Characteristics of Gut Microbiota in Rosacea Patients-A Cross-Sectional, Controlled Pilot Study.

BACKGROUND: Recent studies have suggested a possible connection between rosacea and patients' gut microbiota. OBJECTIVE: To investigate the differences in fecal microbial profiles between patients with rosacea and healthy controls. METHODS: Gut microbiota of 54 rosacea patients (RP) were analyzed using MiSeq 16S rRNA sequencing. Enterotypes, the Firmicutes/Bacteroides (F/B) ratio, the significance of alpha and beta diversity, and differential abundance analysis (DAA) were calculated and compared with age- and gender-matched controls (CP, n = 50). RESULTS: Significant changes in the enterotypes and F/B ratio were observed between the RP and CP (p = 0.017 and p = 0.002, respectively). The RP showed a decreased microbial richness and diversity compared to the CP (Shannon p = 0.012, inverse Simpson p = 0.034). Beta diversity also differed between both groups (PERMANOVA, p = 0.006). Fourteen significantly different taxa were detected according to DAA. Faecalibacterium prausnitzii (coef. -0.0800, p = 0.008), Lachnoospiraceae ND 3007 group sp. (coef. -0.073, p < 0.001), and Ruminococcaceae (coef. -0.072, p = 0.015) were significantly decreased; Oscillobacter sp. (coef. 0.023, p = 0.031), Flavonifractor plautii (coef. 0.011, p = 0.037), and Ruminococccaceae UBA 1819 (coef. 0.010, p = 0.031) were significantly increased in the RP compared to the CP. CONCLUSION: Significant alterations in gut microbiota were present in the RP. Taxonomic shifts and reduced richness and diversity were observed when compared to the CP. Larger prospective studies are needed to investigate correlations with clinical features and to translate these findings into future therapeutic approaches.

Dietary carbohydrate sources differently prime the microbial ecosystem but not the epithelial gene expression profile along the complete gut of young calves.

BACKGROUND: Recent data indicated similar growth performance of young calves fed solely high-quality hay instead of a starter diet based on starchy ingredients. Yet, providing exclusively such distinct carbohydrate sources during early life might specifically prime the microbiota and gene expression along the gut of young calves, which remains to be explored. We investigated the effects of starter diets differing in carbohydrate composition, that is medium- or high-quality hay and without or with 70% concentrate supplementation (on fresh matter basis), across the gastrointestinal tract (GIT) of weaned Holstein calves (100 ± 4 days of age) using 16 S rRNA gene sequencing and analyses of short-chain fatty acids and host epithelial gene expressions. RESULTS: The concentrate supplementation drastically decreased microbial diversity throughout the gut, which was also true to a much lesser extent for high-quality hay when compared to medium-quality hay in the foregut. Similarly, the factor concentrate strongly shaped the diet-associated common core microbiota, which was substantially more uniform along the gut with concentrate supplementation. The fermentation profile shifted towards less acetate but more propionate with concentrate supplementation in almost all gut sections, corresponding with higher abundances of starch-utilizing bacteria, while major fibrolytic clusters declined. Noteworthy, the n-butyrate proportion decreased in the rumen and increased in the colon with concentrate, showing an opposite, gut site-dependent effect. Both dietary factors modestly influenced the host epithelial gene expression. CONCLUSIONS: Concentrate supplementation clearly primed the microbial ecosystem on a starch-targeted fermentation with characteristic genera occupying this niche along the entire GIT of calves, whereas the microbial differentiation due to hay quality was less distinct. Overall, changes in the microbial ecosystem were only marginally reflected in the targeted transcriptional profile of the host epithelium.

Integrated microbiota-host-metabolome approaches reveal adaptive ruminal changes to prolonged high-grain feeding and phytogenic supplementation in cattle.

