Improved extraction of PCR-quality community DNA from digesta and fecal samples

Treatment of corn with lactic acid delayed in vitro ruminal degradation without compromising fermentation: a biological and morphological monitoring study

Grain processed by lactic acid (LA) is known to improve ruminant growth and health. However, the exact mechanism regarding rumen hydrolysis of LA-treated grain is still ambiguous. This experiment was designed to compare the effects of 5% LA treatment on the trophic and morphological variations in corn and to discover the alternations in ruminal hydrolysis between LA-treated and untreated corn macroscopically and microscopically using in vitro fermentation method. The results showed that, compared with untreated corn (CN), corn treated with 5% LA for 48 h (CNLA) experienced a decrease in the dry matter, albumin fraction, aNDFom, and water-soluble carbohydrate content but an increase in the resistant starch content. The in vitro fermentation showed that the pH of CNLA was higher, but dry matter disappearance was lower than that of CN. Most of the fermentation indices were unaffected, except for decreased iso-butyrate and iso-valerate. The abundances of total bacteria, Prevotella spp., Streptococcus bovis, and Selenomonas ruminantium were higher, but those of Ruminococcus flavefaciens and Ruminococcus albus were lower in CNLA than in CN. There were differences in the scanning electron micrographs between CNLA and CN after 3 h of fermentation. This study suggests that treating corn with LA for 48 h can induce changes in its nutrient composition and alter the bacterial flora during subsequent in vitro fermentation. These changes appeared to be crucial contributors to the beneficial effects observed in rumen fermentation.

Rumen microbiome-driven insight into bile acid metabolism and host metabolic regulation

Gut microbes play a crucial role in transforming primary bile acids (BAs) into secondary forms, which influence systemic metabolic processes. The rumen, a distinctive and critical microbial habitat in ruminants, boasts a diverse array of microbial species with multifaceted metabolic capabilities. There remains a gap in our understanding of BA metabolism within this ecosystem. Herein, through the analysis of 9371 metagenome-assembled genomes and 329 cultured organisms from the rumen, we identified two enzymes integral to BA metabolism: 3-dehydro-bile acid delta4,6-reductase (baiN) and the bile acid:Na + symporter family (BASS). Both in vitro and in vivo experiments were employed by introducing exogenous BAs. We revealed a transformation of BAs in rumen and found an enzyme cluster, including L-ribulose-5-phosphate 3-epimerase and dihydroorotate dehydrogenase. This cluster, distinct from the previously known BA-inducible operon responsible for 7α-dehydroxylation, suggests a previously unrecognized pathway potentially converting primary BAs into secondary BAs. Moreover, our in vivo experiments indicated that microbial BA administration in the rumen can modulate amino acid and lipid metabolism, with systemic impacts underscored by core secondary BAs and their metabolites. Our study provides insights into the rumen microbiome's role in BA metabolism, revealing a complex microbial pathway for BA biotransformation and its subsequent effect on host metabolic pathways, including those for glucose, amino acids, and lipids. This research not only advances our understanding of microbial BA metabolism but also underscores its wider implications for metabolic regulation, offering opportunities for improving animal and potentially human health.

Effects of α-amylase and coated α-amylase supplementation on growth performance, nutrient digestion, and rumen fermentation in Holstein bulls

This study evaluated the impacts of α-amylase (AM) and coated α-amylase (CAM) on bull performance, nutrient digestibility, and ruminal fermentation. This study randomized 60 Holstein bulls of 365 ± 11.5 days of age and 457.5 ± 9.35 kg body weight into three groups: without AM addition, adding AM 0.6 g/kg dry matter (DM), and adding CAM 0.6 g AM/kg DM, separately. This whole experimental period was 80 days, including a 20-day adaptation period and a 60-day data and sample acquisition period. In comparison with the unsupplemented control, dry matter intake (DMI) was unaltered; however, average daily gain (ADG) and feed efficiency (FE) were greater for AM or CAM addition. Bulls receiving AM or CAM supply had greater total-tract nutrient digestibility, ruminal total volatile fatty acids (VFA) content, propionate molar proportion, cellulolytic enzyme and AM activities, and the number of microorganisms. In addition, the activities of AM and trypsin in the jejunum and ileum and glucose, albumin, and total protein concentrations in serum were greater for AM or CAM addition compared to the control. When comparing the supplementation mode of AM, bulls receiving CAM addition had greater ADG and FE. The crude protein and starch digestibility and intestinal AM and trypsin activity were higher, while acid detergent fiber (ADF) digestibility was lower for CAM addition than for AM addition. The lower propionate molar proportion and cellobiase and carboxymethyl cellulase activities, together with Ruminococcus albus, Ruminococcus flavefaciens, and Fibrobacter succinogenes populations were observed for CAM addition compared with AM addition. However, there were greater glucose, albumin, and total protein concentrations in serum after adding CAM. According to the data, the supply of AM improved ADG, nutrient digestion, and rumen fermentation. Notably, the optimum supplementation mode was in the form of CAM in bulls.

Prebiotic utilisation provides Lactiplantibacillus plantarum a competitive advantage in vitro, but is not reflected by an increased intestinal fitness

Synbiotics combine the concepts of probiotics and prebiotics to synergistically enhance the health-associated effects of both components. Previously, we have shown that the intestinal persistence of inulin-utilizing L. plantarum Lp900 is significantly increased in rats fed an inulin-supplemented, high-calcium diet. Here we employed a competitive population dynamics approach to demonstrate that inulin and GOS can selectively enrich L. plantarum strains that utilize these substrates for growth during in vitro cultivation, but that such enrichment did not occur during intestinal transit in rats fed a GOS or inulin-supplemented diet. The intestinal persistence of all L. plantarum strains increased irrespective of their prebiotic utilization phenotype, which was dependent on the calcium level of the diet. Analysis of fecal microbiota and intestinal persistence decline rates indicated that prebiotic utilization capacity did not selectively stimulate intestinal persistence in prebiotic supplemented diets. Moreover, microbiota and organic acid profile analyses indicate that the prebiotic utilizing probiotic strains are vastly outcompeted by the endogenous prebiotic-utilizing microbiota, and that the collective enhanced persistence of all L. plantarum strains is most likely explained by their well-established tolerance to organic acids.

Varied microbial community assembly and specialization patterns driven by early life microbiome perturbation and modulation in young ruminants

Perturbations and modulations during early life are vital to affect gut microbiome assembly and establishment. In this study, we assessed how microbial communities shifted during calf diarrhea and with probiotic yeast supplementation (Saccharomyces cerevisiae var. boulardii, SCB) and determined the key bacterial taxa contributing to the microbial assembly shifts using a total of 393 fecal samples collected from 84 preweaned calves during an 8-week trial. Our results revealed that the microbial assembly patterns differed between healthy and diarrheic calves at 6- and 8-week of the trial, with healthy calves being stochastic-driven and diarrheic calves being deterministic-driven. The two-state Markov model revealed that SCB supplementation had a higher possibility to shift microbial assembly from deterministic- to stochastic-driven in diarrheic calves. Furthermore, a total of 23 and 21 genera were specific ecotypes to assembly patterns in SCB-responsive (SCB-fed calves did not exhibit diarrhea) and nonresponsive (SCB-fed calves occurred diarrhea) calves, respectively. Among these ecotypes, the area under a receiver operating characteristic curve revealed that Blautia and Ruminococcaceae UCG 014, two unidentified genera from the Ruminococcaceae family, had the highest predictiveness for microbial assembly patterns in SCB-responsive calves, while Prevotellaceae, Blautia, and Escherichia-Shigella were the most predictive bacterial taxa for microbial assembly patterns in SCB-nonresponsive calves. Our study suggests that microbiome perturbations and probiotic yeast supplementation serving as deterministic factors influenced assembly patterns during early life with critical genera being predictive for assembly patterns, which sheds light on mechanisms of microbial community establishment in the gut of neonatal calves during early life.

Comparative Rumen Metagenome and CAZyme Profiles in Cattle and Buffaloes: Implications for Methane Yield and Rumen Fermentation on a Common Diet

A study was undertaken to compare the rumen microbial community composition, methane yield, rumen fermentation, and CAZyme profiles between cattle and buffaloes. The primary aim of this study was to ascertain the impact of the host species on the above when diet and environmental factors are fixed. A total of 43 phyla, 200 orders, 458 families, and 1722 microbial genera were identified in the study. Bacteroidetes was the most prominent bacterial phylum and constituted >1/3rd of the ruminal microbiota; however, their abundances were comparable between cattle and buffaloes. Firmicutes were the second most abundant bacteria, found to be negatively correlated with the Bacteroidetes. The abundances of Firmicutes as well as the F/B ratio were not different between the two host species. In this study, archaea affiliated with the nine phyla were identified, with Euryarchaeota being the most prominent. Like bacterial phyla, the abundances of Euryarchaeota methanogens were also similar between the cattle and buffaloes. At the order level, Methanobacteriales dominated the archaea. Methanogens from the Methanosarcinales, Methanococcales, Methanomicrobiales, and Methanomassiliicoccales groups were also identified, but at a lower frequency. Methanobrevibacter was the most prevalent genus of methanogens, accounting for approximately three percent of the rumen metagenome. However, their distribution was not different between the two host species. CAZymes affiliated with five classes, namely CBM, CE, GH, GT, and PL, were identified in the metagenome, where the GH class was the most abundant and constituted ~70% of the total CAZymes. The protozoal numbers, including Entodiniomorphs and Holotrichs, were also comparable between the cattle and buffaloes. Results from the study did not reveal any significant difference in feed intake, nutrient digestibility, and rumen fermentation between cattle and buffaloes fed on the same diet. As methane yield due to the similar diet composition, feed ingredients, rumen fermentation, and microbiota composition did not vary, these results indicate that the microbiota community structure and methane emissions are under the direct influence of the diet and environment, and the host species may play only a minor role until the productivity does not vary. More studies are warranted to investigate the effect of different diets and environments on microbiota composition and methane yield. Further, the impact of variable productivity on both the cattle and buffaloes when the diet and environmental factors are fixed needs to be ascertained.

