Description of Olsenella kribbiana sp. nov., an anaerobic bacterium isolated from pig faeces

A short-rod-shaped, obligate anaerobic, Gram-stain-positive bacterium isolated from the faeces of a pig was designated as the strain YH-ols2221T. The analysis of the 16S rRNA gene sequence revealed that the isolate was most closely related to Olsenella phocaeensis DSM 103159T, Olsenella urininfantis KCTC 25755T and Olsenella absiana KCTC 25800T with 96.6-96.7% similarities. The multi-locus sequence tree revealed that the isolate formed a cluster adjacent to O. absiana KCTC 25800T. The average nucleotide identity and the digital DNA-DNA hybridization values for the isolate and the most closely related strains were 71.7-74.1% and 19.9-23.0%, respectively. The main fatty acids identified were C14 : 0, C16 : 0 DMA and C18 : 0  ω9c DMA. The cell wall contained the meso-diaminopimelic acid-based peptidoglycan. The end products of the fermentation were lactic acid and acetic acid. Given the chemotaxonomic, phenotypic and phylogenetic properties, YH-ols2221T (=KCTC 25801T=NBRC 116679T) represents a novel taxon. The name Olsenella kribbiana sp. nov. was proposed.

Transfer of Antioxidant Capacity Through Placenta and Colostrum: β-Carotene and Superoxide Dismutase Collaboratively Enhance Integrated Breeding of Sows and Piglets

Sows and piglets face heightened oxidative stress during gestation and lactation, yet strategies to simultaneously mitigate these challenges remain underexplored. This study investigated the effects of β-carotene and superoxide dismutase (SOD) supplementation on 140 Landrace × Yorkshire sows (parity 3-5) randomly assigned to (1) a control; (2) long-term low-dose treatment (25 mg/kg β-carotene, 4 mg/kg SOD, or both) throughout gestation-lactation; or (3) short-term high-dose treatment (100 mg/kg β-carotene, 14 mg/kg SOD, or both) administered 7 days pre/post-weaning and farrowing. Our data indicate that the antioxidants enhanced the productive performance of both sows and piglets, with the most pronounced effect observed in the long-term, low-dose combined administration of β-carotene and SOD. The composite antioxidants significantly improved the systemic antioxidant capacity in sows, while concurrently reducing the cortisol and lipopolysaccharide concentrations in the serum. This enhancement contributed to elevations in serum progesterone and prolactin levels at day 40 of gestation and farrowing, respectively, ultimately increasing the number of weaned piglets and decreasing the backfat loss. In addition, the compound antioxidants improved the serum antioxidant indices of piglets, increased the growth hormone concentrations, and improved the litter weight gain. Mechanistically, the placental upregulation of CAT, GPX1, and GLUT3, alongside Claudin1, Occludin, and ZO-1 expression, underpinned improved nutrient transport and barrier function. These findings demonstrate that β-carotene and SOD synergistically transfer antioxidant capacity via placental and colostrum pathways, offering a viable strategy for integrated sow-piglet management.

Exogenous ketones exert antiseizure effects and modulate the gut microbiome and mycobiome in a clinically relevant murine model of epilepsy

OBJECTIVE

Despite growing interest in the potential use of exogenous ketones for the treatment of epilepsy, their impact on seizures and the gut microbiome and mycobiome remain unclear.

METHODS

Here, we examined the effects of both oral gavage and subcutaneous (SC) injection of a ketone ester (KE) in spontaneously epileptic Kcna1-null (KO) mice that model seminal aspects of human temporal lobe epilepsy. Electroencephalographic recordings and biochemical analyses were performed in KE-treated KO mice. Fecal microbial and fungal communities were profiled to determine whether the antiseizure activity of KE involves changes in the gut microbiome.

RESULTS

We found that exogenous KE administration by SC injection was more effective than oral gavage in terms of rendering antiseizure effects while generating similar degrees of ketonemia. However, reductions in mean daily seizure counts were accompanied by overall alterations in the fecal bacterial microbiome. Either oral or SC injection imposed a greater impact on the microbiome in male than female mice. In males, oral KE decreased Bacteroidota phylum and genera of Ligilactobacillus and Muribaculaceae, whereas SC injection decreased Bacteroides, Lactobacillus, and Lachnospiraceae. The fecal mycobiome was affected by KE injection to a greater degree than by oral gavage, and more in females than in males, as reflected by an increase in Ascomycota and Saccharomyces. Correlation analysis between microbiome and seizure counts revealed that in mice receiving KE injection, the seizure count was positively correlated with an amplicon sequencing variant of Lactobacillus (Spearman rho = .64, p = .03) and tended toward a negative correlation with Saccharomyces (Spearman rho = -.57, p = .057).

SIGNIFICANCE

Our findings demonstrate that exogenous ketone administration alone can induce antiseizure effects equally via different routes of administration, and that they induce differential shifts in both the bacterial microbiome and mycobiome.

Description of Olsenella absiana sp. nov., an anaerobic bacterium isolated from pig faeces

A short-rod-shaped, obligate anaerobic, Gram-positive bacterium isolated from the faeces of a pig was designated as the strain YH-ols2223T. Analysis of the 16S rRNA gene sequence revealed that the isolate was most closely related to Olsenella urininfantis KCTC 25755T with 97.7% similarity. The multi-locus sequence tree revealed that the isolate formed a sub-cluster within the genus Olsenella. The average nucleotide identity and the digital DNA-DNA hybridization values for the isolate and the most closely related strains were 74.9-76.6% and 20.8-22.5%, respectively. The end products of the fermentation were lactic acid and acetic acid. The main fatty acids identified were C18 : 0 DMA, C18 : 1  ω9c DMA and C18 : 1  ω9c. The cell wall contained the meso-diaminopimelic acid-based peptidoglycan. Given the chemotaxonomic, phenotypic and phylogenetic properties, YH-ols2223T (= KCTC 25800T = NBRC 116680T) represents a novel taxon. The name Olsenella absiana sp. nov. was proposed.

Effects of 5-Aminolevulinic Acid Supplementation on Gas Production, Fermentation Characteristics, and Bacterial Community Profiles In Vitro

To investigate the effect of 5-aminolevulinic acid (5-ALA) on in vitro rumen gas production, fermentation characteristics, and bacterial community profiles, five levels of 5-ALA (0, 100, 500, 1000, and 5000 mg/kg DM) were supplemented into a total mixed ration (concentrate/forage = 40:60) as substrate in an in vitro experiment. Results showed that as the supplementation level of 5-ALA increased, asymptotic gas production (b) decreased linearly and quadratically (p < 0.01) while the dry matter degradation rate increased quadratically (p < 0.01). Meanwhile, the propionate concentration of 72 h incubation fluid increased linearly (p = 0.03) and pH value increased linearly and quadratically (p < 0.01), while the concentrations of butyrate, isobutyrate, valerate, isovalerate, and NH3-N and the ratio of acetate/propionate (A/P) decreased linearly and quadratically (p < 0.05). There was no significant difference in any alpha diversity indices of bacterial communities among the various 5-ALA levels (p < 0.05). PCoA and PERMANOVA analysis revealed that the bacterial profiles showed a statistical difference between the treatment 5-ALA at 1000 mg/kg DM and the other levels except for 5000 mg/kg DM (p < 0.05). Taxonomic classification revealed a total of 18 and 173 bacterial taxa at the phylum and genus level with relative abundances higher than 0.01% in at least half of the samples, respectively. LEfse analysis revealed that 19 bacterial taxa were affected by 5-ALA levels. Correlation analysis showed that Actinobacteriota was positively correlated with the gas production parameter b, the ratio of A/P, and the concentration of butyrate, isovalerate, and NH3-N (p < 0.05) and negatively correlated with pH (p < 0.05). WPS-2 exhibited a negative correlation with the gas production parameter b, the ratio of A/P, and the concentration of butyrate, valerate, isobutyrate, isovalerate, and NH3-N (p < 0.05), along with a weaker positive correlation with pH (p = 0.04). The Bacteroidales BS11 gut group was negatively correlated with the concentration of propionate but positively correlated with gas production parameter b and the concentration of butyrate and NH3-N (p < 0.05). The Lachnospiraceae NK3A20 group was found to have a positive correlation with gas production parameter b, the ratio of A/P, and the concentration of butyrate, isobutyrate, isovalerate, valerate, total VFA, and NH3-N (p < 0.05), but a highly negative correlation with pH (p < 0.01). Differential metabolic pathways analysis suggested that metabolic pathways related to crude protein utilization, such as L-glutamate degradation VIII (to propanoate), L-tryptophan degradation IX, and urea cycle, increased with 5-ALA levels. In summary, including 5-ALA in the diet might improve energy and protein utilization by reducing the abundance of Actinobacteriota, the Bacteroidales BS11 gut group, the Lachnospiraceae NK3A20 group, and certain pathogenic bacteria and increasing the abundance of WPS-2.

Resilience towards organic load and activated sludge variations in co-fermentation for carboxylic acid production

Two perturbations were investigated in acidogenic co-fermentation of waste activated sludge (WAS) and food waste in continuous mesophilic fermenters: increasing the organic loading rate (OLR) and changing the WAS. A control reactor maintained an OLR of 11 gVS/(L·d), while a test reactor had a prolonged OLR change to 18 gVS/(L·d). For each OLR, two WAS were studied. The change in OLR led to differentiated fermentation product profile without compromising the fermentation yields (∼300 mgCOD/gVS). At 11 gVS/(L·d), the product profile was dominated by acetic, butyric, and propionic acids while at 18 gVS/(L·d) it shifted to acetic acid, ethanol, and caproic acid. Reverting the OLR also reverted the fermentation profile. The biomass immigration with the WAS changed the fermentation microbial structure and introduced acetic acid-consuming methanogens, which growth was only delayed by the OLR increase. Microbial monitoring and post-fermentation tests can be used for early detection of acetic acid-consuming events.

Comparative analysis of microbiome in coronal and root caries

BACKGROUND

The global rise in the elderly population has increased the prevalence of root caries. Streptococcus mutans, Lactobacilli and Actinomyces are considered the primary pathogens of dental caries in culture-based studies. This study aimed to investigate bacterial profiles in coronal and root caries lesions and determine the association of specific bacterial genera at each site.