Diets rich in readily fermentable carbohydrates primarily impact microbial composition and activity, but can also impair the ruminal epithelium barrier function. By combining microbiota, metabolome, and gene expression analysis, we evaluated the impact of feeding a 65% concentrate diet for 4 weeks, with or without a phytogenic feed additive (PFA), on the rumen ecosystem of cattle. The breaking point for rumen health seemed to be the second week of high grain (HG) diet, with a dysbiosis characterized by reduced alpha diversity. While we did not find changes in histological evaluations, genes related with epithelial proliferation (IGF-1, IGF-1R, EGFR, and TBP) and ZO-1 were affected by the HG feeding. Integrative analyses allowed us to define the main drivers of difference for the rumen ecosystem in response to a HG diet, identified as ZO-1, MyD88, and genus Prevotella 1. PFA supplementation reduced the concentration of potentially harmful compounds in the rumen (e.g. dopamine and 5-aminovaleric acid) and increased the tolerance of the epithelium toward the microbiota by altering the expression of TLR-2, IL-6, and IL-10. The particle-associated rumen liquid microbiota showed a quicker adaptation potential to prolonged HG feeding compared to the other microenvironments investigated, especially by the end of the experiment.

Winery by-products as a feed source with functional properties: dose-response effect of grape pomace, grape seed meal, and grape seed extract on rumen microbial community and their fermentation activity in RUSITEC.

BACKGROUND: Grape and winery by-products have nutritional values for cattle and also contain functional compounds like phenols, which not only bind to protein but can also directly affect microbiota and their function in the rumen. We characterized the nutritional and functional effects of grape seed meal and grape pomace as well as an effective dosage of grape phenols on ruminal microbiota and fermentation characteristics using a rumen simulation technique. RESULTS: Six diets (each n = 8) were compared including a control diet (CON, no by-product), a positive control diet (EXT, CON + 3.7% grape seed extract on a dry matter (DM) basis), two diets with grape seed meal at 5% (GS-low) and 10% (GS-high), and two diets with grape pomace: at 10% (GP-low) and 20% (GP-high), on a DM basis. The inclusion of the by-product supplied total phenols at 3.4%, 0.7%, 1.4%, 1.3%, and 2.7% of diet DM for EXT, GS-low, GS-high, GP-low, and GP-high, respectively. Diets were tested in four experimental runs. All treatments decreased ammonia concentrations and the disappearances of DM and OM (P < 0.05) compared to CON. EXT and GP-high lowered butyrate and odd- and branch-chain short-chain fatty acids while increased acetate compared to CON (P < 0.05). Treatments did not affect methane formation. EXT decreased the abundance of many bacterial genera including those belonging to the core microbiota. GP-high and EXT consistently decreased Olsenella and Anaerotipes while increased Ruminobacter abundances. CONCLUSION: The data suggest that the inclusion of winery by-products or grape seed extract could be an option for reducing excessive ammonia production. Exposure to grape phenols at a high dosage in an extract form can alter the rumen microbial community. This, however, does not necessarily alter the effect of grape phenols on the microbial community function compared to feeding high levels of winery by-products. This suggests the dominant role of dosage over the form or source of the grape phenols in affecting ruminal microbial activity. In conclusion, supplementing grape phenols at about 3% of diet DM is an effective dosage tolerable to ruminal microbiota.

Sigla storax (Liquidambar orientalis) mitigates in vitro methane production without disturbances in rumen microbiota and nutrient fermentation in comparison to monensin.