Fate of high-risk antibiotic resistance genes in large-scale aquaculture sediments: Geographical differentiation and corresponding drivers

Antibiotic resistance genes (ARGs), emerging environmental contaminants, have become challenges of public health security. However, the distribution and drivers of ARGs, especially high-risk ARGs, in large-scale aquaculture sediments remain unknown. Here, we collected sediment samples from 40 crayfish ponds in seven main crayfish culture provinces in China and then investigated the distribution and risk of ARGs based on high-throughput sequencing and quantitative PCR techniques. Our results suggested that aquaculture sediment was potential reservoir of ARGs and the abundance of aadA-02 was the highest. High-risk ARG (floR) was also prevalent in the sediment and was the most abundant in Jiangsu Province, where opportunistic pathogens were also enriched. The abundance of floR was positively correlated with different environmental factors, such as total phosphorus in water and total carbon in sediment. In addition, Mycobacterium sp., opportunistic pathogenic bacteria, might be potential host for floR. Furthermore, the potential propagation pathway of ARGs was from sediment to crayfish gut, and Bacteroidetes and Proteobacteria might be the main bacterial groups responsible for the proliferation of ARGs. Generally, our results illustrate that pond sediment may be an ARG reservoir of aquatic animals. Meanwhile, our study helps develop valuable strategies for accessing risks and managing ARGs.

Assessing the In Vitro and In Vivo Effect of Supplementation with a Garlic (Allium sativum) and Oregano (Origanum vulgare) Essential Oil Mixture on Digestibility in West African Sheep

This study assessed the impact of a mixture of garlic (Allium sativum) and oregano (Origanum vulgare) essential oils (EOGOs) on in vitro dry matter digestibility (IVDMD) and in vivo apparent nutrient digestibility. Different EOGO inclusion levels were evaluated to assess the dose response and potential effects of the mixture. Three EOGO inclusion levels (0.5, 0.75, and 1 mL/kg of incubated dry matter) were evaluated in vitro, while four treatments (0.5, 0.75, and 1 mL/day of EOGO and a control group) were tested in vivo on 12 West African sheep. A randomized controlled trial was conducted using a 4 × 4 design. Blood parameters (glucose, blood urea nitrogen, and β-hydroxybutyrate) were measured to observe the effect of EOGO on the metabolism. The results showed that the inclusion of EOGO significantly enhanced IVDMD at low levels (p < 0.052) compared with the highest levels in treatments containing 0.5 and 0.75 mL/kg of EOGO dry matter. A higher intake of dry matter (DM), crude protein (CP), and neutral detergent fiber (NDF) (p < 0.05) was observed in the in vivo diets with the inclusion of EOGO. In terms of in vivo apparent digestibility, significant differences were found among treatments in the digestibility coefficients of DM, CP, and NDF. EOGO inclusion increased the digestibility of DM. CP digestibility displayed a cubic effect (p < 0.038), with the lowest values of digestibility observed at 1 mL EOGO inclusion. Additionally, NDF digestibility showed a cubic effect (p < 0.012), with the highest value obtained at 0.75 mL of EOGO inclusion. The inclusion levels above 0.75 mL EOGO showed a cubic effect, which indicates that higher concentrations of EOGO may not be beneficial for the digestibility of CP and NDF. Although no significant difference was observed in total digestible nutrients, a linear trend was observed (p < 0.059). EOGO improved the intake of DM, CP, and NDF. EOGO supplementation improved the digestibility of DM and NDF, with optimal levels observed at 0.5 mL/day. No significant effects were observed in the blood parameters. These results suggest that EOGO has the potential as an additive in ruminal nutrition to improve food digestibility and serve as an alternative to antibiotic additives. The use of EOGO potentially improves fiber digestion and may reduce the use of antibiotics in livestock production. Garlic (A. sativum) and oregano (O. vulgare) essential oils effectively modulated fiber digestibility at 0.75 mL/day. Garlic (A. sativum) and oregano (O. vulgare) essential oils have the potential to improve digestibility at low inclusion levels and serve as an alternative to antibiotic additives. The effectiveness of essential oils is greater in a mixture and at lower doses.

Effects of concentrate levels on intestinal fermentation and the microbial profile in Japanese draft horses

In racehorses, feeding a high-concentrate diet could cause abnormal fermentation in the hindgut. This feeding management regime is not suitable for the nutritional physiology of horses. However, studies on the hindgut environment have yet to be reported in Japanese draft horses, so feeding management needs to be investigated in these horses. Therefore, the objective of this study was to investigate the effects of a high-concentrate diet on hindgut fermentation in Japanese draft horses. Feces were collected from 20 male Japanese draft horses managed by two stables with different feeding designs (65% weight ratio of concentrate feed, HC; 50% weight ratio of concentrate, MC), and fecal metabolic characteristics and the microbiome were analyzed. Higher lactate concentrations and lower fecal pH levels were observed in the HC group (P=0.0011, P=0.0192, respectively). Fecal microbiome analysis revealed a decrease in microbial diversity (P=0.0360) and an increase in the relative abundance of Streptococcus lutetiensis/equinus/infantarius (P=0.0011) in the HC group. On the other hand, fibrolytic bacteria in the MC group had similarities with Clostridium sacchalolyticum and Ruminococcus albus. This study revealed that overfeeding of concentrates induced abnormal fermentation in the hindgut of Japanese draft horses. This suggests that the establishment of a feeding design based on not only the chemical compositions of feeds but also microbial dynamics is needed.

Unveiling Candida albicans intestinal carriage in healthy volunteers: the role of micro- and mycobiota, diet, host genetics and immune response

Candida albicans is a commensal yeast present in the gut of most healthy individuals but with highly variable concentrations. However, little is known about the host factors that influence colonization densities. We investigated how microbiota, host lifestyle factors, and genetics could shape C. albicans intestinal carriage in 695 healthy individuals from the Milieu Intérieur cohort. C. albicans intestinal carriage was detected in 82.9% of the subjects using quantitative PCR. Using linear mixed models and multiway-ANOVA, we explored C. albicans intestinal levels with regard to gut microbiota composition and lifestyle factors including diet. By analyzing shotgun metagenomics data and C. albicans qPCR data, we showed that Intestinimonas butyriciproducens was the only gut microbiota species whose relative abundance was negatively correlated with C. albicans concentration. Diet is also linked to C. albicans growth, with eating between meals and a low-sodium diet being associated with higher C. albicans levels. Furthermore, by Genome-Wide Association Study, we identified 26 single nucleotide polymorphisms suggestively associated with C. albicans colonization. In addition, we found that the intestinal levels of C. albicans might influence the host immune response, specifically in response to fungal challenge. We analyzed the transcriptional levels of 546 immune genes and the concentration of 13 cytokines after whole blood stimulation with C. albicans cells and showed positive associations between the extent of C. albicans intestinal levels and NLRP3 expression, as well as secreted IL-2 and CXCL5 concentrations. Taken together, these findings open the way for potential new interventional strategies to curb C. albicans intestinal overgrowth.

Dietary supplementation of sodium butyrate enhances lactation performance by promoting nutrient digestion and mammary gland development in dairy cows

This experiment was to evaluate the influence of sodium butyrate (SB) addition on milk production, ruminal fermentation, nutrient digestion, and the development and metabolism regulation of the mammary gland in dairy cows. Forty Holstein dairy cows averaging 710 ± 18.5 kg body weight, 72.8 ± 3.66 d in milk (DIM), and 41.4 ± 1.42 kg/d milk production were divided into four treatments blocked by DIM and milk production. Treatments were control group, low SB, medium SB, and high SB with 0, 100, 200 and 300 g/d of SB addition per cow, respectively. The study lasted for 105 d. Production of milk, milk protein and lactose quadratically increased (P < 0.05), while fat-corrected milk, energy-corrected milk and milk fat yields linearly increased (P < 0.05) with increasing SB addition. The digestibility of dietary dry matter, organic matter, and crude protein linearly increased (P < 0.05), whereas the digestibility of ether extract, neutral detergent fibre, and acid detergent fibre quadratically increased (P < 0.05). Ruminal pH quadratically decreased (P = 0.04), while total volatile fatty acids (VFA) quadratically increased (P = 0.03) with increasing SB addition. The acetic acid to propionic acid ratio increased (P = 0.03) linearly due to the unaltered acetic acid molar percentage and a linear decrease in propionic acid molar percentage. Ruminal enzymatic activity of carboxymethyl-cellulase and α-amylase, populations of total bacteria, total anaerobic fungi, total protozoa, Ruminococcus albus, R. flavefaciens, Butyrivibrio fibrisolvens, Fibrobacter succinogenes, and Ruminobacter amylophilus linearly increased (P < 0.05). Blood glucose, urea nitrogen, and non-esterified fatty acids linearly decreased (P < 0.05), while total protein concentration linearly increased (P = 0.04). Moreover, the addition of SB at 200 g/d promoted (P < 0.05) mRNA and protein expression of PPARγ, SREBF1, ACACA, FASN, SCD, CCNA2, CCND1, PCNA, Bcl-2, GPR41, and the ratios of p-Akt/Akt and p-mTOR/mTOR, but decreased (P < 0.05) mRNA and protein expressions of Bax, caspase-3, and caspase-9. The results suggest that milk production and milk fat synthesis increased with SB addition by stimulating rumen fermentation, nutrient digestion, gene and protein expressions concerned with milk fat synthesis and mammary gland development.

