by concentrating water soluble flavour molecules and releasing low fat-solubility volatiles faster. Increasing number of Holstein-Friesians bulls are used for beef production, and this breed is considered to have lower meat quality than purebred and crossbred beef cattle. Therefore, in this study we designed different dietary energy levels and slaughter ages to find ways to improve the meat quality of Holstein-Friesians bulls in beef production. We found that Holstein-Friesians bulls fed with 10.90 and 11.68 MJ/kg metabolizable energy diets, compared to a diet with 10.12 MJ/kg of metabolizable energy, had higher average daily gain, dressing percentage, intramuscular fat content and water holding capacity at 23 or 26 months of age. This study provides a basis to use bulls to produce beef by providing indicators of growth performance, rumen fermentation and ruminal bacteria community, and meat quality.

Abstract

The objective of this study was to evaluate the effects of dietary energy levels on growth performance, rumen fermentation and bacterial community, and meat quality of Holstein-Friesians bulls slaughtered at different ages. Thirty-six Holstein-Friesians bulls (17 months of age) were divided into a 3 × 3 factorial experiment with three energy levels (LE, ME and HE; metabolizable energy is 10.12, 10.90 and 11.68 MJ/kg, respectively) of diets, and three slaughter ages (20, 23 and 26 months). Results indicated that bulls fed with ME and HE diets had higher dry matter intake, average daily gain, and dressing percentage at 23 or 26 months of age. The ME and HE diets also reduced bacterial diversity, altered relative abundances of bacteria and produced lower concentrations of acetate, but higher butyrate and valerate concentrations in rumen fluid. Increasing in dietary energy and slaughter age increased the intramuscular fat (IMF) and water holding capacity. In summary, Holstein-Friesians bulls fed with ME and HE diets, slaughtered at 23 and 26 months of age could be a good choice to produce beef with high IMF. Slaughter age may have less influence than dietary energy in altering fermentation by increasing amylolytic bacteria and decreasing cellulolytic bacteria, and thus, further affecting meat quality.

Correlation of the rumen fluid microbiome and the average daily gain with a dietary supplementation of Allium mongolicum Regel extracts in sheep1

Plant extracts can affect the rumen microbiome and ADG in ruminants, and studies of the association between the rumen microbiome and ADG provide information applicable to improving ruminant growth performance. The objectives were to investigate the effects of Allium mongolicum Regel extracts on the rumen microbiome and ADG and their association in sheep. Forty healthy, male, small-tailed Han sheep (6 mo, 34 ± 3.5 kg body weight) were randomly assigned to 1 of the following 4 dietary treatments: basal diet as control group (CK, n = 10), basal diet supplemented with 3.4 g·sheep-1·d-1A. mongolicum Regel powder extract as PAM group (PAM, n = 10), basal diet supplemented with 10 g·sheep-1·d-1A. mongolicum Regel powder as AM group (AM, n = 10), and basal diet supplemented with 10 g·sheep-1·d-1A. mongolicum Regel powder extract residue as RAM group (RAM, n = 10). The ADG for individual sheep was calculated using the sum of the ADGs observed during the experimental period divided by the number of days in the experimental period. At the end of the experiment, sheep were randomly selected from each treatment for slaughter (n = 6), and the rumen fluids were collected and stored immediately at -80 °C. Illumina HiSeq was subsequently used to investigate the changes in the rumen microbiome profile, and the associations with ADG were analyzed by Spearman correlation coefficient analysis. The results demonstrated that, compared with that in CK group, the ADG in AM and RAM significantly increased (P = 0.0171). The abundances of Tenericutes and Mollicutes ([ρ] = 0.5021, P = 0.0124) were positively correlated with ADG. Within Mollicutes, the abundances of Anaeroplasmatales ([ρ] = 0.5458, P = 0.0058) and Anaeroplasmataceae ([ρ] = 0.5458, P = 0.0058) were positively correlated with ADG. The main negatively correlated bacteria were Saccharibacteria ([ρ] = -0.4762, P = 0.0187) and Betaproteobacteria ([ρ] = -0.5669, P = 0.039). Although Anaeroplasmatales and Anaeroplasmataceae were positively correlated with ADG, Saccharibacteria and Betaproteobacteria were negatively correlated with ADG. In conclusion, supplementation with A. mongolicum Regel powder and extracts will influence the rumen microbiome and increase the ADG.