AIM: The aim of this study was to investigate the in vitro dose-dependent effects of sigla storax (Styrax liquidus) on rumen microbiota and rumen microbial fermentation in comparison to monensin as a positive control. METHODS AND RESULTS: This study was carried out using a rumen simulation model (Rusitec). Treatments consisted of no additive (control), 10 mg l-1 of monensin sodium salt, 100 mg l-1 (Low-Sigla), and 500 mg l-1 (High-Sigla) of sigla storax (n = 6/treatment). In addition to rumen fermentation characteristics, rumen microbial composition was investigated using 16S rRNA sequencing. The methane variables and the acetate to propionate ratio decreased in the both High-Sigla and monensin groups (P < 0.05). High-Sigla had no effect on ammonia, total SCFA and nutrition degradation, while monensin decreased these parameters (P < 0.05). Unlike monensin, the sigla storax treatments did not affect the alpha or beta diversity indexes of the microbiota. The relative abundance of Methanomethylophilaceae and Ruminococcaceae decreased with High-Sigla and monensin (P < 0.05), and Atopobiaceae and Eggerthellaceae decreased with the both doses of sigla storax as well as monensin treatments (P < 0.05). Syntrophococcus, DNF00809, and Kandleria were among the genera that most decreased with High-Sigla and monensin (Q < 0.07) and were strongly positively correlated with methane production (r = 0.52-0.56). CONCLUSIONS: The high dose of sigla storax (500 mg l-1) decreased methane in the rumen ecosystem without adverse effects on nutrient degradation and SCFA production, and without dramatically impacting the microbial composition. Sigla storax might be a novel feed additive to mitigate methane in cattle.

Assessing the Performance of a Novel Stool-Based Microbiome Test That Predicts Response to First Line Immune Checkpoint Inhibitors in Multiple Cancer Types.

The intestinal microbiome is by now an undebatable key player in the clinical outcome of ICI therapies. However, no microbiome profiling method to aid therapy decision is yet validated. We conducted a multi-centric study in patients with stage III/IV melanoma, NSCLC, or RCC receiving ICI treatment. The stool microbiome profile of 63 patients was analyzed with BiomeOne®, a microbiome-based algorithm that anticipates whether a patient will achieve clinical benefit with ICIs prior to therapy initiation. Classification of patient samples as Rs and NRs was achieved with a sensitivity of 81% and a specificity of 50% in this validation cohort. An ICI-favorable response was characterized by an intestinal microbiome rich in bacteria such as Oscillospira sp., Clostridia UCG-014, Lachnospiraceae UCG-010 sp., Prevotella copri, and a decrease in Sutterella sp., Lactobacillales, and Streptococcus sp. Patients who developed immune-related adverse events (irAEs) had an overall increased microbial diversity and richness, and a stool microbiome depleted in Agathobacter. When compared with the programmed death-ligand 1 (PD-L1) expression test in the subcohort of NSCLC patients (n = 38), BiomeOne® exhibited a numerically higher sensitivity (78.6%) in identifying responders when compared with the PD-L1 test (67.9%). This study provides an evaluation of BiomeOne®, the first microbiome-based test for prediction of ICI response, to achieve market authorization. Validation with further indications and expansion to other microbiome-based interventions will be essential to bring microbiome-based diagnostics into standard clinical practice.

Low-Level Tetracycline Resistance Gene tet(O)_3 in Campylobacter jejuni.

Campylobacter (C.) spp. are the most important foodborne, bacterial, and zoonotic pathogens worldwide. Resistance monitoring of foodborne bacterial pathogens is an important tool to control antimicrobial resistance as a part of the "One Health" approach. The detection and functionality of new resistance genes are of paramount importance in applying more effective screening methods based on whole genome sequencing (WGS). Most tetracycline-resistant C. spp. isolates harbor tet(O), a gene that encodes a ribosomal protection protein. Here we describe tet(O)_3, which has been identified in two food isolates of C. jejuni and is very similar to the tet(O) gene in Streptococcus pneumoniae, having a truncated promoter sequence. This gene confers resistance to tetracycline below 1 mg/L, which is the epidemiological cut-off value. We have analyzed the entire genome of these two isolates, together with a C. jejuni isolate found to have high-level resistance to tetracycline. In contrast to the highly resistant isolate, the promoter of tet(O)_3 is highly responsive to tetracycline, as observed by reverse transcription polymerase chain reaction (RT-PCR). In addition, the two isolates possess a CRISPR repeat, fluoroquinolone resistance due to the gyrA point mutation C257T, a ß-lactamase resistance gene blaOXA-184, a multidrug efflux pump CmeABC and its repressor CmeR, but no plasmid. Low-level antibiotic resistant C. jejuni might therefore have an advantage for surviving in non-host environments.