Development of a Protocol for Anaerobic Preparation and Banking of Fecal Microbiota Transplantation Material: Evaluation of Bacterial Richness in the Cultivated Fraction

Fecal microbiota transplantation (FMT) has shown highly variable results in indications beyond recurrent Clostridioides difficile infection. Microbiota dysbiosis in many diseases is characterized by the depletion of strictly anaerobic bacteria, which may be crucial for FMT efficacy. We developed a protocol to ensure anaerobic conditions during the entire transplant preparation and banking process, from material collection to administration. The protocol necessitates an anaerobic cabinet, i.e., a non-standard laboratory equipment. We analyzed the population of viable anaerobes by combining cultivation and 16S rRNA gene profiling during the transplant preparation, and after 4, 8, and 12 months of anaerobic or aerobic storage at -80 °C, 78% of fecal species were captured via cultivation. Our findings suggest that strictly anaerobic transplant preparation and storage may preserve species richness better than oxic conditions, but the overall difference was not significant. However, specific anaerobes such as Neglecta and Anaerotruncus were affected by the oxygen exposure. A storage time of up to 12 months did not affect the presence of cultivated taxa. Noteworthy, our analysis focused on the richness of cultivated anaerobes rather than their abundance, which may have been affected. The benefits of the developed anaerobic protocol in FMT for specific indications remain to be demonstrated in clinical trials.

Identification of intestinal and fecal microbial biomarkers using a porcine social stress model

Understanding the relationships between social stress and the gastrointestinal microbiota, and how they influence host health and performance is expected to have many scientific and commercial implementations in different species, including identification and improvement of challenges to animal welfare and health. In particular, the study of the stress impact on the gastrointestinal microbiota of pigs may be of interest as a model for human health. A porcine stress model based on repeated regrouping and reduced space allowance during the last 4 weeks of the finishing period was developed to identify stress-induced changes in the gut microbiome composition. The application of the porcine stress model resulted in a significant increase in salivary cortisol concentration over the course of the trial and decreased growth performance and appetite. The applied social stress resulted in 32 bacteria being either enriched (13) or depleted (19) in the intestine and feces. Fecal samples showed a greater number of microbial genera influenced by stress than caecum or colon samples. Our trial revealed that the opportunistic pathogens Treponema and Clostridium were enriched in colonic and fecal samples from stressed pigs. Additionally, genera such as Streptococcus, Parabacteroides, Desulfovibrio, Terrisporobacter, Marvinbryantia, and Romboutsia were found to be enriched in response to social stress. In contrast, the genera Prevotella, Faecalibacterium, Butyricicoccus, Dialister, Alloprevotella, Megasphaera, and Mitsuokella were depleted. These depleted bacteria are of great interest because they synthesize metabolites [e.g., short-chain fatty acids (SCFA), in particular, butyrate] showing beneficial health benefits due to inhibitory effects on pathogenic bacteria in different animal species. Of particular interest are Dialister and Faecalibacterium, as their depletion was identified in a human study to be associated with inferior quality of life and depression. We also revealed that some pigs were more susceptible to pathogens as indicated by large enrichments of opportunistic pathogens of Clostridium, Treponema, Streptococcus and Campylobacter. Generally, our results provide further evidence for the microbiota-gut-brain axis as indicated by an increase in cortisol concentration due to social stress regulated by the hypothalamic-pituitary-adrenal axis, and a change in microbiota composition, particularly of bacteria known to be associated with pathogenicity and mental health diseases.

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

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

Rapid Genotyping of Campylobacter coli Strains from Poultry Meat by PFGE, Sau-PCR, and fla-DGGE

The genotyping of Campylobacter coli was done using three methods, pulsed-field gel electrophoresis (PFGE), Sau-polymerase chain reaction (Sau-PCR), and denaturing gradient gel electrophoresis assay of flagellin gene (fla-DGGE) and the characteristics of these assays were compared. The results showed that a total of 53 strains of C. coli were isolated from chicken and duck samples in three markets. All isolates were clustered into 31, 33, and 15 different patterns with Simpson's index of diversity (SID) values of 0.972, 0.974, and 0.919, respectively. Sau-PCR assay was simpler, more rapid, and had higher discriminatory power than PFGE assay. Fla-DGGE assay could detect and illustrate the number of contamination types of C. jejuni and C. coli without cultivation, which saved more time and cost than Sau-PCR and PFGE assays. Therefore, Sau-PCR and fla-DGGE assays are both rapid, economical, and easy to perform, which have the potential to be promising and accessible for primary laboratories in genotyping C. coli strains.

Effects of wheat bran replacement with pomegranate seed pulp on rumen fermentation, gas production, methanogen and protozoa populations of camel and goat rumen using competitive PCR technique: An in vitro study

BACKGROUND

Microbial populations in the rumen play an essential role in the degradation of Cellulosic dietary components and in providing nutrients to the host animal.

OBJECTIVE

This study aims to detect the effect of pomegranate seed pulp (PSP) on rumen fermentation, digestibility and methanogens and the protozoa population (by competitive polymerase chain reaction [PCR]) of the camel and goat rumen fluid.

MATERIALS AND METHODS

PSP was added to the experimental treatments and replaced by wheat bran (0%, 5% and 10%). Rumen fluid was collected from three goats and two camels according to the similarity of sex, breed, origin and time and used for three gas production studies. DNA extraction was performed by the RBB + c method, the ImageJ programme calculated band intensities (target and competing DNA), and line gradients were plotted based on the number of copies and intensity.

RESULTS

Our result showed that diets did not significantly affect the methanogen and protozoa population. Animal species affected microbial populations so that both populations in camels were less than goats. The production of gas and volatile fatty acids was not affected by diets. These two parameters and NH3 concentration and methane production in goats were higher than in camel. The pH of digested dry matter and microbial protein in camels was higher than in goats.

CONCLUSIONS

Therefore, the competitive PCR technique is an effective method for enumerating rumen microbiota. This supplementation can be considered a strategy to achieve performance and environmental benefits.

Effects of different feeding systems on ruminal fermentation, digestibility, methane emissions, and microbiota of Hanwoo steers

This study evaluates how different feeding systems impact ruminal fermentation, methane production, and microbiota of Hanwoo steers native to Korea. In a replicated 2 × 2 crossover design over 29 days per period, eight Hanwoo steers (507.1 ± 67.4 kg) were fed twice daily using a separate feeding (SF) system comprising separate concentrate mix and forage or total mixed rations (TMR) in a 15:85 ratio. The TMR-feeding group exhibited a considerable neutral detergent fiber digestibility increase than the SF group. However, ruminal fermentation parameters and methane production did not differ between two feeding strategies. In addition, TMR-fed steers expressed elevated Prevotellaceae family, Christensenellaceae R-7 group, and an unidentified Veillonellaceae family genus abundance in their rumen, whereas SF-fed steers were rich in the Rikenellaceae RC9 gut group, Erysipelotrichaceae UCG-004, and Succinivibrio. Through linear regression modeling, positive correlations were observed between the Shannon Diversity Index and the SF group's dry matter intake and methane production. Although feeding systems do not affect methane production, they can alter ruminal microbes. These results may guide future feeding system investigations or ruminal microbiota manipulations as a methane-mitigation practice examining different feed ingredients.

Benefits of barley straw as a forage for dairy calves before and after weaning

The aim of this study was to assess the potential consequences on calf intake, performance, behavior, ruminal microbiome, and ruminal epithelium development of combining the inclusion of chopped barley straw and alfalfa hay during the pre- and postweaning periods keeping concentrate to forage ratio constant among dietary treatments. Forty-five Holstein calves (44 ± 5.7 kg of body weight [BW] and 3 ± 1.5 d of age) individually penned were blocked by BW and randomly assigned to a common pellet concentrate fed ad libitum along with one of following forage feeding strategies: barley straw before and after weaning (S-S), barley straw before and alfalfa hay after weaning (S-A), or alfalfa hay before and after weaning (A-A). All calves received the same milk replacer regimen. Forage was supplied in a separated bucket at the rate of 7.5% (preweaning) and 15% (postweaning) of total solid feed intake of the previous day. Feed intake and BW were recorded daily and weekly, respectively. Rumen samples were obtained via a stomach tube at 53, 66, and 87 d and were composite in 3 samples of 5 animals each for subsequent rumen microbiome analysis. A rumen epithelium sample was taken by endoscopy at 90 d to assess gene expression of OCLN, CLDN4, SLC9A1, SLC9A3, SLC16A1, SLC16A4, IL6, and TGFB1. Data were analyzed with a mixed-effects model accounting for the fixed effects of block, forage, week of study, and their interaction, and calf as a random effect. The type of forage fed did not affect concentrate feed, forage, or total DM intake before weaning. However, S-A and A-A calves consumed less concentrate feed and S-A calves grew at a lower rate after weaning than S-S calves. Expression of the gene coding for SLC16A1 in the rumen epithelium was greatest in S-S among treatments. Rumen microbiome did not differ among treatments, while the relative abundance of Acidaminococcus and Selenomas genera increased, while Alloprevotella, Bifidobaterium, Olsenella, and Succiclasticum genera decreased with age. In conclusion, feeding barley straw before and after weaning was more effective than feeding alfalfa hay in promoting concentrate feed intake after weaning and fostering an increase in the expression of SLC16A1 in the rumen epithelium.

Supplementing branched-chain volatile fatty acids in dual-flow cultures varying in dietary forage and corn oil concentrations. I: Digestibility, microbial protein, and prokaryotic community structure

Branched-chain amino acids are deaminated by amylolytic bacteria to branched-chain volatile fatty acids (BCVFA), which are growth factors for cellulolytic bacteria. Our objective was to determine the dietary conditions that would increase the uptake of BCVFA by rumen bacteria. We hypothesized that increased forage would increase cellulolytic bacterial abundance and incorporation of BCVFA into their structure. Supplemental polyunsaturated fatty acids, supplied via corn oil (CO), should inhibit cellulolytic bacteria growth, but we hypothesized that additional BCVFA would alleviate that inhibition. Further, supplemental BCVFA should increase neutral detergent fiber degradation and efficiency of bacterial protein synthesis more with the high forage and low polyunsaturated fatty acid dietary combination. The study was an incomplete block design with 8 dual-flow continuous cultures used in 4 periods with 8 treatments (n = 4 per treatment) arranged as a 2 × 2 × 2 factorial. The factors were: high forage (HF) or low forage (LF; 67 or 33%), without or with supplemental CO (3% dry matter), and without or with 2.15 mmol/d (which included 5 mg/d of 13C each of BCVFA isovalerate, isobutyrate, and 2-methylbutyrate). The isonitrogenous diets consisted of 33:67 alfalfa:orchardgrass pellet, and was replaced with a concentrate pellet that mainly consisted of ground corn, soybean meal, and soybean hulls for the LF diet. The main effect of supplementing BCVFA increased neutral detergent fiber (NDF) degradability by 7.6%, and CO increased NDF degradability only in LF diets. Supplemental BCVFA increased bacterial N by 1.5 g/kg organic matter truly degraded (6.6%) and 0.05 g/g truly degraded N (6.5%). The relative sequence abundance decreased with LF for Fibrobacter succinogenes, Ruminococcus flavefaciens, and genus Butyrivibrio compared with HF. Recovery of the total 13C dose in bacterial pellets decreased from 144 µg/ mg with HF to 98.9 µg/ mg with LF. Although isotope recovery in bacteria was greater with HF, BCVFA supplementation increased NDF degradability and efficiency of microbial protein synthesis under all dietary conditions. Therefore, supplemental BCVFA has potential to improve feed efficiency in dairy cows even with dietary conditions that might otherwise inhibit cellulolytic bacteria.