Investigation of the Potential Effects of Host Genetics and Probiotic Treatment on the Gut Bacterial Community Composition of Aquaculture-raised Pacific Whiteleg Shrimp, Litopenaeus vannamei

This study presents the potential effects of the genetic background and use of probiotics on the gut bacterial composition of Pacific whiteleg shrimp (Litopenaeus vannamei) grown in an indoor aquaculture facility. The strains investigated were Shrimp Improvement Systems (SIS, Islamorada, FL, USA), a strain genetically selected for disease resistance, and an Oceanic Institute (OI, Oahu, HI, USA) strain, selected for growth performance. BioWish 3P (BioWish Technologies, Cincinnati, OH, USA) was the selected probiotic. The study consisted of two separate trials, where all shrimp were raised under standard industry conditions and fed the same diet. Shrimp were stocked in 2920 L production tanks at a density of 200/m³ and acclimated for 14 days. After the acclimation period, triplicate tanks were supplemented daily for a duration of 28 days with probiotics, while three other tanks did not receive any treatment (controls). During the 28-day trial period, there was no statistically supported difference (p > 0.05) in either performance or health status as a result of genetic background or probiotic treatment. However, differences in gut bacterial composition, as assessed by high throughput sequencing of amplicons generated from the V1-V3 region of the bacterial 16S rRNA gene, were observed. The relative abundance of five major operational taxonomic units (OTUs) were found to vary significantly across experimental groups (p < 0.05). Notably, operational taxonomic unit (OTU) SD_Shr-00006 was at its highest abundance in d43 SIS samples, with levels greater than d71 samples of the same genetic line or any of the OI shrimp samples. OTUs for SD_Shr-00098 displayed a similar type of profile, but with highest abundance in the OI genetic line and lowest in the SIS shrimp. SD_Shr-00004 showed an opposite profile, with highest abundance in the SIS d71 samples and lowest in the SIS d43 samples. Together, these results suggest that host genetic background can be an important determinant of gut bacterial composition in aquaculture-raised whiteleg shrimp and indicate that development of strategies to manipulate the microbiome of this important seafood will likely need to be customized depending on the genetic line.

Dynamic Alterations in Yak Rumen Bacteria Community and Metabolome Characteristics in Response to Feed Type

Current knowledge about the relationships between ruminal bacterial communities and metabolite profiles in the yak rumen is limited. This is due to differences in the nutritional and metabolic features between yak and other ordinary cattle combined with difficulties associated with farm-based research and a lack of technical guidance. A comprehensive analysis of the composition and alterations in ruminal metabolites is required to advance the development of modern yak husbandry. In the current study, we characterized the effect of feed type on the ruminal fluid microbiota and metabolites in yak using 16S rRNA gene sequencing and liquid chromatography-mass spectrometry (LC-MS). Bacteroidetes and Firmicutes were the predominant bacterial phyla in the yak rumen. At the genus level, the relative abundance of Bacteroidales BS11 gut group, Prevotellaceae UCG-003, Ruminococcaceae UCG-011, Bacteroidales RF16 group and Ruminococcaceae UCG-010 was significantly (P < 0.01) higher in the forage group compared to that in the concentrate group, while the concentrate group harbored higher proportions of Bacteroidales S24-7 group, Ruminococcaceae NK4A214, Succiniclasticum and Ruminococcus 2. Yak rumen metabolomics analysis combined with enrichment analysis revealed that feed type altered the concentrations of ruminal metabolites as well as the metabolic pattern, and significantly (P < 0.01) affected the concentrations of ruminal metabolites involved in protein digestion and absorption (e.g., L-arginine, ornithine, L-threonine, L-proline and β-alanine), purine metabolism (e.g., xanthine, hypoxanthine, deoxyadenosine and deoxyadenosine monophosphate) and fatty acid biosynthesis (e.g., stearic acid, myristic acid and arachidonic acid). Correlation analysis of the association of microorganisms with metabolite features provides us with a comprehensive understanding of the composition and function of microbial communities. Associations between utilization or production were widely identified between affected microbiota and certain metabolites, and these findings will contribute to the direction of future research in yak.