METHODS

Dentine samples from carious lesions were collected from 22 extracted teeth using an excavator. Microbial DNA was extracted from the samples using a protocol developed for this study. 16S rRNA gene amplicon sequencing was employed for microbial analysis. PCR amplification targeted the V3-V4 region of the bacterial 16S rRNA, and the amplicon sequencing used an Illumina MiSeq system (2 × 300 bp paired-end reads). Statistical analysis was performed by the Phyloseq and DESeq2 packages in R.

RESULTS

In coronal caries, Olsenella, Lactobacillus and Prevotella were the most prevalent genera, comprising approximately 70% of the microbiome community. In the root caries, however, although Olsenella, Prevotella and Lactobacillus remained the dominant genera, they accounted for only half of the microbiome community. This study identified significant differences in alpha diversity indices between the coronal and root caries. LEfSE analysis revealed several unique genera in each caries lesion.

CONCLUSION

The microbiome of root caries lesions was richer and more complex than the coronal caries microbiota. The results suggest that lesion-related variations in the oral microflora may be detected in carious dentine.

Luteolin, a natural flavonoid, exhibits a protective effect on intestinal injury induced by soybean meal in early-weaned piglets

Soybean meal is known to be able to cause intestinal damage and dysfunction in early-weaned piglets. However, research on natural compounds that can alleviate these effects is scarce. In this study, the effect of luteolin, a natural flavonoid, on intestinal health of piglets fed on a soybean meal-based diet was explored. A total of eighteen 21-d-old piglets were selected and randomly divided into 3 groups: a negative control group fed with an animal protein-based diet, a positive control group fed with a soybean meal-based diet, and a luteolin group that was fed with the positive control diet supplemented with luteolin. The results suggested that luteolin supplementation significantly increased the average daily gain and average daily feed intake of early-weaned piglets, while effectively reducing the diarrhea incidence. Additionally, luteolin supplementation lowered the levels of soybean antigen-specific immunoglobulin G and immunoglobulin E anitbodies, increased the superoxide dismutase activity in both sera and small intestine mucosa, and enhanced the total antioxidant capacity in sera. Further research found that luteolin supplementation increased the intestinal villi height and decreased the crypt depth, resulting in an increased ratio of villi to crypts. At the same time, it reduced the concentration of serum diamine oxidase, improving intestinal barrier function. Moreover, luteolin significantly decreased the gene expression of Bax and Caspase-3, reducing cell apoptosis in the intestinal mucosa. Luteolin supplementation also increased the abundance of Actinobacteria at the phylum level, reduced the abundance of Prevotella and increased the abundance of Olsenella at the genus level. In conclusion, the supplementation of luteolin to the soybean meal diet was capable of effectively reducing allergic response, enhancing the antioxidant capacity of early-weaned piglets, protecting their intestinal barrier function, inhibiting intestinal mucosal cell apoptosis, and altering the intestinal microbiota structure, therefore promoting intestinal health and improving production performance in early-weaned piglets.

Enhancing the Conventional Culture: the Evaluation of Several Culture Media and Growth Conditions Improves the Isolation of Ruminal Bacteria

The rumen microbiota is critical in cattle digestion. Still, its low cultivability makes it difficult to study its ecological function and biotechnological potential. To improve the recovery of ruminal microorganisms, this study combined the evaluation of several cultivation parameters with metabarcoding analysis. The parameters tested comprised eight media cultures, three sample dilutions (10-2, 10-6, 10-12), and two incubation times (3 and 7 days). Bacterial populations were determined through Illumina sequencing of 16S rRNA from three biological replicates. The results indicate that none of the culture media recovered all rumen populations and that there was an altered relative abundance of the dominant phyla. In the rumen, Bacteroidetes and Firmicutes comprised 75% and 15% of the relative abundance, respectively, while in the culture media, these were 15% and 60%, respectively. Principal coordinate analysis (PCoA) of the bacterial community revealed significant shifts in population composition due to dilution, with 10-2 and 10-6 dilutions clustered closely while the 10-12 dilution differed markedly. In contrast, incubation duration did not influence population diversity. According to the results, two media, CAN and KNT, were selected based on their ability to recover more similar populations compared to the rumen sample. The metataxonomic study showed that CAN media had consistent reproducibility over time, while KNT showed enrichment of different taxa due to the use of rumen fluid as a substrate. From these, 64 pure cultures were obtained and 54 were identified through 16S rRNA gene sequencing. Being Streptococcus the most frequently isolated genus, this prevalence contrasts with the liquid media composition, underscoring the importance of refining single colony isolation strategies. Although no culture medium could replicate the native rumen bacterial population perfectly, our findings highlight the potential of CAN and KNT media in recovering populations that are more closely aligned to natural rumen conditions. In conclusion, our study emphasizes the importance of integrating molecular approaches in selecting suitable cultivation media and parameters to depict rumen bacteria accurately.

Inhibition of intestinal FXR activity as a possible mechanism for the beneficial effects of a probiotic mix supplementation on lipid metabolism alterations and weight gain in mice fed a high fat diet

Supplementation with probiotics has emerged as a promising therapeutic tool to manage metabolic diseases. We investigated the effects of a mix of Bifidobacterium animalis subsp. lactis LA804 and Lactobacillus gasseri LA806 on high-fat (HF) diet -induced metabolic disease in mice. Supplementation with the probiotic mix in HF diet-fed mice (HF-Pr2) reduced weight and fat mass gains, decreased hepatic lipid accumulation, and lowered plasma triglyceride peak during an oral lipid tolerance test. At the molecular level, the probiotic mix protected against HF-induced rise in mRNA levels of genes related to lipid uptake, metabolism, and storage in the liver and white adipose tissues, and strongly decreased mRNA levels of genes related to inflammation in the white adipose tissue and to oxidative stress in the liver. Regarding intestinal homeostasis, the probiotic mix did not prevent HF-induced gut permeability but slightly modified microbiota composition without correcting the dysbiosis induced by the HF diet. Probiotic supplementation also modified the cecal bile acid (BA) profile, leading to an increase in the Farnesoid-X-Receptor (FXR) antagonist/agonist ratio between BA species. In agreement, HF-Pr2 mice exhibited a strong inhibition of FXR signaling pathway in the ileum, which was associated with lipid metabolism protection. This is consistent with recent reports proposing that inhibition of intestinal FXR activity could be a potent mechanism to overcome metabolic disorders. Altogether, our results demonstrate that the probiotic mix evaluated, when administered preventively to HF diet-fed mice could limit obesity and associated lipid metabolism disorders, likely through the inhibition of FXR signaling in the intestinal tract.

Wheat silage partially replacing oaten hay exhibited greater feed efficiency and fibre digestion despite low feed intake by feedlot lambs

This study aimed to investigate the feeding effect of wheat silage on growth performance, nutrient digestibility, rumen fermentation, and microbiota composition in feedlot lambs. Sixty-four male crossbred Chinese Han lambs (BW = 27.8 ± 0.67 kg, 3 months of age) were randomly assigned to four ration groups with wheat silage replacing 0% (WS0), 36% (WS36), 64% (WS64), and 100% (WS100) of oaten hay on forage dry matter basis. The concentrate-to-forage ratio was 80:20 and the feeding trial lasted 52 d. Increasing wheat silage inclusion linearly decreased dry matter intake by 4% to 27% (P < 0.01). However, increasing the wheat silage replacement of oaten hay by no more than 64% improved the feed efficiency by 14% as noted by the feed-to-gain ratio (P = 0.04). Apparent digestibility of organic matter (P < 0.01), neutral detergent fibre (P = 0.04) and acid detergent fibre (P < 0.01) quadratically increased. Ammonia nitrogen (P = 0.01) decreased while microbial protein production (P < 0.01) increased with the increase of wheat silage inclusion. Total volatile fatty acids concentration increased quadratically with the increase of wheat silage inclusion (P < 0.01), and the highest occurred in WS64. The molar proportion of acetate (P < 0.01) and acetate-to-propionate ratio (P = 0.04) decreased while butyrate (P < 0.01) and isovalerate (P = 0.04) increased. Increasing wheat silage inclusion increased the Firmicutes-to-Bacteroidota ratio by 226% to 357%, resulting in Firmicutes instead of Bacteroidota being the most abundant phylum. The relative abundance of cellulolytic Ruminococcus numerically increased but that of amylolytic Prevotella (P < 0.01) decreased as increasing wheat silage inclusion. Taken together, increasing wheat silage replacement of oaten hay by no more than 64% exhibited greater feed efficiency and fibre digestion despite low feed intake by feedlot lambs due to the change of Firmicutes-to-Bacteroidota ratio in the rumen.

Cooperative interactions between Veillonella ratti and Lactobacillus acidophilus ameliorate DSS-induced ulcerative colitis in mice

Veillonella and Lactobacillus species are key regulators of a healthy gut environment through metabolic cross-feeding, influencing lactic acid and short-chain fatty acid (SCFA) levels, which are crucial for gut health. This study aims to investigate how Veillonella ratti (V. ratti) and Lactobacillus acidophilus (LA) interact with each other and alleviate dextran sulfate sodium (DSS)-induced ulcerative colitis (UC) in a mouse model. We assess their metabolic interactions regarding carbon sources through co-culturing in a modified medium. In the in vitro experiments, V. ratti and LA were inoculated in mono-cultures and co-culture, and viable cell counts, OD600, pH, lactic acid, glucose and SCFAs were measured. For the in vivo experiment, 60 C57BL/6 mice were randomly divided into five groups and administered V. ratti and LA alone or in combination via oral gavage (1 × 109 CFU mL-1 per day per mouse) for 14 days. On the seventh day, 2.5% DSS was added to the drinking water to induce colitis. The effects of these probiotics on UC were evaluated by assessing intestinal barrier integrity and intestinal inflammation in the gut microenvironment. In vitro results demonstrated that co-culturing V. ratti with LA significantly increased viable cell numbers, lactic acid production, and SCFA production, while reducing pH and glucose levels in the medium. In vivo findings revealed that intervention with V. ratti, particularly in combination with LA, alleviated symptoms, including weight loss, colon shortening, and tissue damage. These probiotics mitigated intestinal inflammation by down-regulating pro-inflammatory molecules, such as IL-6, IL-1β, IL-γ, iNOS, and IFN-γ, as well as oxidative stress markers, including MDA and MPO. Concurrently, they upregulated the activity of anti-inflammatory enzymes, namely, SOD and GSH, and promoted the production of SCFAs. The combined intervention of V. ratti and LA significantly increased acetic acid, propionic acid, butyric acid, isobutyric acid, valeric acid, and total SCFAs in cecal contents. Furthermore, the intervention of V. ratti and LA increased the abundance of beneficial bacteria, such as Akkermansia, while reducing the abundance of harmful bacteria, such as Escherichia-Shigella and Desulfovibrio, thereby mitigating excessive inflammation. These findings highlight the enhanced therapeutic effects resulting from the interactions between V. ratti and LA, demonstrating the potential of this combined probiotic approach.