Metabolic network construction reveals probiotic-specific alterations in the metabolic activity of a synthetic small intestinal community

IMPORTANCE

The development of probiotic therapies targeted at the small intestinal microbiota represents a significant advancement in the field of probiotic interventions. This region poses unique opportunities due to its low number of gut microbiota, along with the presence of heightened immune and metabolic host responses. However, progress in this area has been hindered by a lack of detailed understanding regarding the molecular mechanisms through which probiotics exert their effects in the small intestine. Our study, utilizing a synthetic community of three small intestinal bacterial strains and the addition of two different probiotic species, and kynurenine as a representative dietary or endogenously produced compound, highlights the importance of selecting probiotic species with diverse genetic capabilities that complement the functional capacity of the resident microbiota, or alternatively, constructing a multispecies formula. This approach holds great promise for the development of effective probiotic therapies and underscores the need to consider the functional capacity of probiotic species when designing interventions.

Exploring novel alkane-degradation pathways in uncultured bacteria from the North Atlantic Ocean

IMPORTANCE

Petroleum pollution in the ocean has increased because of rapid population growth and modernization, requiring urgent remediation. Our understanding of the metabolic response of native microbial communities to oil spills is not well understood. Here, we explored the baseline hydrocarbon-degrading communities of a subarctic Atlantic region to uncover the metabolic potential of the bacteria that inhabit the surface and subsurface water. We conducted enrichments with a 13C-labeled hydrocarbon to capture the fraction of the community actively using the hydrocarbon. We then combined this approach with metagenomics to identify the metabolic potential of this hydrocarbon-degrading community. This revealed previously undescribed uncultured bacteria with unique metabolic mechanisms involved in aerobic hydrocarbon degradation, indicating that temperature may be pivotal in structuring hydrocarbon-degrading baseline communities. Our findings highlight gaps in our understanding of the metabolic complexity of hydrocarbon degradation by native marine microbial communities.

Exploring the gut microbiota: lifestyle choices, disease associations, and personal genomics

The gut microbiota is a rich and dynamic ecosystem that actively interacts with the human body, playing a significant role in the state of health and disease of the host. Diet, exercise, mental health, and other factors have exhibited the ability to influence the gut bacterial composition, leading to changes that can prevent and improve, or favor and worsen, both intestinal and extra-intestinal conditions. Altered gut microbial states, or 'dysbiosis', associated with conditions and diseases are often characterized by shifts in bacterial abundance and diversity, including an impaired Firmicutes to Bacteroidetes ratio. By understanding the effect of lifestyle on the gut microbiota, personalized advice can be generated to suit each individual profile and foster the adoption of lifestyle changes that can both prevent and ameliorate dysbiosis. The delivery of effective and reliable advice, however, depends not only on the available research and current understanding of the topic, but also on the methods used to assess individuals and to discover the associations, which can introduce bias at multiple stages. The aim of this review is to summarize how human gut microbial variability is defined and what lifestyle choices and diseases have shown association with gut bacterial composition. Furthermore, popular methods to investigate the human gut microbiota are outlined, with a focus on the possible bias caused by the lack of use of standardized methods. Finally, an overview of the current state of personalized advice based on gut microbiota testing is presented, underlining its power and limitations.

Homemade Nucleic Acid Preservation Buffer Proves Effective in Preserving the Equine Faecal Microbiota over Time at Ambient Temperatures

The equine faecal microbiota is often assessed as a proxy of the microbial community in the distal colon, where the microbiome has been linked to states of health and disease in the horse. However, the microbial community structure may change over time if samples are not adequately preserved. This study stored equine faecal samples from n = 10 horses in four preservation treatments at room temperature for up to 150 h and assessed the resulting impact on microbial diversity and the differential abundance of taxa. Treatments included "COLD" (samples packaged with a cool pack), "CLX" (2% chlorhexidine digluconate solution), "NAP" (nucleic acid preservation buffer), and "FTA" (Whatman FTA™ cards). The samples were assessed using 16S rRNA gene sequencing after storage for 0, 24, 72, and 150 h at room temperature under the different treatments. The results showed effective preservation of diversity and community structure with NAP buffer but lower diversity (p = 0.001) and the under-representation of Fibrobacterota in the FTA card samples. The NAP treatment inhibited the overgrowth of bloom taxa that occurred by 72 h at room temperature. The COLD, CLX, and NAP treatments were effective in preserving the faecal microbiota for up to 24 h at room temperature, and the CLX and NAP treatments improved the yield of Patescibacteria and Fibrobacterota in some cases. The cold and CLX treatments were ineffective in preventing community shifts that occurred by 72 h at room temperature. These findings demonstrate the suitability of the COLD, NAP, and CLX treatments for the room temperature storage of equine faeces for up to 24 h and of NAP buffer for up to 150 h prior to processing.

Effect of feeding Yucca schidigera extract and a live yeast on the rumen microbiome and performance of dairy cows fed a diet excess in rumen degradable nitrogen

Nitrogen (N) loss from livestock agriculture via ammonia and nitrous oxide can reduce feed efficiency, production and negatively affect the environment. One option to reduce N loss is to add dietary supplements such as Yucca schidigera extract which has ammonia-binding properties and contains antimicrobial steroidal saponins, or Saccharomyces cerevisiae yeast, which can stabilise rumen pH and promote fibre degradation, increasing microbial growth and demand for degradable N. To determine the effect of Yucca schidigera extract when fed alone or in combination with a live yeast on the performance, rumen metabolism, microbiome and N balance, six rumen cannulated dairy cows were fed a mixed ration (C), mixed ration with Y. schidigera extract (De-Odorase®, Alltech®; 5 g/cow/day; D), or mixed ration with Y. schidigera extract (5 g/day) and Saccharomyces cerevisiae (Yea-Sacc®, Alltech®, 1 g/cow per day; DY), in a 3 × 3 Latin rectangle design study with three periods of 49-day duration. Digesta samples were collected via the ruminal cannula during the final week of each period and separated into liquid (LPD) and solid (SPD) phases for microbiome analysis using 16S rRNA amplicon sequencing. DM intake was 0.8 kg/d lower (P < 0.05) in cows fed DY than C or D, with milk protein concentration 1.7 g/kg higher in C than D or DY. There was a beta diversity (Bray Curtis) clustering of the LPD in cows fed D or DY compared to C (P < 0.05), driven by an increase in Prevotella ruminicola-related operational taxonomic units (OTUs), and a decrease in P. brevis and P. bryantii OTUs. A methanogen OTU, Methanobrevibacter olleyae, was decreased in cows fed D or DY and an unclassified species of Gammaproteobacteria was increased in DY (LDA > 2.0, P < 0.05) compared to C. Rumen pH, ammonia and total VFA concentration were not affected by treatment (P > 0.05) but the concentration of propionate and iso-butyrate were lower at 1700 and 2000 h in cows fed DY compared to C (P < 0.05). Measurements of N balance were unaffected by supplementation with D or DY, and there was no effect of treatment on slurry pH. In conclusion, supplementing with an extract of Yucca schidigera either alone or in combination with a live yeast had only a small effect on performance, with Yucca schidigera altering species associated with carbohydrate and protein metabolism, and reduced Methanobrevibacter olleyae which is involved in methanogenesis.

Multi-breed host rumen epithelium transcriptome and microbiome associations and their relationship with beef cattle feed efficiency

Understanding host-microbial interactions in the rumen and its influence on desirable production traits may lead to potential microbiota manipulation or genetic selection for improved cattle feed efficiency. This study investigated the host transcriptome and its correlation with the rumen archaea and bacteria differential abundance of two pure beef cattle breeds (Angus and Charolais) and one composite beef hybrid (Kinsella) divergent for residual feed intake (RFI; low-RFI vs. high-RFI). Using RNA-Sequencing of rumen tissue and 16S rRNA gene amplicon sequencing, differentially expressed genes (FDR ≤ 0.05, |log2(Fold-change) >|2) and differentially abundant (p-value < 0.05) archaea and bacteria amplicon sequence variants (ASV) were determined. Significant correlations between gene expression and ASVs (p-value < 0.05) were determine using Spearman correlation. Interesting associations with muscle contraction and the modulation of the immune system were observed for the genes correlated with bacterial ASVs. Potential functional candidate genes for feed efficiency status were identified for Angus (CCL17, CCR3, and CXCL10), Charolais (KCNK9, GGT1 and IL6), and Kinsella breed (ESR2). The results obtained here provide more insights regarding the applicability of target host and rumen microbial traits for the selection and breeding of more feed efficient beef cattle.

Longitudinal observational study protocol - Preterm Infants: Microbiome Establishment, Neuro-CrossTalk and Origins (PIMENTO)

INTRODUCTION

Very preterm infants are at risk of abnormal microbiome colonisation in the first weeks to months of life. Several important associated factors have been identified including gestational age, mode of delivery, antibiotic exposure and feeding. Preterm infants are at risk of a number of pathologies for which the microbiome may play a central role, including necrotising enterocolitis and sepsis. The objective of this study is to determine detailed microbiome changes that occur around implementation of different management practices including empiric antibiotic use, advancement of feeds and administration of probiotics during admission to the neonatal intensive care unit.