Diet and phytogenic supplementation substantially modulate the salivary proteome in dairy cows.

Phytogenic compounds may influence salivation or salivary properties. However, their effects on the bovine salivary proteome have not been evaluated. We investigated changes in the bovine salivary proteome due to transition from forage to high-concentrate diet, with and without supplementation with a phytogenic feed additive. Eight non-lactating cows were fed forage, then transitioned to a 65% concentrate diet (DM basis) over a week. Cows were control (n = 4, CON) or supplemented with a phytogenic feed additive (n = 4, PHY). Proteomic analysis was conducted using liquid chromatography coupled with mass spectrometry. We identified 1233 proteins; 878 were bovine proteins, 189 corresponded to bacteria, and 166 were plant proteins. Between forage and high-concentrate, 139 proteins were differentially abundant (P < 0.05), with 48 proteins having a log2FC difference > |2|. The salivary proteome reflected shifts in processes involving nutrient utilization, body tissue accretion, and immune response. Between PHY and CON, 195 proteins were differently abundant (P < 0.05), with 37 having a log2FC difference > |2|; 86 proteins were increased by PHY, including proteins involved in smell recognition. Many differentially abundant proteins correlated (r > |0.70|) with salivary bicarbonate, total mucins or pH. Results provide novel insights into the bovine salivary proteome using a non-invasive approach, and the association of specific proteins with major salivary properties influencing rumen homeostasis. SIGNIFICANCE: Phytogenic compounds may stimulate salivation due to their olfactory properties, but their effects on the salivary proteome have not been investigated. We investigated the effect of high-concentrate diets and supplementation with a phytogenic additive on the salivary proteome of cows. We show that analysis of cows' saliva can be a non-invasive approach to detect effects occurring not only in the gut, but also systemically including indications for gut health and immune response. Thus, results provide unique insights into the bovine salivary proteome, and will have a crucial contribution to further understand animal response in terms of nutrient utilization and immune activity due to the change from forage to a high-energy diet. Additionally, our findings reveal changes due to supplementation with a phytogenic feed additive with regard to health and olfactory stimulation. Furthermore, findings suggest an association between salivary proteins and other components like bicarbonate content.

Progressive microbial adaptation of the bovine rumen and hindgut in response to a step-wise increase in dietary starch and the influence of phytogenic supplementation.

Microbial composition and activity in the gastrointestinal tract (GIT) of cattle has important implications for animal health and welfare, driving the focus of research toward ways to modify their function and abundance. However, our understanding of microbial adaption to nutritional changes remains limited. The aim of this study was to examine the progressive mechanisms of adaptation in the rumen and hindgut of cattle receiving increasing amounts of starch with or without dietary supplementation of a blended phytogenic feed additive (PFA; containing menthol, thymol and eugenol). We used 16S rRNA gene amplicon sequencing to assess the microbial composition and predicted metabolic pathways in ruminal solid and liquid digesta, and feces. Furthermore, we employed targeted liquid chromatography-mass spectrometry methods to evaluate rumen fluid metabolites. Results indicated a rapid microbial adaptation to diet change, starting on the second day of starch feeding for the particle associated rumen liquid (PARL) microbes. Solid rumen digesta- and feces-associated microbes started changing from the following day. The PARL niche was the most responsive to dietary changes, with the highest number of taxa and predicted pathways affected by the increase in starch intake, as well as by the phytogenic supplementation. Despite the differences in the microbial composition and metabolic potential of the different GIT niches, all showed similar changes toward carbohydrate metabolism. Metabolite measurement confirmed the high prevalence of glucose and volatile fatty acids (VFAs) in the rumen due to the increased substrate availability and metabolic activity of the microbiota. Families Prevotellaceae, Ruminococcaceae and Lachnospiraceae were found to be positively correlated with carbohydrate metabolism, with the latter two showing wide-ranging predicted metabolic capabilities. Phytogenic supplementation affected low abundant taxa and demonstrated the potential to prevent unwanted implications of feeding high-concentrate diet, such as reduction of microbial diversity. The inclusion of 50% concentrate in the diet caused a major shift in microbial composition and activity in the GIT of cattle. This study demonstrated the ability of microorganisms in various GIT niches to adjust differentially, yet rapidly, to changing dietary conditions, and revealed the potential beneficial effects of supplementation with a PFA during dietary adaptation.