In-situ production of lactate driving the biotransformation of waste activated sludge to medium-chain fatty acid

Medium-chain fatty acids (MCFAs) have drawn great attention due to their high energy density and superior hydrophobicity. Waste activated sludge (WAS) has been documented as a renewable feedstock for MCFAs production via anaerobic fermentation. However, MCFAs production from WAS depends on exogenous addition of electron donor (ED, e.g., lactate) for chain elongation (CE) bioprocess, which results in increased economic cost and limited practical application. In this study, a novel biotechnology was proposed to produce MCFAs from WAS with in-situ self-formed lactate by inoculating Yoghurt starter powder containing with Lactobacillales cultures. The batch experimental results revealed that the lactate was in-situ generated from WAS and the maximum production of MCFAs increased from 1.17 to 3.99 g COD/L with the increased addition of Lactobacillales cultures from 6✕107 to 2.3✕108 CFU/mL WAS. In continuous long-term test over 97 days, average MCFA production reached up to 3.94 g COD/L with a caproate yield of 82.74% at sludge retention time (SRT) 12 days, and the average MCFA production increased to 5.87 g COD/L with 69.28% caproate and 25.18% caprylate at SRT 15 days. A comprehensive analysis of the metagenome and metatranscriptome demonstrated that the genus of Lactobacillus and Streptococcus were capable of producing lactate from WAS and upgrading to MCFAs. Moreover, another genus, i.e., Candidatus Promineofilum, was firstly revealed that it might be responsible for lactate and MCFAs production. Further investigation of related microbial pathways and enzyme expression suggested that D-lactate dehydrogenase and pyruvate ferredoxin oxidoreductase contributed to lactate and acetyl-CoA production, which were the crucial steps for MCFAs generation and were most actively expressed. This study provides a conceptual framework of MCFAs from WAS with endogenous ED, potentially enhancing the energy recovery from WAS treatment.

Long-term influence of chloroxylenol on anaerobic microbial community: Performance, microbial interaction, and antibiotic resistance gene behaviors

The use of antibacterial and disinfection products is increasing in recent years. Para-chloro-meta-xylenol (PCMX), a widely used antimicrobial agent, has been detected in various environments. Herein, the impacts of PCMX with long-term exposure on anaerobic sequencing batch reactors were investigated. The high concentration (50 mg/L, GH group) PCMX severely inhibited the nutrient removal process, and the low concentration group (0.5 mg/L, GL group) slightly affected the removal efficiency which was recovered after 120 days of adaptation compared to the control group (0 mg/L, GC group). Cell viability tests indicated that PCMX inactivated the microbes. A significant reduction in bacterial α-diversity was observed in the GH but not the GL group. The microbial communities were shifted upon PCMX exposure, among which Olsenella, Novosphingobium, and Saccharibacteria genera incertae Sedis became the predominant genera in the GH groups. Network analyses showed that PCMX significantly reduced the complexity and interactions of the microbial communities, consistent with the negative impacts on bioreactor performance. Real-time PCR analysis indicated that PCMX affected the behavior of antibiotic resistance genes (ARGs), and the relationship between ARGs and bacterial genera gradually became complicated after long-term exposure. Most detected ARGs decreased on Day 60 but increased on Day 120 especially in the GL group, implying the potential risk of environment-relevant concentration of PCMX in the ecosystems. This study provides new insights into the understanding of the impacts and risks of PCMX on wastewater treatment processes.

Microbiota and Nutrient Portraits of European Roe Deer (Capreolus capreolus) Rumen Contents in Characteristic Southern German Habitats

Roe deer (Capreolus capreolus) are found in various habitats, from pure forest cultures to agricultural areas and mountains. In adapting to the geographically and seasonally differentiating food supply, they depend, above all, on an adapted microbiome. However, knowledge about the microbiome of wild ruminants still needs to be improved. There are only a few publications for individual species with a low number of samples. This study aims to identify a core microbiota for Bavarian roe deer and present nutrient and microbiota portraits of the individual habitat types. This study investigated the roe deer's rumen (reticulorumen) content from seven different characteristic Bavarian habitat types. The focus was on the composition of nutrients, fermentation products, and the rumen bacterial community. A total of 311 roe deer samples were analysed, with the most even possible distribution per habitat, season, age class, and gender. Significant differences in nutrient concentrations and microbial composition were identified for the factors habitat, season, and age class. The highest crude protein content (plant protein and microbial) in the rumen was determined in the purely agricultural habitat (AG), the highest value of non-fibre carbohydrates in the alpine mountain forest, and the highest fibre content (neutral detergent fibre, NDF) in the pine forest habitat. Maximum values for fibre content go up to 70% NDF. The proportion of metabolites (ammonia, lactate, total volatile fatty acids) was highest in the Agriculture-Beech-Forest habitat (ABF). Correlations can be identified between adaptations in the microbiota and specific nutrient concentrations, as well as in strong fluctuations in ingested forage. In addition, a core bacterial community comprising five genera could be identified across all habitats, up to 44% of total relative abundance. As with all wild ruminants, many microbial genera remain largely unclassified at various taxonomic levels. This study provides a more in-depth insight into the diversity and complexity of the roe deer rumen microbiota. It highlights the key microorganisms responsible for converting naturally available nutrients of different botanical origins.

"Get the best out of what comes in" - adaptation of the microbiota of chamois (Rupicapra rupicapra) to seasonal forage availability in the Bavarian Alps

As an inhabitant of the Alps, chamois are exposed to significant climatic changes throughout the year and are also strongly confronted with changing forage availability. Besides horizontal and vertical migratory movements as an adaptation, it undergoes physiological transformations and dynamic changes in the ruminal microbiota. The following study used 48 chamois of different ages and genders to investigate to which extent the ingested food plants, the resulting crude nutrients in the rumen (reticulorumen) contents, and the bacterial microbiota in the rumen and their fermentation products were influenced by the changes over the seasons. Very little is known about the microbiota of wild ruminants, and many bacterial taxa could only be determined to certain taxonomic levels in this study. However, adapted microbiota reflects the significant changes in the ingested forage and the resulting crude nutrients. For some taxa, our results indicated potential functional relationships. In addition, 15 genera were identified, representing almost 90% of the relative abundance, forming the central part of the microbial community throughout the year. The successful and flexible adaptation of chamois is reflected in the chamois rumen's nutrient and microbial profile. This is also the first study that analyzes the microbiota of the chamois using rumen samples and considers the microbiota in a seasonal comparison.

Effect of grape pomace supplement on growth performance, gastrointestinal microbiota, and methane production in Tan lambs

Grape pomace (GP), a by-product in wine production, is nutritious and can be used as a feed ingredient for ruminants; however, its role in shaping sheep gastrointestinal tract (GIT) microbiota is unclear. We conducted a controlled trial using a randomized block design with 10 Tan lambs fed a control diet (CD) and 10 Tan lambs fed a pelleted diet containing 8% GP (dry matter basis) for 46 days. Rumen, jejunum, cecum, and colon bacterial and archaeal composition were identified by 16S rRNA gene sequencing. Dry matter intake (DMI) was greater (p < 0.05) in the GP than CD group; however, there was no difference in average daily gain (ADG, p < 0.05) and feed conversion ratio (FCR, p < 0.05) between the two groups. The GP group had a greater abundance of Prevotella 1 and Prevotella 7 in the rumen; of Sharpe, Ruminococcaceae 2, and [Ruminococcus] gauvreauii group in the jejunum; of Ruminococcaceae UCG-014 and Romboutsia in the cecum, and Prevotella UCG-001 in the colon; but lesser Rikenellaceae RC9 gut group in the rumen and cecum, and Ruminococcaceae UCG-005 and Ruminococcaceae UCG-010 in the colon than the CD group. The pathways of carbohydrate metabolism, such as L-rhamnose degradation in the rumen, starch and glycogen degradation in the jejunum, galactose degradation in the cecum, and mixed acid fermentation and mannan degradation in the colon were up-graded; whereas, the pathways of tricarboxylic acid (TCA) cycle VIII, and pyruvate fermentation to acetone in the rumen and colon were down-graded with GP. The archaeal incomplete reductive TCA cycle was enriched in the rumen, jejunum, and colon; whereas, the methanogenesis from H2 and CO2, the cofactors of methanogenesis, including coenzyme M, coenzyme B, and factor 420 biosynthesis were decreased in the colon. The study concluded that a diet including GP at 8% DM did not affect ADG or FCR in Tan lambs. However, there were some potential benefits, such as enhancing propionate production by microbiota and pathways in the GIT, promoting B-vitamin production in the rumen, facilitating starch degradation and amino acid biosynthesis in the jejunum, and reducing methanogenesis in the colon.

The long-term gut bacterial signature of a wild primate is associated with a timing effect of pre- and postnatal maternal glucocorticoid levels

BACKGROUND

During development, elevated levels of maternal glucocorticoids (GCs) can have detrimental effects on offspring morphology, cognition, and behavior as well as physiology and metabolism. Depending on the timing of exposure, such effects may vary in strength or even reverse in direction, may alleviate with age, or may concern more stable and long-term programming of phenotypic traits. Maternal effects on gut bacterial diversity, composition, and function, and the persistence of such effects into adulthood of long-lived model species in the natural habitats remain underexplored.