METHODS AND ANALYSIS

A single-site, longitudinal observational study of infants born less than 32 weeks gestation, including collection of maternal samples around delivery and breastmilk and infant samples from admission through discharge from the neonatal unit.

ETHICS AND DISSEMINATION

The protocol was approved by the Clinical Research Ethics Committee of the Cork Teaching Hospitals.The findings from this study will be disseminated in peer-reviewed journals, during scientific conferences, and directly to the study participants. Sequencing data will be deposited in public databases.

TRIAL REGISTRATION NUMBER

NCT05803577.

Effects of the Use of Rice Grain on Growth Performances, Blood Metabolites, Rumen Fermentation, and Rumen Microbial Community in Fattening Hanwoo Steers

This study aimed to assess the influence of rice grain in the total mixed ration (TMR) on the growth performance, blood metabolites, rumen fermentation, and rumen microbial community of fattening Hanwoo steers. Two experimental diets were prepared: (i) a TMR containing 33% dry matter (DM) corn grains (Corn TMR) and (ii) a TMR containing 33% DM rice grains (Rice TMR). Twenty-two Hanwoo steers (body weight [BW], 498 ± 32 kg; months, 17 ± 0.5) were distributed into two treatment groups in a completely randomized block design according to BW. The Rice TMR group had a higher final BW and DM intake (DMI) compared to those in the Corn TMR group (p < 0.01). However, no difference was observed in the average daily gain (ADG) and feed conversion ratio (FCR) between the two treatments. For the rumen fermentation parameters, the molar portion of butyrate in the Rice TMR was higher than in the Corn TMR (p < 0.01). Streptococcus bovis tended to be higher in the Rice TMR (p = 0.09). The results of this study suggest that using rice grain as the primary starch source in TMRs may be an alternative option for fattening Hanwoo steers.

Saccharomyces cerevisiae boulardii accelerates intestinal microbiota maturation and is correlated with increased secretory IgA production in neonatal dairy calves

Neonatal calves have a limited capacity to initiate immune responses due to a relatively immature adaptive immune system, which renders them susceptible to many on-farm diseases. At birth, the mucosal surfaces of the intestine are rapidly colonized by microbes in a process that promotes mucosal immunity and primes the development of the adaptive immune system. In a companion study, our group demonstrated that supplementation of a live yeast probiotic, Saccharomyces cerevisiae boulardii (SCB) CNCM I-1079, to calves from birth to 1 week of age stimulates secretory IgA (sIgA) production in the intestine. The objective of the study was to evaluate how SCB supplementation impacts the intestinal microbiota of one-week-old male calves, and how changes in the bacterial community in the intestine relate to the increase in secretory IgA. A total of 20 calves were randomly allocated to one of two treatments at birth: Control (CON, n = 10) fed at 5 g/d of carrier with no live yeast; and SCB (n = 10) fed at 5 g of live SCB per day (10 × 109 CFU/d). Our study revealed that supplementing calves with SCB from birth to 1 week of age had its most marked effects in the ileum, increasing species richness and phylogenetic diversity in addition to expediting the transition to a more interconnected bacterial community. Furthermore, LEfSe analysis revealed that there were several differentially abundant taxa between treatments and that SCB increased the relative abundance the family Eubacteriaceae, Corynebacteriaceae, Eggerthellaceae, Bacillaceae, and Ruminococcaceae. Furthermore, network analysis suggests that SCB promoted a more stable bacterial community and appears to reduce colonization with Shigella. Lastly, we observed that the probiotic-driven increase in microbial diversity was highly correlated with the enhanced secretory IgA capacity of the ileum, suggesting that the calf's gut mucosal immune system relies on the development of a stable and highly diverse microbial community to provide the necessary cues to train and promote its proper function. In summary, this data shows that supplementation of SCB promoted establishment of a diverse and interconnected microbiota, prevented colonization of Escherichia Shigella and indicates a possible role in stimulating humoral mucosal immunity.

Prophylactic feeding of neomycin to Holstein calves alters gut microbiota, bile acid metabolism, and expression of genes involved in immunometabolic regulation

The objective of this study was to evaluate the effects of prophylactic neomycin administration on Holstein bull calves' intestinal microbiota, bile acid (BA) metabolism, and transcript abundance of genes related to BA metabolism. A total of 36 calves were blocked by body weight and assigned to either non-medicated milk replacer (CTL), or neomycin for 14 days (ST) or 28 days (LT) in their milk replacer. At the end of the study, calves were euthanized to collect tissue and digesta samples from the gastrointestinal tract, liver, and adipose tissue for analysis of intestinal microbial diversity, bile acid concentration and profile in various body tissues, and gene expression related to bile acid, lipid, carbohydrate metabolism, and inflammation. Calves that received prophylactic administration of neomycin for 28 d (LT) had reduced species richness (chao1 index), and tended to have reduced phylogenetic diversity in the ileum tissue. The relative abundance of Lactobacillus, and Bifidobacterium in ileum and colon digesta were decreased in LT compared with CTL. Concentrations of primary, secondary, and total BA were increased by ST in ileal tissue. In plasma, ST and LT treatments had lower concentrations of secondary BA. Gene expression of the BA receptor FXR was increased in ileum and liver by LT compared to CTL. The expression of FXR and TGR5 in the liver was increased in the ST group compared with CTL, and in adipose tissue, 5 genes related to triglyceride, gluconeogenesis, and immune activation were differentially expressed between CTL and ST. In conclusion, we provide evidence that prophylactic administration of neomycin leads to aberrant changes in BA concentration and profile in different compartments of the enterohepatic system through a process that possibly entails antimicrobial disruption of key bacterial groups, which persists even after cessation of neomycin administration. Additionally, we uncovered an apparent link between dysregulated BA metabolism and changes in lipid metabolism and immune activation in adipose tissue and liver.

Gut, oral, and nasopharyngeal microbiota dynamics in the clinical course of hospitalized infants with respiratory syncytial virus bronchiolitis

Introduction

Respiratory syncytial virus (RSV) is the most common cause of bronchiolitis and hospitalization in infants worldwide. The nasopharyngeal microbiota has been suggested to play a role in influencing the clinical course of RSV bronchiolitis, and some evidence has been provided regarding oral and gut microbiota. However, most studies have focused on a single timepoint, and none has investigated all three ecosystems at once.

Methods

Here, we simultaneously reconstructed the gut, oral and nasopharyngeal microbiota dynamics of 19 infants with RSV bronchiolitis in relation to the duration of hospitalization (more or less than 5 days). Fecal samples, oral swabs, and nasopharyngeal aspirates were collected at three timepoints (emergency room admission, discharge and six-month follow-up) and profiled by 16S rRNA amplicon sequencing.

Results

Interestingly, all ecosystems underwent rearrangements over time but with distinct configurations depending on the clinical course of bronchiolitis. In particular, infants hospitalized for longer showed early and persistent signatures of unhealthy microbiota in all ecosystems, i.e., an increased representation of pathobionts and a depletion of typical age-predicted commensals.

Discussion

Monitoring infant microbiota during RSV bronchiolitis and promptly reversing any dysbiotic features could be important for prognosis and long-term health.

Comparison of four DNA extraction methods for 16s rRNA microbiota profiling of human faecal samples

OBJECTIVE

Growth in large population-based studies assessing contributions of the gut microbiota to health and disease requires high-throughput sample processing and analysis methods. This study assessed the impact that modifications to a commercially available magnetic bead based, semi-automated DNA extraction kit had on determination of microbial composition, relative to an established in-house method involving a combination of mechanical and chemical lysis. DNA was extracted from faecal samples from healthy adults (n = 12; 34-69 years), microbial composition was determined by V3-V4 16s rRNA sequencing and compared between extraction methods.

RESULTS

Diversity metrics did not differ between extraction methods. Differences in the relative abundance of key phyla, including a significantly lower abundance of the Firmicutes (p = 0.004) and higher relative abundance of the Bacteroidetes (p = 0.005) and Proteobacteria (p = 0.008) phyla were noted where the DNA extraction did not include additional chemical and mechanical lysis. Principal coordinate analysis of family and genera level data also suggested a potential for sample pre-processing to impact microbial composition. Observations of the potential for skewed microbial composition profiles from samples prepared using a semi-automated DNA extraction kit without additional sample pre-processing highlights a need for consideration of standardisation of methodological approaches to increase the comparability of microbial compositional data.

An Immobilized Form of a Blend of Essential Oils Improves the Density of Beneficial Bacteria, in Addition to Suppressing Pathogens in the Gut and Also Improves the Performance of Chicken Breeding

Antimicrobial growth promoters (AGP) are used in chicken production to suppress pathogens in the gut and improve performance, but such products tend to suppress beneficial bacteria while favoring the development and spread of antimicrobial resistance. A green alternative to AGP with the ability to suppress pathogens, but with an additional ability to spare beneficial gut bacteria and improve breeding performance is urgently required. We investigated the effect of supplementation of a blend of select essential oils (cinnamon oil, carvacrol, and thyme oil, henceforth referred to as EO; at two doses: 200 g/t and 400 g/t feed) exhibiting an ability to spare Lactobacillus while exhibiting strong E. coli inhibition ability under in vitro tests and immobilized in a sunflower oil and calcium alginate matrix, to broiler chickens and compared the effects with those of a probiotic yeast (Y), an AGP virginiamycin (V), and a negative control (C). qPCR analysis of metagenomic DNA from the gut content of experimental chickens indicated a significantly (p < 0.05) lower density of E. coli in the EO groups as compared to other groups. Amplicon sequence data of the gut microbiome indicated that all the additives had specific significant effects (DESeq2) on the gut microbiome, such as enrichment of uncultured Clostridia in the V and Y groups and uncultured Ruminococcaceae in the EO groups, as compared to the control. LEfSe analysis of the sequence data indicated a high abundance of beneficial bacteria Ruminococcaceae in the EO groups, Faecalibacterium in the Y group, and Blautia in the V group. Supplementation of the immobilized EO at the dose rate of 400 g/ton feed improved body weight gain (by 64 g/bird), feed efficiency (by 5 points), and cellular immunity (skin thickness response to phytoheamagglutinin lectin from Phaseolus vulgaris by 58%) significantly (p < 0.05), whereas neither yeast nor virginiamycin showed a significant effect on performance parameters. Expression of genes associated with gut barrier and immunity function such as CLAUDIN1, IL6, IFNG, TLR2A, and NOD1 were significantly higher in the EO groups. This study showed that the encapsulated EO mixture can improve the density of beneficial microbes in the gut significantly, with concomitant suppression of potential pathogens such as E.coli and improved performance and immunity, and hence, has a high potential to be used as an effective alternative to AGP in poultry.