Feeding Essential Oils to Neonatal Holstein Dairy Calves Results in Increased Ruminal Prevotellaceae Abundance and Propionate Concentrations

Since antibiotic use in animal production has become a public health concern, great efforts are being dedicated to find effective and viable alternatives. While essential oils (EO) have become attractive candidates for use in the livestock industry, their mode of action and microbial targets in food animals remain largely uncharacterized. To gain further insight, we investigated the rumen environment of neonatal calves fed calf starter pellets and milk replacer supplemented with a commercial blend of EO. Propionate concentrations were not only found to be higher in EO-fed calves compared to controls (P < 0.05), but ruminal bacterial communities also differed greatly. For instance, the abundance of Firmicutes was significantly lower in samples from EO-fed calves than in controls, which appeared to be mostly due to lower Lachnospiraceae levels (P < 0.05). In contrast, Bacteriodetes were more abundant in EO-fed calves compared to controls, which was primarily the result of higher Prevotellaceae (P < 0.05). Notably, two bacterial operational taxonomic units (OTUs) were significantly more abundant in EO-fed calves; SD_Bt-00966 was found to be a close relative of Prevotella ruminicola (97%), while SD_Bt-00978 likely corresponded to an uncharacterized species of Gammaproteobacteria. In addition, Pearson correlation and canonical correspondence analyses revealed potential associations between other ruminal bacterial OTUs and either short chain fatty acids (SCFA) parameters or metrics for calf growth. Together, these results support that EO supplementation in growing dairy calves can modulate rumen function through SCFA production and growth of specific rumen bacterial groups.

Impact of Aquaculture Practices on Intestinal Bacterial Profiles of Pacific Whiteleg Shrimp Litopenaeus vannamei

Considering the crucial role of the gut microbiome in animal health and nutrition, solutions to shrimp aquaculture challenges, such as improving disease resistance and optimizing growth on lower cost feeds, may lie in manipulation of their microbial symbionts. However, achieving this goal will require a deeper understanding of shrimp microbial communities and how their composition is influenced by diet formulation, environmental conditions, and host factors. In this context, the current study investigated the intestinal bacterial communities of the Pacific whiteleg shrimp (Litopenaeus vannamei—the most widely aquaculture-farmed shrimp worldwide) reared in indoor aquaculture facilities and outdoor pond systems. While samples showed very consistent intestinal bacterial community profiles within each production system, major differences were uncovered between the two practices. Indeed, bacteria affiliated with Rhodobacteraceae (Proteobacteria) and Actinobacteria were significantly more abundant in indoor samples (84.4% vs. 5.1%; 3.0% vs. 0.06%, respectively), while Vibrionaceae (Proteobacteria), Firmicutes, Fusobacteria and Cyanobacteria were predominant in pond samples (0.03% vs. 44.8%; 0.7% vs. 36.0%; 0.0% vs. 7.9%; 0.001% vs. 1.6%, respectively). Accordingly, the abundance of 11 of the 12 most prominent Operational Taxonomic Units (OTUs) were found to be statistically different between the two production environments. Together, these results indicate that aquaculture practices greatly influence the intestinal bacterial profile of the whiteleg shrimp, and further suggest that bacterial communities of this economically important crustacean could be effectively manipulated using diet composition or environmental conditions.

Tibet kefir milk decreases fat deposition by regulating the gut microbiota and gene expression of Lpl and Angptl4 in high fat diet-fed rats

The role of Tibet kefir milk (TKM) feeding on fat deposition was investigated in high-fat diet (HFD)-fed human flora-associated (HFA) rats. TKM feeding reduced abdominal fat mass from 33.9 g to 24.0 g and serum triglyceride (TG) from 0.75 mmol/L to 0.47 mmol/L, and caused lipoprotein lipase (LPL) to decrease from 395.8 ± 36.0 ng/L to 362.3 ± 64.4 ng/L in fat and increase from 287.3 ± 40.8 ng/L to 329.8 ± 48.5 ng/L and 312.5 ± 22.0 to 375.1 ± 30.8 ng/L in liver and serum, respectively. Likewise, TMK feeding down-regulated Lpl gene expression in fat and Angptl4 (angiopoietin-like protein-4, also known as fasting-induced adipose factor) gene expression in liver, and up-regulated Angptl4 gene expression in fat. Sequence analysis showed that the Firmicutes/Bacteroidetes proportion and Verrucomicrobia at the phylum level, Akkermansia, Escherichia and Oscillospira at the genus level, as well as Escherichia coli at the species level were positively regulated by TKM. The results indicated that TKM decreased abdominal fat deposition and serum TG by regulating Lpl and Angptl4 at the transcriptional level. The microbiota groups mentioned above were regulated by TKM at the same time and may be the potential intervention targets to reduce fat deposition.