RESULTS

In a cross-sectional sample of infant, juvenile, and adult Assamese macaques, the timing of exposure to elevated maternal GCs during ontogeny was associated with the gut bacterial community of the offspring. Specifically, naturally varying maternal GC levels during early but not late gestation or lactation were associated with reduced bacterial richness. The overall effect of maternal GCs during early gestation on the gut bacterial composition and function exacerbated with offspring age and was 10 times stronger than the effect associated with exposure during late prenatal or postnatal periods. Instead, variation in maternal GCs during the late prenatal or postnatal period had less pronounced or less stable statistical effects and therefore a weaker effect on the entire bacterial community composition, particularly in adult individuals. Finally, higher early prenatal GCs were associated with an increase in the relative abundance of several potential pro-inflammatory bacteria and a decrease in the abundance of Bifidobacterium and other anti-inflammatory taxa, an effect that exacerbated with age.

CONCLUSIONS

In primates, the gut microbiota can be shaped by developmental effects with strong timing effects on plasticity and potentially detrimental consequences for adult health. Together with results on other macaque species, this study suggests potential detrimental developmental effects similar to rapid inflammaging, suggesting that prenatal exposure to high maternal GC concentrations is a common cause underlying both phenomena. Our findings await confirmation by metagenomic functional and causal analyses and by longitudinal studies of long-lived, ecologically flexible primates in their natural habitat, including developmental effects that originate before birth. Video Abstract.

Microbiome and metabolome associated with white spot lesions in patients treated with clear aligners

White spot lesions (WSLs) have long been a noteworthy complication during orthodontic treatment. Recently, an increasing number of orthodontists have found that adolescents undergoing orthodontic treatment with clear aligners are at a higher risk of developing WSLs. The oral microbiota and metabolites are considered the etiologic and regulatory factors of WSLs, but the specific impact of clear aligners on the oral microbiota and metabolites is unknown. This study investigated the differences in the salivary microbiome and metabolome between adolescents with and without WSLs treated with clear aligners. Fifty-five adolescents (aged 11-18) with Invisalign appliances, 27 with and 28 without WSLs, were included. Saliva samples were analyzed using 16S rRNA gene sequencing and ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS); the data were further integrated for Spearman correlation analysis. The relative abundances of 14 taxa, including Actinobacteria, Actinomycetales, Rothia, Micrococcaceae, Subdoligranulum, Capnocytophaga, Azospira, Olsenella, Lachnoanaerobaculum, and Abiotrophia, were significantly higher in the WSL group than in the control group. Metabolomic analysis identified 27 potential biomarkers, and most were amino acids, including proline and glycine. The metabolites were implicated in 6 metabolic pathways, including alanine, aspartate and glutamate metabolism; glycine, serine and threonine metabolism; and aminoacyl-tRNA biosynthesis. There was a correlation between the salivary microbial and metabolomic datasets, reflecting the impact of clear aligners on the metabolic activity of the oral flora. A concordant increase in the levels of Lachnoanaerobaculum, Rothia, Subdoligranulum and some amino acids had predictive value for WSL development. In summary, when adolescents undergo long-term clear aligner therapy with poor oral hygiene habits, clear aligners can disrupt the balance of the oral microecosystem and lead to oral microbiota dysbiosis, thereby increasing the risk of developing WSLs. Our findings might contribute to the understanding of the pathogenesis of WSLs and provide candidate biomarkers for the diagnosis and treatment of WSLs associated with clear aligners.

An Update on Novel Taxa and Revised Taxonomic Status of Bacteria Isolated from Domestic Animals Described in 2018 to 2021

Novel bacterial taxonomy and nomenclature revisions can have significant impacts on clinical practice, disease epidemiology, and veterinary microbiology laboratory operations. Expansion of research on the microbiota of humans, animals, and insects has significant potential impacts on the taxonomy of organisms of clinical interest. Implications of taxonomic changes may be especially important when considering zoonotic diseases. Here, we address novel taxonomy and nomenclature revisions of veterinary significance. Noteworthy discussion centers around descriptions of novel mastitis pathogens in Streptococcaceae, Staphylococcaceae, and Actinomycetaceae; bovine reproductive tract pathogens in Corynebacteriaceae; novel members of Mannheimia spp., Leptospira spp., and Mycobacterium spp.; the transfer of Ochrobactrum spp. to Brucella spp.; and revisions to the genus Mycoplasma.

High-Dose Vitamin E Supplementation Can Alleviate the Negative Effect of Subacute Ruminal Acidosis in Dairy Cows

The aim of this trial was to assess whether the supplementation of vitamin E (VE) in high-concentrate diets could improve the fermentation and blood metabolism in the rumen of dairy cows, thereby modulating the degree of the subacute ruminal acidosis (SARA) response and improving the performance. Seven Holstein cows (four fitted with ruminal cannulas) were fed three diets (total mixed rations) during three successive periods (each lasted for 18 d): (1) the control diet (CON); (2) a high-grain (HG) diet, which was the control diet supplied with a 15% finely ground wheat diet (FGW); and (3) a high-VE diet (HGE), which was the control diet provided with a 15% FGW and 12,000 IU of VE/head per day. The results indicated that VE was able to alleviate the reduction in the dry matter intake (DMI) and milk fat yield in cows caused by HG diets. The supplementation of VE significantly reduced the levels of lipopolysaccharide (LPS), histamine (HIS), and the total volatile fatty acid (TVFA) in the rumen. The supplementation of VE observably increased the antioxidant capacity of the milk and plasma. In addition, VE markedly reduced the plasma levels of endotoxin, HIS, and pro-inflammatory factors. The supplementation of VE significantly enriched the differential metabolites of the purine metabolism, cysteine, methionine metabolism, and ABC transporter synthesis pathway in the serum. The supplementation of VE also significantly increased the relative abundance of Succiniclasticum and decreased the relative abundance of Treponema, thus reducing the production of TVFA in the rumen. In conclusion, considering that the cows in this trial had high ketone levels (BHBA > 2.3 mmol/L), we found that VE could improve the rumen fermentation and blood metabolism by modulating the relative abundance of rumen microorganisms, thereby mitigating a range of adverse effects caused by SARA.

A westernized diet changed the colonic bacterial composition and metabolite concentration in a dextran sulfate sodium pig model for ulcerative colitis

Introduction

Ulcerative colitis (UC) is characterized by chronic inflammation in the colonic epithelium and has a blurred etiology. A western diet and microbial dysbiosis in the colon were reported to play a role in UC development. In this study, we investigated the effect of a westernized diet, i.e., increasing fat and protein content by including ground beef, on the colonic bacterial composition in a dextran sulfate sodium (DexSS) challenged pig study.

Methods

The experiment was carried out in three complete blocks following a 2×2 factorial design including 24 six-week old pigs, fed either a standard diet (CT) or the standard diet substituted with 15% ground beef to simulate a typical westernized diet (WD). Colitis was induced in half of the pigs on each dietary treatment by oral administration of DexSS (DSS and WD+DSS, respectively). Samples from proximal and distal colon and feces were collected.

Results and discussion

Bacterial alpha diversity was unaffected by experimental block, and sample type. In proximal colon, WD group had similar alpha diversity to CT group and the WD+DSS group showed the lowest alpha diversity compared to the other treatment groups. There was a significant interaction between western diet and DexSS for beta diversity, based on Bray-Curtis dissimilarly. The westernized diet and DexSS resulted in three and seven differentially abundant phyla, 21 and 65 species, respectively, mainly associated with the Firmicutes and Bacteroidota phyla followed by Spirochaetota, Desulfobacterota, and Proteobacteria. The concentration of short-chain fatty acids (SCFA) was lowest in the distal colon. Treatment had a slight effect on the estimates for microbial metabolites that might have valuable biological relevance for future studies. The concentration of putrescine in the colon and feces and that of total biogenic amines was highest in the WD+DSS group. We conclude that a westernized diet could be a potential risk factor and an exacerbating agent for UC by reducing the abundance of SCFA-producing bacteria, increasing the abundance of pathogens such as Helicobacter trogontum, and by increasing the concentration of microbial proteolytic-derived metabolites in the colon.

Microbial colonization dynamics of the postnatal digestive tract of Bos indicus calves

The rumen and the jejunum of calves have distinct functional roles; the former is in the storage and fermentation of feed, and the latter is in transporting digesta to the ileum. It is unknown how nutrition changes the evolution of the microbiome of these organs after birth. We sequenced and characterized the entire microbiome of the rumen and the jejunum from Bos indicus calves of the Mexican Tropics to study their dynamics at Days 0, 7, 28, and 42 after birth. Operational taxonomic units (OTUs) belonging to 185 and 222 genera from 15 phylum were observed in the organs, respectively. The most abundant OTUs were Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. We observed that proteobacterial species were outcompeted after the first week of life by Bacteroidetes and Firmicutes in the rumen and the jejunum, respectively. Moreover, Prevotella species were found to predominate in the rumen (36% of total OTUs), while the jejunum microbiome is composed of small proportions of several genera. Presumably, their high relative abundance assists in specialized functions and is more likely in fermentation since they are anaerobes. In summary, the rumen and the jejunum microbiomes were outcompeted by new microbiomes in a dynamic process that begins at birth.