Gut Microbiota, Metabolome, and Body Composition Signatures of Response to Therapy in Patients with Advanced Melanoma

Despite the recent breakthroughs in targeted and immunotherapy for melanoma, the overall survival rate remains low. In recent years, considerable attention has been paid to the gut microbiota and other modifiable patient factors (e.g., diet and body composition), though their role in influencing therapeutic responses has yet to be defined. Here, we characterized a cohort of 31 patients with unresectable IIIC-IV-stage cutaneous melanoma prior to initiation of targeted or first-line immunotherapy via the following methods: (i) fecal microbiome and metabolome via 16S rRNA amplicon sequencing and gas chromatography/mass spectrometry, respectively, and (ii) anthropometry, body composition, nutritional status, physical activity, biochemical parameters, and immunoprofiling. According to our data, patients subsequently classified as responders were obese (i.e., with high body mass index and high levels of total, visceral, subcutaneous, and intramuscular adipose tissue), non-sarcopenic, and enriched in certain fecal taxa (e.g., Phascolarctobacterium) and metabolites (e.g., anethole), which were potentially endowed with immunostimulatory and oncoprotective activities. On the other hand, non-response was associated with increased proportions of Streptococcus, Actinomyces, Veillonella, Dorea, Fusobacterium, higher neutrophil levels (and a higher neutrophil-to-lymphocyte ratio), and higher fecal levels of butyric acid and its esters, which also correlated with decreased survival. This exploratory study provides an integrated list of potential early prognostic biomarkers that could improve the clinical management of patients with advanced melanoma, in particular by guiding the design of adjuvant therapeutic strategies to improve treatment response and support long-term health improvement.

In vitro Effects of Cellulose Acetate on Fermentation Profiles, the Microbiome, and Gamma-aminobutyric Acid Production in Human Stool Cultures

Gamma-aminobutyric acid (GABA) is considered as a potential candidate substance that mediates the effects of intestinal bacteria on human mental health. In the present study, we evaluated the effect of water-soluble cellulose acetate (WSCA), a type of cellulose ester, on fermentation and microbial profiles, and GABA production in human stool cultures prepared from fresh feces from volunteers. In addition, the GABA-producing ability of Bacteroides uniformis, which can utilize WSCA, was evaluated in a pure-culture study. All incubations were conducted anaerobically. WSCA supplementation increased (P < 0.05) acetate and propionate production and decreased (P < 0.05) the pH in human fecal cultures. WSCA significantly altered the microbiota, selectively increasing the relative abundance of B. uniformis (P < 0.05). Pure-culture study results revealed that B. uniformis produces GABA, possibly via a glutamate-dependent acid resistance system under low pH conditions. In conclusion, WSCA could be a potential prebiotic material that is fermented by intestinal bacteria and increases short-chain fatty acid and GABA production in the human gut. Bacteroides uniformis might play an important role in both WSCA degradation and GABA production in the intestine.

Metagenomic approach to infer rumen microbiome derived traits of cattle

Ruminants enable the conversion of indigestible plant material into animal consumables, including dairy products, meat, and valuable fibers. Microbiome research is gaining popularity in livestock species because it aids in the knowledge of illnesses and efficiency processes in animals. In this study, we use WGS metagenomic data to thoroughly characterize the ruminal ecosystem of cows to infer positive and negative livestock traits determined by the microbiome. The rumen of cows from Argentina were described by combining different gene biomarkers, pathways composition and taxonomic information. Taxonomic characterization indicated that the two major phyla were Bacteroidetes and Firmicutes; in third place, Proteobacteria was highly represented followed by Actinobacteria; Prevotella, and Bacteroides were the most abundant genera. Functional profiling of carbohydrate-active enzymes indicated that members of the Glycoside Hydrolase (GH) class accounted for 52.2 to 55.6% of the total CAZymes detected, among them the most abundant were the oligosaccharide degrading enzymes. The diversity of GH families found suggested efficient hydrolysis of complex biomass. Genes of multidrug, macrolides, polymyxins, beta-lactams, rifamycins, tetracyclines, and bacitracin resistance were found below 0.12% of relative abundance. Furthermore, the clustering analysis of genera and genes that correlated to methane emissions or feed efficiency, suggested that the cows analysed could be regarded as low methane emitters and clustered with high feed efficiency reference animals. Finally, the combination of bioinformatic analyses used in this study can be applied to assess cattle traits difficult to measure and guide enhanced nutrition and breeding methods.

Effects of grain-based diets on the rumen and fecal bacterial communities of the North American bison (Bison bison)

To overcome the challenges of pasture-finishing of bison, producers commonly feed them with higher energy, grain-based diets to reach the desired market weight. However, decades of research on domesticated ruminants have shown that such diets can have profound effects on the composition of gut microbial communities. To gain further insight, the 16S rRNA gene-based study described in this report aimed to compare the composition of ruminal and fecal bacterial communities from two herds of bison heifers (n = 20/herd) raised on different ranches that were both transitioned from native pasture to a grain-based, free-choice diet for ~100 days prior to slaughter. Comparative analyses of operational taxonomic unit (OTU) composition, either by alpha diversity indices, principal coordinate analysis (PCoA), or on the most abundant individual OTUs, showed the dramatic effect of a diet on the composition of both rumen and fecal bacterial communities in bison. Indeed, feeding a grain-based diet resulted in a lower number of rumen and fecal bacterial OTUs, respectively, compared to grazing on pasture (p < 0.05). PCoA revealed that the composition of the rumen and fecal bacterial communities from the two herds was more similar when they were grazing on native pastures compared to when they were fed a grain-based, free-choice diet. Finally, a comparative analysis of the 20 most abundant OTUs from the rumen and fecal communities further showed that the representation of all these species-level bacterial groups differed (p < 0.05) between the two dietary treatments. Together, these results provide further insights into the rumen and fecal microbiomes of grazing bison and their response to grain-based diet regimens commonly used in intensive ruminant production systems.

Screening macroalgae for mitigation of enteric methane in vitro

This study investigated the effects of 67 species of macroalgae on methanogenesis and rumen fermentation in vitro. Specimens were analyzed for their effect on ruminal fermentation and microbial community profiles. Incubations were carried out in an automated gas production system for 24-h and macroalgae were tested at 2% (feed dry matter basis) inclusion rate. Methane yield was decreased 99% by Asparagopsis taxiformis (AT) when compared with the control. Colpomenia peregrina also decreased methane yield 14% compared with control; no other species influenced methane yield. Total gas production was decreased 14 and 10% by AT and Sargassum horneri compared with control, respectively. Total volatile fatty acid (VFA) concentration was decreased between 5 and 8% by 3 macroalgae, whereas AT reduced it by 10%. Molar proportion of acetate was decreased 9% by AT, along with an increase in propionate by 14%. Asparagopsis taxiformis also increased butyrate and valerate molar proportions by 7 and 24%, respectively, whereas 3 macroalgae species decreased molar proportion of butyrate 3 to 5%. Vertebrata lanosa increased ammonia concentration, whereas 3 other species decreased it. Inclusion of AT decreased relative abundance of Prevotella, Bacteroidales, Firmicutes and Methanobacteriaceae, whereas Clostridium, Anaerovibrio and Methanobrevibacter were increased. Specific gene activities for Methanosphaera stadtmane and Methanobrevibacter ruminantium were decreased by AT inclusion. In this in vitro study, Asparagopsis taxiformis was most effective in decreasing methane concentration and yield, but also decreased total gas production and VFA concentration which indicates overall inhibition of ruminal fermentation. No other macroalgae were identified as potential mitigants of enteric methane.

A pilot study of dietary fibres on pathogen growth in an ex vivo colonic model reveals their potential ability to limit vancomycin-resistant Enterococcus expansion

Aim: Dietary fibre is important for shaping gut microbiota. The aim of this pilot study was to investigate the impact of dietary fibres on pathogen performance in the presence of gut microbiota. Methods: In an ex vivo gut model, pooled faecal samples were spiked with a cocktail of representative gastrointestinal pathogens and fermented with yeast β-glucan for 24 hours, after which 16S rRNA amplicon sequencing and short-chain and branched-chain fatty acid (SCFA and BCFA) analyses were performed. In addition, oat β-glucan, arabinoxylan, yeast β-glucan, and galactooligosaccharides were each tested against individual representative pathogens and pathogen growth was assessed via qPCR. Glucose served as a control carbon source. Results: Based on 16S rRNA amplicon sequencing, yeast β-glucan selected for higher proportions of Bacteroides (P = 0.0005, ~6 fold) and Clostridia (P = 0.005, ~3.6 fold) while species of Escherichia/Shigella (P = 0.021, ~2.8 fold) and Lactobacillus (P = 0.007, ~ 15.7-fold) were higher in glucose. Pathogen relative abundance did not differ between glucose and yeast β-glucan. In the absence of pathogens, higher production of BCFAs (P = 0.002) and SCFAs (P = 0.002) fatty acids was observed for fibre group(s). For individual pathogens, yeast β-glucan increased growth of Escherichia coli, Salmonella typhimurium, and Listeria monocytogenes (P < 0.05), arabinoxylan increased S. typhimurium (P < 0.05). Tested fibres decreased vancomycin-resistant Enterococcus faecium (P < 0.05), with yeast β-glucan causing a 1-log reduction (P < 0.01), while galactooligosaccharides decreased L. monocytogenes (P < 0.05). Conclusion: Tested fibres differentially influenced the growth of pathogens, but yeast β-glucan could represent a dietary strategy to help limit vancomycin-resistant enterococci (VRE) expansion in the gut.