Characterization of presence and activity of microRNAs in the rumen of cattle hints at possible host-microbiota cross-talk mechanism.

MicroRNAs (miRNAs), as important post-transcriptional regulators, are ubiquitous in various tissues. The aim of this exploratory study was to determine the presence of miRNAs in rumen fluid, and to investigate the possibility of miRNA-mediated cross-talk within the ruminal ecosystem. Rumen fluid samples from four cannulated Holstein cows were collected during two feeding regimes (forage and high-grain diet) and DNA and RNA were extracted for amplicon and small RNA sequencing. Epithelial biopsies were simultaneously collected to investigate the co-expression of miRNAs in papillae and rumen fluid. We identified 377 miRNAs in rumen fluid and 638 in rumen papillae, of which 373 were shared. Analysis of microbiota revealed 20 genera to be differentially abundant between the two feeding regimes, whereas no difference in miRNAs expression was detected. Correlations with at least one genus were found for 170 miRNAs, of which, 39 were highly significant (r > |0.7| and P < 0.01). Both hierarchical clustering of the correlation matrix and WGCNA analysis identified two main miRNA groups. Putative target and functional prediction analysis for the two groups revealed shared pathways with the predicted metabolic activities of the microbiota. Hence, our study supports the hypothesis of a cross-talk within the rumen at least partly mediated by miRNAs.

Shift of dietary carbohydrate source from milk to various solid feeds reshapes the rumen and fecal microbiome in calves.

The transition from milk to solid diets drastically impacts the gut microbiome of calves. We explored the microbial communities of ruminal fluid and feces of Holstein calves when fed milk on d 7 of life, and when fed solid feeds based on either medium- or high-quality hay with or without concentrate inclusion (70% in fresh matter) on d 91. Ruminal fluid and feces had distinct microbial compositions already on d 7, showing that niche specialization in early-life gut is rather diet-independent. Changes between d 7 and d 91 were accompanied by a general increase in microbial diversity. Solid diets differed largely in their carbohydrate composition, being reflected in major changes on d 91, whereby concentrate inclusion was the main driver for differences among groups and strongly decreased microbial diversity in both matrices. Fecal enterotyping revealed two clusters: concentrate-supplemented animals had an enterotype prevalent in Prevotella, Succinivibrio and Anaerovibrio, whereas the enterotype of animals without concentrate was dominated by fibrolytic Ruminococcaceae. Hay quality also affected microbial composition and, compared to medium-quality, high-quality hay reduced alpha-diversity metrics. Concluding, our study revealed that concentrate inclusion, more than hay quality, dictates the establishment of niche-specific, microbial communities in the rumen and feces of calves.

Characterization of microbial intolerances and ruminal dysbiosis towards different dietary carbohydrate sources using an in vitro model.

AIM: This study aimed to characterize the critical points for determining the development of dysbiosis associated with feed intolerances and ruminal acidosis. METHODS AND RESULTS: A metabologenomics approach was used to characterize dynamic microbial and metabolomics shifts using the rumen simulation technique (RUSITEC) by feeding native cornstarch (ST), chemically modified cornstarch (CMS), or sucrose (SU). SU and CMS elicited the most drastic changes as rapidly as 4 h after feeding. This was accompanied by a swift accumulation of d-lactate, and the decline of benzoic and malonic acid. A consistent increase in Bifidobacterium and Lactobacillus as well as a decrease in fibrolytic bacteria was observed for both CMS and ST after 24 h, indicating intolerances within the fibre degrading populations. However, an increase in Lactobacillus was already evident in SU after 8 h. An inverse relationship between Fibrobacter and Bifidobacterium was observed in ST. In fact, Fibrobacter was positively correlated with several short-chain fatty acids, while Lactobacillus was positively correlated with lactic acid, hexoses, hexose-phosphates, pentose phosphate pathway (PENTOSE-P-PWY), and heterolactic fermentation (P122-PWY). CONCLUSIONS: The feeding of sucrose and modified starches, followed by native cornstarch, had a strong disruptive effect in the ruminal microbial community. Feed intolerances were shown to develop at different rates based on the availability of glucose for ruminal microorganisms. SIGNIFICANCE AND IMPACT OF THE STUDY: These results can be used to establish patterns of early dysbiosis (biomarkers) and develop strategies for preventing undesirable shifts in the ruminal microbial ecosystem.