In Situ Rumen Degradation Characteristics and Bacterial Colonization of Corn Silages Differing in Ferulic and p-Coumaric Acid Contents

In plant cell wall, ferulic acid (FA) and p-coumaric acid (pCA) are commonly linked with arabinoxylans and lignin through ester and ether bonds. These linkages were deemed to hinder the access of rumen microbes to cell wall polysaccharides. The attachment of rumen microbes to plant cell wall was believed to have profound effects on the rate and the extent of forage digestion in rumen. The objective of this study was to evaluate the effect of bound phenolic acid content and their composition in corn silages on the nutrient degradability, and the composition of the attached bacteria. Following an in situ rumen degradation method, eight representative corn silages with different FA and pCA contents were placed into nylon bags and incubated in the rumens of three matured lactating Holstein cows for 0, 6, 12, 24, 36, 48, and 72 h, respectively. Corn silage digestibility was assessed by in situ degradation methods. As a result, the effective degradability of dry matter, neutral detergent fibre, and acid detergent fibre were negatively related to the ether-linked FA and pCA, and their ratio in corn silages, suggesting that not only the content and but also the composition of phenolic acids significantly affected the degradation characteristics of corn silages. After 24 h rumen fermentation, Firmicutes, Actinobacteria, and Bacteroidota were observed as the dominant phyla in the bacterial communities attached to the corn silages. After 72 h rumen fermentation, the rumen degradation of ester-linked FA was much greater than that of ester-linked pCA. The correlation analysis noted that Erysipelotrichaceae_UCG-002, Olsenella, Ruminococcus_gauvreauii_group, Acetitomaculum, and Bifidobacterium were negatively related to the initial ether-linked FA content while Prevotella was positively related to the ether-linked FA content and the ratio of pCA to FA. In summary, the present results suggested that the content of ether-linked phenolic acids in plant cell walls exhibited a more profound effect on the pattern of microbial colonization than the fibre content.

Effect of feeding raw potato starch on the composition dynamics of the piglet intestinal microbiome

OBJECTIVE

Raw potato starch (RPS) is resistant to digestion, escapes absorption, and is metabolized by intestinal microflora in the large intestine and acts as their energy source. In this study, we compared the effect of different concentrations of RPS on the intestinal bacterial community of weaned piglets.

METHODS

Male weaned piglets (25-days-old, 7.03±0.49 kg) were either fed a corn/soybean-based control diet (CON, n = 6) or two treatment diets supplemented with 5% RPS (RPS5, n = 4) or 10% RPS (RPS10, n = 4) for 20 days and their fecal samples were collected. The day 0 and 20 samples were analyzed using a 16S rRNA gene sequencing technology, followed by total genomic DNA extraction, library construction, and high-throughput sequencing. After statistical analysis, five phyla and 45 genera accounting for over 0.5% of the reads in any of the three groups were further analyzed. Furthermore, short-chain fatty acids (SCFAs) in the day 20 fecal samples were analyzed using gas chromatography.

RESULTS

Significant changes were not observed in the bacterial composition at the phylum level even after 20 d post feeding (dpf); however, the abundance of Intestinimonas and Barnesiella decreased in both RPS treatment groups compared to the CON group. Consumption of 5% RPS increased the abundance of Roseburia (p<0.05) and decreased the abundance of Clostridium (p<0.01) and Mediterraneibacter (p< 0.05). In contrast, consumption of 10% RPS increased the abundance of Olsenella (p<0.05) and decreased the abundance of Campylobacter (p<0.05), Kineothrix (p<0.05), Paraprevotella (p<0.05), and Vallitalea (p<0.05). Additionally, acetate (p<0.01), butyrate (p<0.05), valerate (p = 0.01), and total SCFAs (p = 0.01) were upregulated in the RPS5 treatment group.

CONCLUSION

Feeding 5% RPS altered bacterial community composition and promoted gut health in weaned piglets. Thus, resistant starch as a feed additive may prevent diarrhea in piglets during weaning.

Effect of pH dynamic control on ethanol-lactic type fermentation (ELTF) performance of glucose

This study proposed a new ethanol-lactic type fermentation (ELTF) and explored the optimal control strategy. Using batch experiments, the effects of pH, temperature and organic loading (OL) on ELTF were investigated. The sum of ethanol and lactic acid yield was highest at whole-control pH value of 4.0, 35°C temperature and OL of 33 gCOD/L. To improve ELTF, the dynamic pH control in the long-term CSTR was adjusted at 4.0 (1-28 days), 5.0 (29-44 days) and 4.0 (46-62 days) successively. The high concentration of ethanol and lactic acid was 8190.5 mg/L at 16th day of pH 4.0. At pH of 5.0, the average acidogenesis rate and total concentration of fermentation products increased 111.0% and 128.0%, respectively. Organisms of Lactobacillus and Bifidobacterium were the predominant bacteria in reactor. It can achieve the directional regulation of ELTF and provides parameter support for the application of two-phase anaerobic digestion.

Granulimonas faecalis gen. nov., sp. nov., and Leptogranulimonas caecicola gen. nov., sp. nov., novel lactate-producing Atopobiaceae bacteria isolated from mouse intestines, and an emended description of the family Atopobiaceae

Two strictly anaerobic, Gram-stain-positive, non-motile bacteria (strains OPF53T and TOC12T) were isolated from mouse intestines. Strains OPF53T and TOC12T grew at pH 5.5–9.0 and 5.0–9.0, respectively, and at temperatures of 30–45 °C. The cell morphologies of these strains were short rods and rods, respectively, and the cells possessed intracellular granules. The major cellular fatty acids of OPF53T were C18  :  1 cis 9 and C18  :  1 cis 9 dimethyl acetal, whereas those of TOC12T were C18  :  0 and C18  :  1 cis 9. In OPF53T, the main end-products of modified peptone–yeast extract–glucose (PYG) fermentation were lactate, formate and butyrate, whereas, in addition to these acids, TOC12T also produced hydrogen. The genomes of OPF53T and TOC12T were respectively 2.2 and 2.0 Mbp in size with a DNA G+C contents of 69.1 and 58.7 %. The 16S rRNA gene sequences of OPF53T and TOC12T showed the highest similarity to members of the family Atopobiaceae , namely, Olsenella phocaeensis Marseille-P2936T (94.3 %) and Olsenella umbonata KCTC 15140T (93.2 %), respectively. Phylogenetic analyses revealed that both isolates formed distinct lineages from other genera of the family Atopobiaceae . In addition, the two strains were characterized by relatively low 16S rRNA gene sequence similarity (93.4 %) and can be distinguished by their distinctive traits (including cell shape, DNA G+C content, and major fatty acids profiles). On the basis of their polyphasic taxonomic properties, these isolates represent two noel species of two novel genera within the family Atopobiaceae , for which the names Granulimonas faecalis gen. nov., sp. nov. (OPF53T=JCM 35015T=KCTC 25474T) and Leptogranulimonas caecicola gen. nov., sp. nov. (TOC12T=JCM 35017T=KCTC 25472T) are proposed.

Bile Salt Hydrolases with Extended Substrate Specificity Confer a High Level of Resistance to Bile Toxicity on Atopobiaceae Bacteria

The bile resistance of intestinal bacteria is among the key factors responsible for their successful colonization of and survival in the mammalian gastrointestinal tract. In this study, we demonstrated that lactate-producing Atopobiaceae bacteria (Leptogranulimonas caecicola TOC12T and Granulimonas faecalis OPF53T) isolated from mouse intestine showed high resistance to mammalian bile extracts, due to significant bile salt hydrolase (BSH) activity. We further succeeded in isolating BSH proteins (designated LcBSH and GfBSH) from L. caecicola TOC12T and G. faecalis OPF53T, respectively, and characterized their enzymatic features. Interestingly, recombinant LcBSH and GfBSH proteins exhibited BSH activity against 12 conjugated bile salts, indicating that LcBSH and GfBSH have much broader substrate specificity than the previously identified BSHs from lactic acid bacteria, which are generally known to hydrolyze six bile salt isomers. Phylogenetic analysis showed that LcBSH and GfBSH had no affinities with any known BSH subgroup and constituted a new BSH subgroup in the phylogeny. In summary, we discovered functional BSHs with broad substrate specificity from Atopobiaceae bacteria and demonstrated that these BSH enzymes confer bile resistance to L. caecicola TOC12T and G. faecalis OPF53T.

Target and Enhance Ethanol and Butyrate Production from Anaerobic Fermentation via the pH and Organic Loading Rate Combined Strategy

The large capacity production and low utilization rate increase the difficulty of fruit and vegetable wastes (FVW) treatment. Efficient and targeted recovery strategies can solve these problems. This study investigated and proposed combined strategies via pH and organic loading rate (OLR) to target and enhance ethanol- and butyrate-dominant acidogenic production in the FVW mixed culture fermentation. Under pH 4.0, OLR 18 gCOD/(L∙d), and mesophilic (35 °C), ethanol-dominant fermentation was formed. The long-term operation (168 days) showed that the highest ethanol yield was 0.33 g/gCOD which was greater than that in other studies. Also, the hydrolysis rate of ethanol-type fermentation reached 74.5%. Besides, butyrate-type fermentation was stable at yield 0.39 g/gCOD following conditions: pH 6.0, OLR 28 gCOD/(L∙d), and 35 °C, of which hydrolysis and acidogenic rate were 78.0% and 62.0%, respectively. The high relative abundance of Lactobacillus, Olsenella, and Bifidobacterium played positive role in achieving ethanol, butyrate, and lactate production among various metabolic pathways. The results revealed the pH value together with OLR was the valid parameter to affect product formation and composition during FVW fermentation.

Biorefining food waste through the anaerobic conversion of endogenous lactate into caproate: A fragile balance between microbial substrate utilization and product inhibition

New technologies development and renewable source exploitation are key tools to realize the European Green Deal and to boost the bio-based economy. In this context, fermentation of organic residues as food waste is an efficient method to obtain marketable products such as carboxylic acids widely applied in industrial production. Under favourable thermodynamic conditions, short chain fatty acids deriving from primary fermentation could be biologically converted into medium-chain fatty acids as caproate via chain elongation (CE) process, by using ethanol or lactate as electron donors. This study evaluates the effectivity of producing caproate from Food Waste extract rich in organics with in situ electron donor production. The test carried out at OLR 15 gCOD L^-1d^-1 showed high Volatile Fatty Acids (from acetic to caproic acid) yields (0.37 g g^-1COD_fed), with a maximum caproate concentration of 8 g L^-1. The associated microbiome was composed by lactate-producing bacteria (Corynebacterium, Lactobacillus, and Olsenella) and by chain elongators (Clostridiaceae and Caproiciproducens). By stressing the system with OLR increase up to 20 gCOD L^-1d^-1, the CE process was inhibited by the high concentration of caproate (low occurrence of Clostridiaceae and Caproiciproducens). Nevertheless, after few days of stop-feeding regime imposed to the system, the microbiome restored its capability to proceed with lactate-based CE pathways. Different batch tests carried out with the inhibited biomass at increasing initial caproate concentration confirmed its impact on lactate utilization kinetics.