Integrated meta-omics analyses reveal a role of ruminal microorganisms in ketone body accumulation and ketosis in lactating dairy cows

The extent to which a nutrition-related disorder such as ketosis alters the ruminal microbiota or whether microbiota composition is related to ketosis and potential associations with host metabolism is unknown. We aimed to evaluate variations occurring in the ruminal microbiota of ketotic and nonketotic cows in the early postpartum period, and how those changes may affect the risk of developing the disease. Data on milk yield, dry matter intake (DMI), body condition score, and blood β-hydroxybutyrate (BHB) concentrations at 21 d postpartum were used to select 27 cows, which were assigned (n = 9 per group) to a clinical ketotic (CK, 4.10 ± 0.72 mmol BHB/L, DMI 11.61 ± 0.49 kg/d, ruminal pH 7.55 ± 0.07), subclinical ketotic (SK, 1.36 ± 0.12 mmol BHB/L, DMI 15.24 ± 0.34 kg/d, ruminal pH 7.58 ± 0.08), or control (NK, 0.88 ± 0.14 mmol BHB/L, DMI 16.74 ± 0.67/d, ruminal pH 7.61 ± 0.03) group. Cows averaged 3.6 ± 0.5 lactations and a body condition score of 3.11 ± 0.34 at the time of sampling. After blood serum collection for metabolomics analysis (¹H nuclear magnetic resonance spectra), 150 mL of ruminal digesta was collected from each cow using an esophageal tube, paired-end (2 × 300 bp) sequencing of isolated DNA from ruminal digesta was performed via Illumina MiSeq, and sequencing data were analyzed using QIIME2 (v 2020.6) to measure the ruminal microbiota composition and relative abundance. Spearman correlation coefficients were used to evaluate relationships between relative abundance of bacterial genera and concentrations of serum metabolites. There were more than 200 genera, with approximately 30 being significant between NK and CK cows. Succinivibrionaceae UCG 1 taxa decreased in CK compared with NK cows. Christensenellaceae (Spearman correlation coefficient = 0.6), Ruminococcaceae (Spearman correlation coefficient = 0.6), Lachnospiraceae (Spearman correlation coefficient = 0.5), and Prevotellaceae (Spearman correlation coefficient = 0.6) genera were more abundant in the CK group and were highly positively correlated with plasma BHB. Metagenomic analysis indicated a high abundance of predicted functions related to metabolism (37.7%), genetic information processing (33.4%), and Brite hierarchies (16.3%) in the CK group. The 2 most important metabolic pathways for butyrate and propionate production were enriched in CK cows, suggesting increased production of acetyl coenzyme A and butyrate and decreased production of propionate. Overall, the combined data suggested that microbial populations may be related to ketosis by affecting short-chain fatty acid metabolism and BHB accumulation even in cows with adequate feed intake in the early postpartum period.

Early feeding leads to molecular maturation of the gut mucosal immune system in suckling piglets

Introduction

Diet-microbiota-host interactions are increasingly studied to comprehend their implications in host metabolism and overall health. Keeping in mind the importance of early life programming in shaping intestinal mucosal development, the pre-weaning period can be utilised to understand these interactions in suckling piglets. The objective of this study was to investigate the consequences of early life feeding on the time-resolved mucosal transcriptional program as well as mucosal morphology.

Methods

A customised fibrous feed was provided to piglets (early-fed or EF group; 7 litters) from five days of age until weaning (29 days of age) in addition to sow's milk, whereas control piglets (CON; 6 litters) suckled mother's milk only. Rectal swabs, intestinal content, and mucosal tissues (jejunum, colon) were obtained pre- and post-weaning for microbiota analysis (16S amplicon sequencing) and host transcriptome analysis (RNA sequencing).

Results

Early feeding accelerated both microbiota colonisation as well as host transcriptome, towards a more "mature state", with a more pronounced response in colon compared to jejunum. Early feeding elicited the largest impact on the colon transcriptome just before weaning (compared to post-weaning time-points), exemplified by the modulation of genes involved in cholesterol and energy metabolism and immune response. The transcriptional impact of early feeding persisted during the first days post-weaning and was highlighted by a stronger mucosal response to the weaning stress, via pronounced activation of barrier repair reactions, which is a combination of immune activation, epithelial migration and "wound-repair" like processes, compared to the CON piglets.

Discussion

Our study demonstrates the potential of early life nutrition in neonatal piglets as a means to support their intestinal development during the suckling period, and to improve adaptation during the weaning transition.

A Comparative Analysis of the Fecal Bacterial Communities of Light and Heavy Finishing Barrows Raised in a Commercial Swine Production Environment

For commercial swine producers, the natural variation in body weight amongst pigs in a herd presents a challenge in meeting the standards of meat processors who incentivize target carcass weights by offering more favorable purchase prices. Body weight variation in a swine herd is evident as early as birth, and it is typically maintained throughout the entire production cycle. Amongst the various factors that can affect growth performance, the gut microbiome has emerged as an important factor that can affect efficiency, as it contributes to vital functions such as providing assimilable nutrients from feed ingredients that are inedible to the host, as well as resistance to infection by a pathogen. In this context, the objective of the study described in this report was to compare the fecal microbiomes of light and heavy barrows (castrated male finishing pigs) that were part of the same research herd that was raised under commercial conditions. Using high-throughput sequencing of amplicons generated from the V1-V3 regions of the 16S rRNA gene, two abundant candidate bacterial species identified as operational taxonomic units (OTUs), Ssd-1085 and Ssd-1144, were found to be in higher abundance in the light barrows group. Ssd-1085 was predicted to be a potential strain of Clostridium jeddahitimonense, a bacterial species capable of utilizing tagatose, a monosaccharide known to act as a prebiotic that can enhance the proliferation of beneficial microorganisms while inhibiting the growth of bacterial pathogens. OTU Ssd-1144 was identified as a candidate strain of C. beijerinckii, which would be expected to function as a starch utilizing symbiont in the swine gut. While it remains to be determined why putative strains of these beneficial bacterial species would be in higher abundance in lower weight pigs, their overall high levels in finishing pigs could be the result of including ingredients such as corn and soybean-based products in swine diets. Another contribution from this study was the determination that these two OTUs, along with five others that were also abundant in the fecal bacterial communities of the barrows that were analyzed, had been previously identified in weaned pigs, suggesting that these OTUs can become established as early as the nursery phase.

Oral administration of Pinus koraiensis cone essential oil reduces rumen methane emission by altering the rumen microbial composition and functions in Korean native goat (Capra hircus coreanae)

This study aimed to investigate Pinus koraiensis cone essential oil (PEO) as a methane (CH₄) inhibitor and determine its impact on the taxonomic and functional characteristics of the rumen microbiota in goats. A total of 10 growing Korean native goats (Capra hircus coreanae, 29.9 ± 1.58 kg, male) were assigned to different dietary treatments: control (CON; basal diet without additive) and PEO (basal diet +1 g/d of PEO) by a 2 × 2 crossover design. Methane measurements were conducted every 4 consecutive days for 17-20 days using a laser CH₄ detector. Samples of rumen fluid and feces were collected during each experimental period to evaluate the biological effects and dry matter (DM) digestibility after PEO oral administration. The rumen microbiota was analyzed via 16S rRNA gene amplicon sequencing. The PEO oral administration resulted in reduced CH₄ emission (eructation CH₄/body weight^0.75, p = 0.079) without affecting DM intake; however, it lowered the total volatile fatty acids (p = 0.041), molar proportion of propionate (p = 0.075), and ammonia nitrogen (p = 0.087) in the rumen. Blood metabolites (i.e., albumin, alanine transaminase/serum glutamic pyruvate transaminase, creatinine, and triglyceride) were significantly affected (p < 0.05) by PEO oral administration. The absolute fungal abundance (p = 0.009) was reduced by PEO oral administration, whereas ciliate protozoa, total bacteria, and methanogen abundance were not affected. The composition of rumen prokaryotic microbiota was altered by PEO oral administration with lower evenness (p = 0.054) observed for the PEO group than the CON group. Moreover, PICRUSt2 analysis revealed that the metabolic pathways of prokaryotic bacteria, such as pyruvate metabolism, were enriched in the PEO group. We also identified the Rikenellaceae RC9 gut group as the taxa potentially contributing to the enriched KEGG modules for histidine biosynthesis and pyruvate oxidation in the rumen of the PEO group using the FishTaco analysis. The entire co-occurrence networks showed that more nodes and edges were detected in the PEO group. Overall, these findings provide an understanding of how PEO oral administration affects CH₄ emission and rumen prokaryotic microbiota composition and function. This study may help develop potential manipulation strategies to find new essential oils to mitigate enteric CH₄ emissions from ruminants.

Differences in Faecal Microbiome Taxonomy, Diversity and Functional Potential in a Bovine Cohort Experimentally Challenged with Mycobacterium avium subsp. paratuberculosis (MAP)

Mycobacterium avium subspecies paratuberculosis (MAP) is the causative agent of Johne's disease in ruminants, a chronic enteritis which results in emaciation and eventual loss of the animal. Recent advances in metagenomics have allowed a more in-depth study of complex microbiomes, including that of gastrointestinal tracts, and have the potential to provide insights into consequences of the exposure of an animal to MAP or other pathogens. This study aimed to investigate taxonomic diversity and compositional changes of the faecal microbiome of cattle experimentally challenged with MAP compared to an unexposed control group. Faecal swab samples were collected from a total of 55 animals [exposed group (n = 35) and a control group (n = 20)], across three time points (months 3, 6 and 9 post-inoculation). The composition and functional potential of the faecal microbiota differed across time and between the groups (p < 0.05), with the primary differences, from both a taxonomic and functional perspective, occurring at 3 months post inoculation. These included significant differences in the relative abundance of the genera Methanobrevibacter and Bifidobacterium and also of 11 other species (4 at a higher relative abundance in the exposed group and 7 at a higher relative abundance in the control group). Correlations were made between microbiome data and immunopathology measurements and it was noted that changes in the microbial composition correlated with miRNA-155, miR-146b and IFN-ɣ. In summary, this study illustrates the impact of exposure to MAP on the ruminant faecal microbiome with a number of species that may have relevance in veterinary medicine for tracking exposure to MAP.