Short-term exposure to the mycotoxins zearalenone or fumonisins affects rumen fermentation and microbiota, and health variables in cattle.

Zearalenone (ZEN) and fumonisins (FUM) jeopardize fertility and health in cattle; yet, their toxigenic effects on rumen health and microbiota, both being crucial for animal health, are not clarified. This study determined the effects of a short-term exposure to ZEN or FUM on the rumen ecosystem, and further evaluated acute implications on health parameters. Six cows were fed a basal diet with 40% grain (dry matter basis) and exposed to either 5 mg of ZEN or 20 mg of FUM daily for two consecutive days each, separated by a 7-days washout period. The exposure to ZEN or FUM led to a reduction of Lachnospiraceae and Prevotellaceae in the rumen. Similarly, ZEN lowered the ruminal pH and total short-chain fatty acid concentration, despite increased rumination activity of the cows. Fumonisins increased the number of observed features and significantly impacted ß-diversity structure and metagenome predicted function. At the systemic level, FUM exposure suggested an immediate hepatotoxic effect, as evidenced by increased liver enzyme concentrations, which were accompanied by altered heart and respiratory rates. Similarly, ZEN increased the body temperature up to a mild fever. Concluding, short-term exposure to ZEN and FUM can harm the rumen ecosystem and acutely impair systemic health.

Bovine rumen epithelial miRNA-mRNA dynamics reveals post-transcriptional regulation of gene expression upon transition to high-grain feeding and phytogenic supplementation.

The rumen epithelium has a pivotal role in nutrient uptake and host health. This study aimed to explore the role of microRNAs (miRNAs) in the epithelial transcriptome during diet transition from forage to high-grain feeding and the modulation through supplementation with a phytogenic feed additive. Rumen biopsies were collected from 9 ruminally-cannulated non-lactating Holstein cows fed a baseline forage diet (FD) and then transitioned to high-grain feeding (HG; 65% concentrate on a dry matter basis). Cows were randomly allocated into a control group (CON, n = 5) and a group supplemented with a phytogenic feed additive (PHY, n = 4). MiRNA and mRNA sequencing was performed in parallel and transcripts were analyzed for differential expression, pathway enrichment analysis, and miRNA-mRNA interaction networks. We identified 527 miRNAs shared by all samples of the rumen epithelium, from which, bta-miR-21-5p, bta-miR-143 and bta-miR-24-3p were the most expressed. Six miRNAs were differentially expressed between CON and PHY and 8 miRNAs between FD and HG feeding, which were mainly associated with fat metabolism. Transcriptome analysis identified 9481 differentially expressed genes (DEGs) between FD and HG, whereas PHY supplementation resulted in 5 DEGs. DEGs were mainly involved in epithelium development and morphogenesis. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways associated with tricarboxylic acid and short chain fatty acid (SCFA) metabolism were enriched in DEGs between diets. MiRNA target prediction and anti-correlation analysis was used to construct networks and identify DEGs targeted by DE miRNAs responsive to diet or PHY. This study allowed the identification of potential miRNA regulation mechanisms of gene expression during transition from FD to HG feeding and phytogenic supplementation, evidencing a direct role of miRNAs in host responses to nutrition.

Fungal species and mycotoxins in mouldy spots of grass and maize silages in Austria.