Short Chain Fatty Acids and Bacterial Taxa Associated with Reduced Salmonella enterica serovar I 4,[5],12:i:- Shedding in Swine Fed a Diet Supplemented with Resistant Potato Starch

Salmonella enterica serovar I 4,[5],12:i:- is a foodborne pathogen of concern because many isolates are multidrug-resistant (resistant to ≥3 antimicrobial classes) and metal tolerant. In this study, three in-feed additives were individually tested for their ability to reduce Salmonella I 4,[5],12:i:- shedding in swine: resistant potato starch (RPS), high amylose corn starch, and a fatty acid blend, compared with a standard control diet over 21 days. Only RPS-fed pigs exhibited a reduction in Salmonella fecal shedding, different bacterial community compositions, and different cecal short chain fatty acid (SCFA) profiles relative to control animals. Within the RPS treatment group, pigs shedding the least Salmonella tended to have greater cecal concentrations of butyrate, valerate, caproate, and succinate. Additionally, among RPS-fed pigs, several bacterial taxa (Prevotella_7, Olsenella, and Bifidobacterium, and others) exhibited negative relationships between their abundances of and the amount of Salmonella in the feces of their hosts. Many of these same taxa also had significant positive associations with cecal concentrations of butyrate, valerate, caproate, even though they are not known to produce these SCFAs. Together, these data suggest the RPS-associated reduction in Salmonella shedding may be dependent on the establishment of bacterial cross feeding interactions that result in the production of certain SCFAs. However, directly feeding a fatty acid mix did not replicate the effect. RPS supplementation could be an effective means to reduce multidrug-resistant (MDR) S. enterica serovar I 4,[5],12:i:- in swine, provided appropriate bacterial communities are present in the gut. IMPORTANCE Prebiotics, such as resistant potato starch (RPS), are types of food that help to support beneficial bacteria and their activities in the intestines. Salmonella enterica serovar I 4,[5],12:i:- is a foodborne pathogen that commonly resides in the intestines of pigs without disease, but can make humans sick if unintentionally consumed. Here we show that in Salmonella inoculated pigs, feeding them a diet containing RPS altered the colonization and activity of certain beneficial bacteria in a way that reduced the amount of Salmonella in their feces. Additionally, within those fed RPS, swine with higher abundance of these types of beneficial bacteria had less Salmonella I 4,[5],12:i:- in their feces. This work illustrates likely synergy between the prebiotic RPS and the presence of certain gut microorganisms to reduce the amount of Salmonella in the feces of pigs and therefore reduce the risk that humans will become ill with MDR Salmonella serovar I 4,[5],12:i:-.

Dietary Melanoidins from Biscuits and Bread Crust Alter the Structure and Short-Chain Fatty Acid Production of Human Gut Microbiota

Melanoidins are the products of the Maillard reaction between carbonyl and amino groups of macromolecules and are readily formed in foods, especially during heat treatment. In this study we utilized the three-stage Human Gut Simulator system to assess the effect of providing melanoidins extracted from either biscuits or bread crust to the human gut microbiota. Addition of melanoidins to the growth medium led to statistically significant alterations in the microbial community composition, and it increased short-chain fatty acid and antioxidant production by the microbiota. The magnitude of these changes was much higher for cultures grown with biscuit melanoidins. Several lines of evidence indicate that such differences between these melanoidin sources might be due to the presence of lipid components in biscuit melanoidin structures. Because melanoidins are largely not degraded by human gastrointestinal enzymes, they provide an additional source of microbiota-accessible nutrients to our gut microbes.

Olsenella intestinalis sp. nov., isolated from cow feces

A Gram-stain-negative, anaerobic, non-motile, rod-shaped bacterium, designated as BGYT1^T, was isolated from the feces of a cow in Andong, Republic of Korea. It was studied using a polyphasic method to determine its taxonomic position. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain BGYT1^T formed a lineage within the genus Olsenella and was most closely related to O. umbonate KCTC 15140^T (98.2%). The complete genome sequence of strain BGYT1^T was 2,476,083 bp long with a G + C content of 66.9 mol% and contained 1835 genes and 8 contigs. The N50 value was 604,117 bp. There were 50 tRNAs, 6 rRNAs (5S, 16S, 23S), 1778 CDSs and 2 BGCs and 1 tmRNA. The values for ANI (76.8%), AAI (67.3%), and dDDH (22.2%) compared to the closest related species were all below the threshold for bacterial species delineation. In addition, genes encoding the cell wall degrading enzymes such as chitinases, β-1,3 glucanases, and proteases were also detected. The strain was able to grow at pH 6.0-8.0 (optimum, pH 7.0), in the presence of 0.5-1.5% NaCl (optimum, 0.5%, w/v) and at the temperature range of 35-40 °C (optimum, 35 °C). The predominant fatty acids were C_16:0 DMA (20.2%), C_16:0 (20.2%), C_18:0 (10.5%) and C_18:1 cis 9 (17.0%). The polar lipids consisted of an unidentified phospholipid, four unidentified glycolipids and three unidentified lipids. Based on its phenotypic analyses, phylogenetic and physiological characteristics, strain BGYT1^T represented a novel species within the genus Olsenella, for which the name Olsenella intestinalis sp. nov. is proposed. The type strain is BGYT1^T (= KCTC 25379^T = GDMCC 1.3011^T).

Dietary Cysteamine Supplementation Remarkably Increased Feed Efficiency and Shifted Rumen Fermentation toward Glucogenic Propionate Production via Enrichment of Prevotella in Feedlot Lambs

Cysteamine (CS) is an essential nutritional regulator that improves the productive performance of animals by regulating somatotropic hormone secretion. To investigate the fattening potential and effects of CS on rumen microbial fermentation, 48 feedlot lambs were randomly assigned to four groups and fed diets supplemented with different CS concentrations (0, 20, 40, and 60 mg/kg BW). An increase in dietary CS concentrations linearly increased the average daily gain (ADG) and dry matter intake (p < 0.05) but decreased the feed-to-gain ratio (p < 0.01). For the serum hormone, increasing the dietary CS concentration linearly decreased somatostatin and leptin concentration (p < 0.01) but linearly increased the concentration of growth hormone and insulin-like growth factor 1 (p < 0.01). Regarding rumen fermentation, ruminal pH, ammonia-N, and butyrate content did not differ among the four treatments, although dietary CS supplementation linearly increased microbial protein and propionate and decreased the amount of acetate (p < 0.05). Furthermore, an increase in dietary CS concentrations quadratically decreased the estimated methane production and methane production per kg ADG (p < 0.05). High-throughput sequencing revealed that increased dietary CS concentrations quadratically increased Prevotella (p < 0.05), and Prevotella and norank_f__norank_o__Clostridia_UCG-014 were positively correlated with growth performance and rumen fermentation in a Spearman correlation analysis (r > 0.55, p < 0.05). Overall, a CS concentration higher than 20 mg/kg BW produced growth-promoting effects by inhibiting somatostatin concentrations and shifting the rumen toward glucogenic propionate fermentation by enriching Prevotella. In addition, Prevotella and norank_f__norank_o__Clostridia_UCG-014 were positively correlated with growth performance in lambs.

Olsenella uli-induced pneumonia: a case report

BACKGROUND

Olsenella uli is anaerobic or microaerophilic bacteria, commonly found in oral cavity or gastrointestinal tract, which has not been reported to be associated with lower respiratory tract infection. Herein, we report the first case of Olsenella uli infection in the lung.

CASE PRESENTATION

A 70-year-old male farmer with no history of other respiratory tract diseases developed a cough with bloody sputum three times a day without obvious causes or other concomitant symptoms. After a period of treatment with empirical antibiotic, his condition did not improve. The computed tomography (CT) and lung biopsy results indicated bilateral pneumonia, and Olsenella uli was identified by micromorphology, sequence analysis and mass spectrometry analysis recovered from sputum. Ceftazidime, a third generation cephalosporin was used for the treatment, and the patient recovered after 10 days.

CONCLUSIONS

Our report suggests a causative role of gingival bacteria in the pathogenesis of pneumonia, thus early diagnosis and prompt antibiotic therapy may play a role in the treatment of Olsenella uli induced pneumonia.

Effects of diets with various levels of forage rape (Brassica napus) on growth performance, carcass traits, meat quality and rumen microbiota of Hu lambs

BACKGROUND

Apart from being an oil crop, forage rape (Brassica napus) can be used to feed ruminants. The objective of this study was to investigate the effects of pelleted total mixed ration (TMR) diets with various levels of forage rape on growth performance, carcass traits, meat quality, meat nutritional value and rumen microbiota of Hu lambs, which was important for the efficient utilization of forage rape and alleviating the shortage of high-quality forage in China.

RESULTS

Lambs fed on diets with 200-400 g kg^-1 forage rape had greater average daily gain (ADG) and lower feed conversion ratio (FCR) than those fed on diets with 0-100 g kg^-1 of forage rape (P < 0.05). As dietary forage rape levels increased, the content of intramuscular α-linolenic acid and a variety of amino acids in the muscle increased linearly (P < 0.05). No difference was found in carcass traits or meat quality among the dietary treatments (P > 0.05). However, the inclusion of forage rape increased the relative abundance of cellulolytic bacteria and short-chain fatty acid producers, including Succiniclasticum, Fibrobacter and members of the Lachnospiraceae. Besides, Succiniclasticum was found to be positively correlated with the final body weight of lambs.

CONCLUSION

TMR diets that included 200-400 g kg^-1 forage rape could improve the growth performance of lambs, and elevated the content of intramuscular α-linolenic acid and a variety of amino acids in the muscle, accompanied by increased abundance of cellulolytic bacteria in the rumen.