Metabolic influence of core ciliates within the rumen microbiome

Protozoa comprise a major fraction of the microbial biomass in the rumen microbiome, of which the entodiniomorphs (order: Entodiniomorphida) and holotrichs (order: Vestibuliferida) are consistently observed to be dominant across a diverse genetic and geographical range of ruminant hosts. Despite the apparent core role that protozoal species exert, their major biological and metabolic contributions to rumen function remain largely undescribed in vivo. Here, we have leveraged (meta)genome-centric metaproteomes from rumen fluid samples originating from both cattle and goats fed diets with varying inclusion levels of lipids and starch, to detail the specific metabolic niches that protozoa occupy in the context of their microbial co-habitants. Initial proteome estimations via total protein counts and label-free quantification highlight that entodiniomorph species Entodinium and Epidinium as well as the holotrichs Dasytricha and Isotricha comprise an extensive fraction of the total rumen metaproteome. Proteomic detection of protozoal metabolism such as hydrogenases (Dasytricha, Isotricha, Epidinium, Enoploplastron), carbohydrate-active enzymes (Epidinium, Diplodinium, Enoploplastron, Polyplastron), microbial predation (Entodinium) and volatile fatty acid production (Entodinium and Epidinium) was observed at increased levels in high methane-emitting animals. Despite certain protozoal species having well-established reputations for digesting starch, they were unexpectedly less detectable in low methane emitting-animals fed high starch diets, which were instead dominated by propionate/succinate-producing bacterial populations suspected of being resistant to predation irrespective of host. Finally, we reaffirmed our abovementioned observations in geographically independent datasets, thus illuminating the substantial metabolic influence that under-explored eukaryotic populations have in the rumen, with greater implications for both digestion and methane metabolism.

Multi-omics reveals that the host-microbiome metabolism crosstalk of differential rumen bacterial enterotypes can regulate the milk protein synthesis of dairy cows

BACKGROUND

Dairy cows' lactation performance is the outcome of the crosstalk between ruminal microbial metabolism and host metabolism. However, it is still unclear to what extent the rumen microbiome and its metabolites, as well as the host metabolism, contribute to regulating the milk protein yield (MPY).

METHODS

The rumen fluid, serum and milk of 12 Holstein cows with the same diet (45% coarseness ratio), parity (2-3 fetuses) and lactation days (120-150 d) were used for the microbiome and metabolome analysis. Rumen metabolism (rumen metabolome) and host metabolism (blood and milk metabolome) were connected using a weighted gene co-expression network (WGCNA) and the structural equation model (SEM) analyses.

RESULTS

Two different ruminal enterotypes, with abundant Prevotella and Ruminococcus, were identified as type1 and type2. Of these, a higher MPY was found in cows with ruminal type2. Interestingly, [Ruminococcus] gauvreauii group and norank_f_Ruminococcaceae (the differential bacteria) were the hub genera of the network. In addition, differential ruminal, serum and milk metabolome between enterotypes were identified, where the cows with type2 had higher L-tyrosine of rumen, ornithine and L-tryptophan of serum, and tetrahydroneopterin, palmitoyl-L-carnitine, S-lactoylglutathione of milk, which could provide more energy and substrate for MPY. Further, based on the identified modules of ruminal microbiome, as well as ruminal serum and milk metabolome using WGCNA, the SEM analysis indicated that the key ruminal microbial module1, which contains the hub genera of the network ([Ruminococcus] gauvreauii group and norank_f_Ruminococcaceae) and high abundance of bacteria (Prevotella and Ruminococcus), could regulate the MPY by module7 of rumen, module2 of blood, and module7 of milk, which contained L-tyrosine and L-tryptophan. Therefore, in order to more clearly reveal the process of rumen bacterial regulation of MPY, we established the path of SEM based on the L-tyrosine, L-tryptophan and related components. The SEM based on the metabolites suggested that [Ruminococcus] gauvreauii group could inhibit the energy supply of serum tryptophan to MPY by milk S-lactoylglutathione, which could enhance pyruvate metabolism. Norank_f_Ruminococcaceae could increase the ruminal L-tyrosine, which could provide the substrate for MPY.

CONCLUSION

Our results indicated that the represented enterotype genera of Prevotella and Ruminococcus, and the hub genera of [Ruminococcus] gauvreauii group and norank_f_Ruminococcaceae could regulate milk protein synthesis by affecting the ruminal L-tyrosine and L-tryptophan. Moreover, the combined analysis of enterotype, WGCNA and SEM could be used to connect rumen microbial metabolism with host metabolism, which provides a fundamental understanding of the crosstalk between host and microorganisms in regulating the synthesis of milk composition.

Modulatory Effects of A1 Milk, A2 Milk, Soy, and Egg Proteins on Gut Microbiota and Fermentation

Milk can be divided into A1 and A2 types according to β-casein variants, and there is a debate about whether A1 milk consumption exacerbates gut environments. This study examined the cecum microbiota and fermentation in mice fed A1 casein, A2 casein, mixed casein (commercial casein), soy protein isolate, and egg white. The cecum acetic acid concentration was higher, and the relative abundances of Muribaculaceae and Desulfovibrionaceae were greater in mice fed A1 versus A2 casein. The other parameters of cecum fermentation and microbiota composition were similar among the mice fed A1, A2, and mixed caseins. The differences were more distinctive among the three caseins, soy, and egg feedings. Chao 1 and Shannon indices of the cecum microbiota were lowered in egg white-fed mice, and the microbiota of mice fed milk, soy, and egg proteins were separately grouped by principal coordinate analysis. Mice fed the three caseins were characterized by a high abundance of Lactobacillaceae and Clostridiaceae, those fed soy were characterized by Corynebacteriaceae, Muribaculaceae, and Ruminococcaceae, and those fed egg white were characterized by Eggerthellaceae, Rikenellaceae, and Erysipelatoclostridiaceae. Thus, although several differences can arise between A1 and A2 caseins in terms of their modulatory effects on gut environments, the differences between milk, soy, and egg proteins can be more distinctive and are worth further consideration.

Effects of Curcumin on Growth Performance, Ruminal Fermentation, Rumen Microbial Protein Synthesis, and Serum Antioxidant Capacity in Housed Growing Lambs

This experiment was conducted to investigate growth performance, ruminal fermentation, rumen microbial protein synthesis, and serum antioxidant capacity with different doses of curcumin (CUR) included in the diet of housed growing lambs. Forty-eight four-month-old Dorper × Thin-tailed Han F₁ crossbred male lambs (body weight = 20.89 ± 1.15 kg, age = 120 ± 10 days; mean ± SD) were randomly divided into four groups for a single-factor, completely randomized experiment. Treatments comprised the following: the basal diet supplemented with 0 (Control), 300 mg/kg (300 CUR), 600 mg/kg (600 CUR), or 900 mg/kg (900 CUR) CUR, respectively. The results showed that dietary CUR increased average daily gain (ADG), and the 300 CUR group evidenced the highest value. There were no significant effects on dry matter intake (DMI) and DMI/ADG. Lambs in the 300 CUR group showed higher totals of volatile fatty acids (VFA) and acetate than other groups, while decreased valerate was observed with supplementary CUR. The ruminal pH and ammonia N (NH₃-N) concentration decreased with increasing CUR, with the greatest effect in the 300 CUR group. The quadratic effects were found in pectinase, carboxymethyl cellulose, and protease, with the greatest value in the 300 CUR group. The microbial populations of total bacteria and Ruminococcus albus also responded quadratically, and the methanogens, protozoan, and Fibrobacter succinogenes populations decreased linearly with increasing CUR. Lambs receiving additional CUR showed increased Prevotella ruminicola population. Microbial protein (MCP) synthesis was promoted by supplementary CUR. As supplementation with CUR increased, the serum activity of total antioxidant capacity (T-AOC), superoxide dismutase (SOD), and glutathione peroxidase (GSH-Px) was enhanced, with the greatest value in the 300 CUR group. In conclusion, dietary CUR improved ruminal fermentation, promoted rumen microbial protein (MCP) synthesis, and enhanced serum antioxidant activity, as well as promoting growth performance in housed growing lambs.

Protocol for a prospective cohort study exploring the gut microbiota of infants with congenital heart disease undergoing cardiopulmonary bypass (the GuMiBear study)

INTRODUCTION

The gut microbiota develops from birth and matures significantly during the first 24 months of life, playing a major role in infant health and development. The composition of the gut microbiota is influenced by several factors including mode of delivery, gestational age, feed type and treatment with antibiotics. Alterations in the pattern of gut microbiota development and composition can be associated with illness and compromised health outcomes.Infants diagnosed with 'congenital heart disease' (CHD) often require surgery involving cardiopulmonary bypass (CPB) early in life. The impact of this type of surgery on the integrity of the gut microbiome is poorly understood. In addition, these infants are at significant risk of developing the potentially devastating intestinal condition necrotising enterocolitis.

METHODS AND ANALYSIS

This study will employ a prospective cohort study methodology to investigate the gut microbiota and urine metabolome of infants with CHD undergoing surgery involving CPB. Stool and urine samples, demographic and clinical data will be collected from eligible infants based at the National Centre for Paediatric Cardiac Surgery in Ireland. Shotgun metagenome sequencing will be performed on stool samples and urine metabolomic analysis will identify metabolic biomarkers. The impact of the underlying diagnosis, surgery involving CPB, and the influence of environmental factors will be explored. Data from healthy age-matched infants from the INFANTMET study will serve as a control for this study.

ETHICS AND DISSEMINATION

This study has received full ethical approval from the Clinical Research Ethics Committee of Children's Health Ireland, GEN/826/20.