Fungi and mycotoxins in silage can have detrimental consequences for both cattle and human health. This pilot study identified, via the routinary direct plating method, the dominant cultivable fungi in mouldy grass silages (GS) (n = 19) and maize silages (MS) (n = 28) from Austria. The profiles of regulated, modified, and emerging mycotoxins together with other fungal metabolites were analysed via LC-(ESI)MS/MS. Penicillium roqueforti, Saccharomyces spp., Geotrichum candidum, Aspergillus fumigatus and Monascus ruber were the most frequent fungal organisms identified. Other species including Mucor circinelloides, Fusarium spp. and Paecilomyces niveus were detected at lower frequencies. The presence of complex mixtures of toxic and potentially toxic compounds was evidenced by high levels and occurrences (≥ 50%) of Penicillium-produced compounds such as mycophenolic acid (MPA), roquefortines (ROCs), andrastins (ANDs) and marcfortine A. Mouldy silages contained toxins commonly produced by genus Fusarium (e.g. zearalenone (ZEN) and trichothecenes), Alternaria (like tenuazonic acid (TeA) and alternariol (AHO)) and Aspergillus (such as sterigmatocystin (STC)). Compared to those in GS, mouldy spots in MS presented significantly higher fungal counts and more diverse toxin profiles, in addition to superior levels of Fusarium spp., Penicillium spp. and total fungal metabolites. Generally, no correlation between mould counts and corresponding metabolites was detected, except for the counts of P. roqueforti, which were positively correlated with Penicillium spp. metabolites in mouldy MS. This study represents a first assessment of the fungal diversity in mouldy silage in Austria and highlights its potential role as a substantial contributor to contamination with complex mycotoxin mixtures in cattle diets.

Supplementing a Clay Mineral-Based Feed Additive Modulated Fecal Microbiota Composition, Liver Health, and Lipid Serum Metabolome in Dairy Cows Fed Starch-Rich Diets.

Starch-rich diets are a commonly adopted strategy in order to sustain high milk yields in dairy cows. However, these diets are known to increase the risk of gut dysbiosis and related systemic health disorders. This study aimed to evaluate the effects of supplementing a clay mineral-based feed additive (CM; Mycofix® Plus, BIOMIN) on fecal microbiota structure, fecal short-chain fatty acid (SCFA) fermentation, serum metabolome, and liver health in primiparous (PP, n = 8) and multiparous (MP, n = 16) early-lactation Simmental cows (737 ± 90 kg of live body weight). Cows were randomly assigned to either a control or CM group (55 g per cow and day) and transitioned from a diet moderate in starch (26.3 ± 1.0%) to a high starch diet (32.0 ± 0.8%). Supplementation of CM reversed the decrease in bacterial diversity, richness, and evenness (p < 0.05) during high-starch diet, demonstrating that CM supplementation efficiently eased hindgut dysbiosis. The CM treatment reduced levels of Lactobacillus in PP cows during starch-rich feeding and elevated fecal pH, indicating a healthier hindgut milieu compared with that in control. Butyrate and propionate levels were modulated by CM supplementation, with butyrate being lower in CM-treated MP cows, whereas propionate was lower in MP but higher in PP cows. Supplementing CM during high-starch feeding increased the concentrations of the main primary bile salts and secondary bile acids in the serum and improved liver function in cows as indicated by reduced levels of glutamate dehydrogenase and γ-glutamyl-transferase, as well as higher serum albumin and triglyceride concentrations. These changes and those related to lipid serum metabolome were more pronounced in PP cows as also corroborated by relevance network analysis.

Unveiling the Bovine Epimural Microbiota Composition and Putative Function.