Gastrointestinal Tract and Dietary Fiber Driven Alterations of Gut Microbiota and Metabolites in Durco × Bamei Crossbred Pigs

Gastrointestinal tract and dietary fiber (DF) are known to influence gut microbiome composition. However, the combined effect of gut segment and long-term intake of a high fiber diet on pig gut microbiota and metabolite profiles is unclear. Here, we applied 16S rRNA gene sequencing and untargeted metabolomics to investigate the effect of broad bean silage on the composition and metabolites of the cecal and jejunal microbiome in Durco × Bamei crossbred pigs. Twenty-four pigs were allotted to four graded levels of DF chow, and the content of jejunum and cecum were collected. Our results demonstrated that cecum possessed higher α-diversity and abundance of Bacteroidetes, unidentified Ruminococcaceae compared to jejunum, while jejunum possessed higher abundance of Lactobacillus, Streptococcus. DF intake significantly altered diversity of the bacterial community. The abundance of Bacteroidetes and Turicibacter increased with the increase of DF in cecum and jejunum respectively. Higher concentrations of amino acids and conjugated bile acids were detected in the jejunum, whereas free bile acids and fatty acids were enriched in the cecum. The concentrations of fatty acids, carbohydrate metabolites, organic acids, 2-oxoadipic acid, and succinate in cecum were higher in the high DF groups. Overall, the results indicate that the composition of bacteria and the microbiota metabolites were distinct in different gut segments. DF had a significant influence on the bacterial composition and structure in the cecum and jejunum, and that the cecal metabolites may further affect host health, growth, and slaughter performance.

Developmental changes of nutrient digestion in young lambs are influenced by weaning and associated with intestinal microbiota

Understanding the effects of weaning on the changes of digestive function could help to design efficient intervention strategies for promoting the development of the lamb during the early stages of life. In this study, 24 lambs were divided into two groups (control group, lambs were not weaned; and weaning group, lambs were weaned at 21 days of age). The growth, nutrient digestion, gastrointestinal enzyme activity, plasma biochemical indicators, and intestinal microbiota at 7-49 days were determined, as well as the impact of early weaning. The nutrient digestion changed rapidly with age, especially at 14-28 days (p < 0.05). Weaning reduced the dry matter (DM), crude protein (CP), and ether extract (EE) intake and digestion, but increased the starch, neutral detergent fiber (NDF), and acid detergent fiber (ADF) intake and digestion (p < 0.05). Weaning did not affect the overall jejunal microbiota (p > 0.05), but affected the relative abundance of certain bacteria taxa (p < 0.05). Lactic acid-producing bacteria, such as Olsenella, Bacillus, Sharpea, and Bifidobacterium are closely related to CP or EE digestion and growth performance (p < 0.05). In summary, we delineated the pattern of nutrient digestion and intestinal microbiota development in young lambs, and the impact of early weaning.

Nutrient Digestibility, Microbial Fermentation, and Response in Bacterial Composition to Methionine Dipeptide: An In Vitro Study

Simple Summary

The rumen microbiota plays an important role in maintaining microbiota homeostasis and promoting milk production synthesis through utilizing amino acids and non-protein nitrogen. Furthermore, various nitrogen sources have shown distinct effects on microbial growth rates. The methionine dipeptide (MD) is a bioactive peptide consisting of two methionine (Met) residues linked by a peptide bond. Although the role of MD in milk protein synthesis is established, little is known about its role in bacterial fermentation. The present study demonstrates that the various nitrogen sources could reshape microbiota differently, and MD could be more efficient than free Met in the rumen to support acetate producer growth. Our study provides some new insights into the relationship between ruminal microbiota of dairy cows and small peptides and points to potential strategies to effectively enhance the health condition and digestion ability of dairy cows.

Abstract

It is well known that the methionine dipeptide (MD) could enhance the dairy cows milking performance. However, there is still a knowledge gap of the effects of MD on the rumen fermentation characteristics, microbiota composition, and digestibility. This experiment was conducted to determine the effect of different nitrogen sources with a total mixed ration on in vitro nutrient digestibility, fermentation characteristics, and bacterial composition. The treatments included 5 mg urea (UR), 25.08 mg methionine (Met), 23.57 mg MD, and no additive (CON) in fermentation culture medium composed of buffer solution, filtrated Holstein dairy cow rumen fluid, and substrate (1 g total mixed ration). Nutrient digestibility was measured after 24 h and 48 h fermentation, and fermentation parameters and microbial composition were measured after 48 h fermentation. Digestibility of dry matter, crude protein, neutral detergent fiber (NDF), and acid detergent fiber (ADF) in the MD group at 48 h were significantly higher than in the CON and UR groups. The total volatile fatty acid concentration was higher in the MD group than in the other groups. In addition, 16S rRNA microbial sequencing results showed MD significantly improved the relative abundances of Succinivibrio, Anaerotruncus, and Treponema_2, whereas there was no significant difference between Met and UR groups. Spearman’s correlation analysis showed the relative abundance of Succinivibrio and Anaerotruncus were positively correlated with gas production, NDF digestibility, ADF digestibility, and acetate, propionate, butyrate, and total volatile fatty acid concentrations. Overall, our results suggested that the microbiota in the fermentation system could be affected by additional nitrogen supplementation and MD could effectively enhance the nutrient utilization in dairy cows.

Reclassification of Olsenella gallinarum as Thermophilibacter gallinarum comb. nov. and description of Thermophilibacter immobilis sp. nov., isolated from the mud in a fermentation cellar used for the production of Chinese Luzhou-flavour Baijiu

A novel Gram-stain-positive, strictly anaerobic, elliptical, non-motile and non-flagellated bacterium, designed LZLJ-2^T, was isolated from the mud in a fermentation cellar used for the production of Chinese Luzhou-flavour Baijiu. Growth occurred at 28-45 °C (optimum, 37 °C), at pH 6.0-7.0 (optimum, pH 6.0) and with concentrations of NaCl up to 2 % (w/v; optimum, 0 %). On the basis of 16S rRNA gene sequence similarity, strain LZLJ-2^T belonged to the genus Thermophilibacter and was most closely related to Thermophilibacter mediterraneus Marseille-P3256^T (similarity 96.9 %), Olsenella gallinarum ClaCZ62^T (similarity 96.6 %) and Thermophilibacter provencensis Marseille-P2912^T (similarity 96.4 %). In addition, strain LZLJ-2^T had high similarity to the genus Olsenella, including Olsenella profusa DSM 13989^T (similarity 94.9 %), Olsenella umbonata DSM 22620^T (similarity 94.9 %), Olsenella uli ATCC 49627^T (similarity 94.22 %), Tractidigestivibacter scatoligenes DSM 28304^T (similarity 93.9 %) and Paratractidigestivibacter faecalis KCTC 15699^T (similarity 93.25 %). Comparative genome analysis showed that orthoANI values between strain LZLJ-2^T and Thermophilibacter mediterraneus Marseille-P3256^T, Olsenella gallinarum ClaCZ62^T, Thermophilibacter provencensis Marseille-P2912^T, Olsenella profusa DSM 13989^T, Olsenella umbonata DSM 22620^T, Olsenella uli ATCC 49627^T, Tractidigestivibacter scatoligenes DSM 28304^T and Paratractidigestivibacter faecalis KCTC 15699^T were 78.68, 78.99, 78.29, 73.40, 74.00, 74.30, 75.08 and 77.23 %, and the genome-to-genome distance values were respectively 22.3, 22.5, 22.4, 19.6, 20.5, 19.7, 20.5 and 21.5 %. The genomic DNA G+C content of strain LZLJ-2^T was 65.21 mol%. The predominant cellular fatty acids (>10 %) of strain LZLJ-2^T were C_18 : 1 cis 9 (33.7 %), C_14 : 0 (22.0 %) and C_18 : 1 cis 9 DMA (13.5 %). d-Glucose, sucrose, mannose, maltose, lactose (weak), salicin, glycerol (weak), cellobiose and trehalose (weak) could be used by strain LZLJ-2^T as sole carbon sources. Enzyme activity results showed positive reactions with valine arylamidase, leucine arylamidase, crystine arylamidase, acid phosphatase, alkaline phosphatase, esterase (C4) (weakly positive), naphthol-AS-BI-phosphohydrolase, α-glucosidase and β-glucosidase. The major end products of glucose fermentation were lactic acid and acetic acid. It produced skatole from indole acetic acid, and produced p-cresol from modified peptone-yeast extract medium with glucose. Based on the 16S rRNA gene trees as well as the genome core gene tree, it is suggested that Olsenella gallinarum are transferred to genus Thermophilibacter as Thermophilibacter gallinarum comb. nov. Based on phenotypic, genotypic and phylogenetic data, strain LZLJ-2^T is considered to represent a novel species of the genus Thermophilibacter, for which the name Thermophilibacter immobilis sp. nov. is proposed. The type strain is LZLJ-2^T (=KCTC 25162^T=JCM 34224^T).

Multispecies probiotics alter fecal short-chain fatty acids and lactate levels in weaned pigs by modulating gut microbiota

Short-chain fatty acids (SCFAs) are metabolic products produced during the microbial fermentation of non-digestible fibers and play an important role in metabolic homeostasis and overall gut health. In this study, we investigated the effects of supplementation with multispecies probiotics (MSPs) containing Bacillus amyloliquefaciens, Limosilactobacillus reuteri, and Levilactobacillus brevis on the gut microbiota, and fecal SCFAs and lactate levels of weaned pigs. A total of 38 pigs weaned at 4 weeks of age were fed either a basal diet or a diet supplemented with MSPs for 6 weeks. MSP administration significantly increased the fecal concentrations of lactate (2.3-fold; p < 0.01), acetate (1.8-fold; p < 0.05), and formate (1.4-fold; p < 0.05). Moreover, MSP supplementation altered the gut microbiota of the pigs by significantly increasing the population of potentially beneficial bacteria such as Olsenella, Catonella, Catenibacterium, Acidaminococcus, and Ruminococcaceae. MSP supplementation also decreased the abundance of pathogenic bacteria such as Escherichia and Chlamydia. The modulation of the gut microbiota was observed to be strongly correlated with the changes in fecal SCFAs and lactate levels. Furthermore, we found changes in the functional pathways present within the gut, which supports our findings that MSP modulates the gut microbiota and SCFAs levels in pigs. The results support the potential use of MSPs to improve the gut health of animals by modulating SCFAs production.

Ruminal effects of excessive dietary sulphur in feedlot cattle

Sulphur (S) dietary excess can limit productive performance and increase polioencephalomalacia (PEM) incidence in feedlot cattle (FC). Sulphur excess ingested is transformed to hydrogen sulphide (H₂ S) by sulfo-reducing ruminal bacteria (SRB), being high ruminal H₂ S concentration responsible for aforementioned damages. As the ruminal mechanisms involved in H₂ S concentrations increase have not been elucidated, this study aimed to evaluate the ruminal environment, and the association between ruminal H₂ S and dissimilatory SRB (DSRB) concentration in FC experimentally subjected to S dietary excess. Twelve crossbred steers were randomly assigned to one of two dietary S levels (6 animals per treatment): low (LS, 0.19% S) and high (HS, 0.39% S obtained by sodium sulfate inclusion at 0.86%). The study lasted 38 days, and on days 0, 22 and 38, ruminal gas samples were taken to quantify H₂ S concentration, and ruminal fluid to determine total bacteria, DSRB, protozoa, volatile fatty acid and ammonia nitrogen concentration. For ruminal H₂ S concentration, S dietary × sampling day interaction was significant (p < 0.001), so that the greater concentration was observed on days 22 and 38 with the HS diet. The remaining ruminal parameters were not affected by dietary S level, and no significant correlation between H₂ S and DSRB concentrations was observed. The ruminal adaptation that maximizes H₂ S production in FC consuming S excess does not seem to be associated with biological or biochemical alterations, nor DSRB concentration changes. The microbial diversity and ruminal environment were resilient to the S excess evaluated, suggesting that 0.39% of dietary S achieved by 0.86% sodium sulfate addition, could be used without disturbances on digestion nor health of FC.

pH regulation of the first phase could enhance the energy recovery from two-phase anaerobic digestion of food waste

The effect of pH regulation in phase I on hydrolysis and acidogenesis rate, metabolites production, microbial community, and the overall energy recovery efficiency during two-phase anaerobic digestion (AD) of food waste (FW) was investigated. pH strongly affected the acidogenesis rate and the yield of the fermentation products. The highest acidogenesis efficiency (60.4%) and total volatile fatty acids (VFA)/ethanol concentration (12.4 g/L) were obtained at pH 8 during phase I. Microbial community analysis revealed that Clostridium IV was enriched at pH 8, relating to the accumulation of butyrate. Also, Clostridium sensu stricto played a crucial role in hydrogen production and was abundant at pH 6, resulting in the highest hydrogen yield (212.2 ml/g VS). In phase II, the highest cumulative methane yield (412.6 ml/g VS) was obtained at pH 8. By considering the hydrogen and methane production stages, the highest energy yield (22.8 kJ/g VS, corresponding to a 76.4% recovery efficiency) was generated at pH 8, which indicates that pH 8 was optimal for energy recovery during two-phase AD of FW. Overall, the results demonstrated the possibility of increasing the energy recovery from FW by regulating the pH in the hydrolysis/acidogenesis phase based on the two-phase AD system. PRACTITIONER POINTS: pH 8 was suitable for hydrolysis, acidogenesis, and methanogenesis. High hydrogen yields were obtained at pH 5-8 (about 200 ml/d). Clostridium sensu stricto might have played a crucial role in hydrogen production. High methane production (about 400 ml/g VS) was obtained at pH 7-9. pH 8 was optimal for energy recovery from FW with an efficiency of 76.4% (22.8 kJ/g VS).

Complete Genome Sequence of Atopobiaceae Bacterium Strain P1, Isolated from Mouse Feces

Atopobiaceae bacterium strain P1 (Actinobacteria, Coriobacteriales) was isolated from mouse feces. Here, we report the complete genome sequence of this strain, which has a total size of 2,028,478 bp and a G+C content of 58.6%.

Analysis of Host Jejunum Transcriptome and Associated Microbial Community Structure Variation in Young Calves with Feed-Induced Acidosis

Diet-induced acidosis imposes a health risk to young calves. In this study, we aimed to investigate the host jejunum transcriptome changes, along with its microbial community variations, using our established model of feed-induced ruminal acidosis in young calves. Eight bull calves were randomly assigned to two diet treatments beginning at birth (a starch-rich diet, Aci; a control diet, Con). Whole-transcriptome RNA sequencing was performed on the jejunum tissues collected at 17 weeks of age. Ribosomal RNA reads were used for studying microbial community structure variations in the jejunum. A total of 853 differentially expressed genes were identified (402 upregulated and 451 downregulated) between the two groups. The cell cycle and the digestion and absorption of protein in jejunal tissue were affected by acidosis. Compared to the control, genera of Campylobacter, Burkholderia, Acidaminococcus, Corynebacterium, and Olsenella significantly increased in abundance in the Aci group, while Lachnoclostridium and Ruminococcus were significantly lower in the Aci group. Expression changes in the AXL gene were associated with the abundance variations of a high number of genera in jejunum. Our study provided a snapshot of the transcriptome changes in the jejunum and its associated meta-transcriptome changes in microbial communities in young calves with feed-induced acidosis.

Microbial mechanism of enhancing methane production from anaerobic digestion of food waste via phase separation and pH control

Phase separation and pH control are commonly used to improve methane production during anaerobic digestion (AD) of food waste, but their influencing mechanisms have not been fully discovered through microbial analysis. In this study, single-phase AD (SPAD), two-phase AD without pH control (TPAD-pHUC), and TPAD with fermentation pH controlled at 6.0 and 4.5 were conducted. The results showed that phase separation decreased the ratio of total bacteria to total archaea in the methanogenic phase. At the organic loading rate (OLR) of 1.9 g/(L·d), methanogenesis was dominated by acetoclastic Methanosaeta in both SPAD and TPAD-pHUC, while elevated Methanoculleus and active hydrogen production initiated a shift from the acetoclastic to hydrogenotrophic pathway in SPAD as OLR increased, eventually resulting in excessive acidification at OLR 3.2 g/(L·d). TPAD-pHUC was dominated by Methanosaeta with scarce hydrogen production genes, and thus maintained a delicate balance between fewer acidogens and methanogens at OLR 3.2-3.7 g/(L·d). TPAD with pH control exhibited higher methane yield (460-482 ml/g) at OLR 1.9 g/(L·d) due to the enhancement of protein degradation and the conversion from methylated compounds to methane by Methanosarcina. High Na⁺ concentration facilitated the proliferation of hydrogen production bacteria, but inhibited acetoclastic methanogenesis at OLR 2.4 g/(L·d). In comparison with SPAD and pH control, TPAD without pH control, integrating 4 d acidogenesis and 22 d methanogenesis, exhibited the best and steady performance at OLR 3.7 g/(L·d) with methane production exceeding 370 ml/g.

Investigation of Immunomodulatory and Gut Microbiota-Altering Properties of Multicomponent Nutraceutical Prepared from Lactic Acid Bacteria, Bovine Colostrum, Apple Production By-Products and Essential Oils

Dietary components, such as lactic acid bacteria (LAB), bovine colostrum, apple production by-products, and essential oils, can favorably alter the host immune system and gut microbiota, however, their cumulative effect as multicomponent nutraceutical supplement has not been investigated. Therefore, the present study is the first one to evaluate a combination of LAB, bovine colostrum, dehydrated apple pomace, and essential oils for their immunomodulatory and prebiotic properties in the swine model. This study shows that supplementary feeding of pigs using multicomponent nutraceutical resulted in a statistically significant decrease in proportions of T cytotoxic and double-positive (CD4⁺CD8^+low) cells within the CD3⁺ cell population at 28 DPI, compared to the beginning of the experiment (0DPI). Conversely, a statistically significant increase in proportions of B cells (accompanied by an increase in IgG concentration) and macrophage/monocyte cells within viable cell population at 28 DPI, compared to the beginning of the experiments, was observed. Furthermore, changes in the bacterial composition of gut microbiota in pigs fed with multicomponent nutraceutical changed significantly, with a 1.78 times higher number of probiotic strains (Bifidobacterium, Streptococcus, Faecilbacterium) at the end of the experiment, compared to control group animals. This study shows a positive effect of the nutraceutical formula used on the changes of gut microbiota by facilitating an increase in probiotic bacteria strains and possible anti-inflammatory properties.

New human-associated species of the family Atopobiaceae and proposal to reclassify members of the genus Olsenella

Five novel bacterial strains, Marseille-P1476^T (=CSURP1476^T=DSM 100642^T), Marseille-P3256^T (=CSURP3256^T=CECT 9977^T), Marseille-P2936^T (=CSURP2936^T=DSM 103159^T), Marseille-P2912^T (=CSURP2912^T=DSM 103345^T) and Marseille-P3197^T (=CSURP3197^T=CCUG 71847^T), were isolated from various human specimens. These five strains were not identified at the species level by matrix-assisted laser desorption/ionization time of flight mass spectrometry. Following 16S rRNA gene sequence comparisons with the GenBank database, the highest nucleotide sequence similarities of all studied strains were obtained to members of the paraphyletic genus Olsenella. A polyphasic taxono-genomic strategy (16S rRNA gene-based and core genome-based phylogeny, genomic comparison, phenotypic and biochemical characteristics) enabled us to better classify these strains and reclassify Olsenella species. Among the studied strains, Marseille-P1476^T, Marseille-P2936^T and Marseille-P3197^T belonged to new species of the genus Olsenella for which we propose the names Olsenella massiliensis sp. nov., Olsenella phocaeensis sp. nov. and Olsenella urininfantis sp. nov., respectively. Strains Marseille-P2912^T and Marseille-P3256^T belonged to a new genus for which the names Thermophilibacter provencensis gen. nov., sp. nov. and Thermophilibacter mediterraneus gen. nov., sp. nov. are proposed, respectively. We also propose the creation of the genera Parafannyhessea gen. nov., Tractidigestivibacter gen. nov. and Paratractidigestivibacter gen. nov. and the reclassification of Olsenella umbonata as Parafannyhessea umbonata comb. nov., Olsenella scatoligenes as Tractidigestivibacter scatoligenes comb. nov., and Olsenella faecalis as Paratractidigestivibacter faecalis comb. nov.