Numerous studies have used the 16S rRNA gene target in an attempt to characterize the structure and composition of the epimural microbiota in cattle. However, comparisons between studies are challenging, as the results show large variations associated with experimental protocols and bioinformatics methodologies. Here, we present a meta-analysis of the rumen epimural microbiota from 11 publicly available amplicon studies to assess key technical and biological sources of variation between experiments. Using the QIIME2 pipeline, 332 rumen epithelial microbiota samples were analyzed to investigate community structure, composition, and functional potential. Despite having a significant impact on microbial abundance, country of origin, farm, hypervariable region, primer set, animal variability, and biopsy location did not obscure the identification of a core microbiota. The bacterial genera Campylobacter, Christensenellaceae R-7 group, Defluviitaleaceae UCG-011, Lachnospiraceae UCG-010, Ruminococcaceae NK4A214 group, Ruminococcaceae UCG-010, Ruminococcaceae UCG-014, Succiniclasticum, Desulfobulbus, and Comamonas spp. were found in nearly all epithelium samples (>90%). Predictive analysis (PICRUSt) was used to assess the potential functions of the epithelial microbiota. Regularized canonical correlation analysis identified several pathways associated with the biosynthesis of precursor metabolites in Campylobacter, Comamonas, Desulfobulbus, and Ruminococcaceae NK4A214, highlighting key metabolic functions of these microbes within the epithelium.

Natural Occurrence of Escherichia coli-Infecting Bacteriophages in Clinical Samples.

The interaction between bacteriophages, bacteria and the human host as a tripartite system has recently captured attention. The taxonomic diversity of bacteriophages, as a natural parasite of bacteria, still remains obscure in human body biomes, representing a so-called "viral dark matter." Here, we isolated and characterized coliphages from blood, urine and tracheal aspirates samples collected at a tertiary care hospital in Austria. Phages were more often isolated from blood, followed by urine and tracheal aspirates. Phylogenetic analysis and genome comparisons allowed the identification of phages belonging to the Tunavirinae subfamily, and to the Peduovirus and Tequintavirus genera. Tunavirinae phages cluster together and are found in samples from 14 patients, suggesting their prevalence across a variety of human samples. When compared with other phage genomes, the highest similarity level was at 87.69% average nucleotide identity (ANI), which suggests that these are in fact a newly isolated phage species. Tequintavirus phages share a 95.90% with phage 3_29, challenging the ANI threshold currently accepted to differentiate phage species. The isolated phages appear to be virulent, with the exception of the Peduovirus members, which are integrative and seem to reside as prophages in bacterial genomes.

Characterization of Bacteria and Inducible Phages in an Intensive Care Unit.

Intensive care units (ICUs) are critical locations for the transmission of pathogenic and opportunistic microorganisms. Bacteria may develop a synergistic relationship with bacteriophages and more effectively resist various stresses, enabling them to persist despite disinfection and antimicrobial treatment. We collected 77 environmental samples from the surroundings of 12 patients with infection/colonizations by Escherichia coli, Staphylococcus aureus or Klebsiella spp in an ICU in Austria. Surface swabs were tested for lytic phages and bacterial isolates for mitomycin C-inducible prophages. No lytic bacteriophages were detected, but S. aureus was isolated from the surroundings of all patients. About 85% of the colonies isolated from surface samples were resistant to antimicrobials, with 94% of them multidrug resistant. Two inducible temperate bacteriophages-myovirus vB_EcoM_P5 and siphovirus vB_SauS_P9-were recovered from two clinical isolates. Staphylococci phage vB_SauS_P9 lysed S. aureus isolates from the surface swabs collected from the surroundings of three patients. No transductants were obtained on propagation in phage-sensitive antimicrobial-resistant isolates. The two phages were sensitive to 0.25% (v/v) of the disinfectant TPH Protect, which eliminated viable phages after 15 min. Coliphage vB_EcoM_P5 was inactivated at 70 °C and staphylococci phage vB_SauS_P9 at 60 °C after 60 min.

Draft Genome Sequence of Escherichia coli DSM 12242, a Highly Efficient Host Strain for the Isolation of Somatic Coliphages.

Here, we report the draft genome sequence and characterization of the commercial strain Escherichia coli DSM 12242 (=ATCC 13706/60 =NZRM 3262) derived from strain C (ATCC 13706), which is suitable for the isolation of coliphages from environmental and clinical samples.