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.

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.

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.

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.

Evaluation of circulating microRNA profiles in blood as potential candidate biomarkers in a subacute ruminal acidosis cow model - a pilot study

BACKGROUND

Subacute ruminal acidosis (SARA) is a metabolic disorder often observed in high-yielding dairy cows, that are fed diets high in concentrates. We hypothesized that circulating miRNAs in blood of cows could serve as potential candidate biomarkers to detect animals with metabolic dysbalances such as SARA. MicroRNAs (miRNAs) are a class of small non-coding RNAs, serving as regulators of a plethora of molecular processes. To test our hypothesis, we performed a pilot study with non-lactating Holstein-Friesian cows fed a forage diet (FD; 0% concentrate, n = 4) or a high-grain diet (HG; 65% concentrate, n = 4) to induce SARA. Comprehensive profiling of miRNA expression in plasma and leucocytes were performed by next generation sequencing (NGS). The success of our model to induce SARA was evaluated based on ruminal pH and was evidenced by increased time spent with a pH threshold of 5.8 for an average period of 320 min/d.

RESULTS

A total of 520 and 730 miRNAs were found in plasma and leucocytes, respectively. From these, 498 miRNAs were shared by both plasma and leucocytes, with 22 miRNAs expressed exclusively in plasma and 232 miRNAs expressed exclusively in leucocytes. Differential expression analysis revealed 10 miRNAs that were up-regulated and 2 that were down-regulated in plasma of cows when fed the HG diet. A total of 63 circulating miRNAs were detected exclusively in the plasma of cows with SARA, indicating that these animals exhibited a higher number and diversity of circulating miRNAs. Considering the total read counts of miRNAs expressed when fed the HG diet, differentially expressed miRNAs ( log₂ fold change) and known function, we have identified bta-miR-11982, bta-miR-1388-5p, bta-miR-12034, bta-miR-2285u, and bta-miR-30b-3p as potential candidates for SARA-biomarker in cows by NGS. These were further subjected to validation using small RNA RT-qPCR, confirming the promising role of bta-miR-30b-3p and bta-miR-2285.

CONCLUSION

Our data demonstrate that dietary change impacts the release and expression of miRNAs in systemic circulation, which may modulate post-transcriptional gene expression in cows undergoing SARA. Particularly, bta-miR-30b-3p and bta-miR-2285 might serve as promising candidate biomarker predictive for SARA and should be further validated in larger cohorts.

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.

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.

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 fiber 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 (SCFA), 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 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 β-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.

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.

Feeding dairy cows bakery by-products enhanced nutrient digestibility, but affected fecal microbial composition and pH in a dose-dependent manner

We reported recently that adding bakery by-products (BP) to the diets of dairy cows up to 30% improved performance and rumen pH, but caused major shifts in the nutrient profile and availability, likely modifying nutrient degradation patterns throughout the gastrointestinal tract. The aim of this study was to investigate the effects of the gradual replacement of cereals by BP on the apparent total-tract digestibility (ATTD), the fermentation patterns, and the microbial community in feces of dairy cows. Twenty-four mid-lactating Simmental cows (149 ± 22.3 days in milk, 756 ± 89.6 kg of initial body weight) were fed a total mixed ration ad libitum (fresh feed was offered twice per day) containing a 50:50 ratio of forage to concentrate (dry matter basis) throughout the experiment. The trial lasted 5 wk, whereby the first week was used for baseline measurements, in which all cows received the same diet, without BP. Cows were then randomly allocated into 3 groups differing in the BP content of diets (0% BP, 15% BP, and 30% BP on a DM basis) and fed for 4 wk. Fecal samples were taken for analysis of pH, volatile fatty acids (VFA), and 16S rRNA gene sequencing. The inclusion of BP resulted in an increase of ether extract and sugars, and a reduction of starch and neutral detergent fiber in the diet. Feeding BP linearly increased the ATTD of almost all nutrients resulting in up to 2 kg more digestible organic matter intake (DOMI). Increasing BP level up to 30% increased fecal total VFA concentration and decreased the pH. The proportion of butyrate in feces increased linearly, but the proportion of all other VFA was not affected by BP-feeding. The richness and diversity indices of the fecal microbiota linearly declined by the inclusion of BP. The cellulolytic phyla Fibrobacteres decreased, whereas amylolytic phyla, such as Proteobacteria, increased. Overall, results showed that feeding BP linearly increased ATTD and DOMI, but impaired fecal microbial diversity and pH. In the interest of the optimization of BP inclusion in the dairy cows' feeding, a dietary level between 15 to 30% of BP might be a better compromise than 30% in terms of an enhanced DOMI and performance with still lowered risk of hindgut dysbiosis, but this will require further investigations.

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.

Distinct serum metabolomic signatures of multiparous and primiparous dairy cows switched from a moderate to high-grain diet during early lactation

INTRODUCTION

Feeding of high-grain diets is common in cows during early lactation, but increases the odds of metabolic derailments, which can likely be detected as undesirable shifts in the serum metabolome signature.

OBJECTIVES

The present study aimed to identify the metabolic signatures of the serum metabolome of early lactation dairy cows switched from a moderate to a high-grain diet.

METHODS

Targeted ESI-LC-MS/MS-based metabolomics was used to characterize metabolic alterations in the serum of early lactation multiparous (MP, n = 16) and primiparous (PP, n = 8) Simmental cows, according to parity and feeding phase. Data were analysed using different data mining approaches.

RESULTS

Carnitine, acetylcarnitine, propionoylcarnitine, amino acid related compounds cis-4-hydroxyproline, trans-4-hydroxyproline, proline betaine, lysophosphatidylcholine PC a C16:1 and phosphatidylcholine PC ae C36:0 were identified as the key metabolites distinguishing MP from PP cows. A different serum metabolite composition during moderate and high-grain diet was also evident. Notably, cows fed high grain diet had higher serum concentrations of primary bile acids and triglycerides, but lower levels of conjugated bile acids and carboxylic acids during the first week in grain. Amino acids valine, cystine and taurine together with lysophosphatidylcholine PC a C26:0 and several phosphatidylcholines were classified as important features for cluster separation.

CONCLUSIONS

Our study greatly expands earlier observations on dietary effects on serum metabolome composition of cows. The altered metabolomic fingerprints clearly distinguishable by diet and cow parity hold potential to be used as early diagnostic tools for cows experiencing grain-induced metabolic disturbances.

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.

Mycobacterial Response to Organic Solvents and Possible Implications on Cross-Resistance With Antimicrobial Agents

Mycobacterium vaccae, a bacterium found in soil, has been receiving attention as adjuvant to antituberculosis treatment, vaccines and immunotherapies and even as antidepressant. This bacterium is also able to degrade several pollutants, including aromatic compounds. The increasing presence of organic solvents in the environment may lead to M. vaccae adapted populations. A possible relationship between solvent tolerance and decreased susceptibility to other types of chemicals, including antibiotics, may pose a problem during opportunistic infections. The present study thus aimed at assessing if solvent adapted cells presented higher tolerance to antibiotics and efflux pump inhibitors (EPIs). M. vaccae cells were able to thrive and grow in the presence of up 20% (v/v) glycerol, 5% (v/v) ethanol, 1% (v/v) methyl tert-butyl ether (MTBE) and 0.1% (v/v) toluene. During adaptation to increasing concentration of ethanol and MTBE, the cells changed their fatty acid profile, zeta potential and morphology. Adapted cells acquired an improved tolerance toward the EPIs thioridazine and omeprazole, but became more susceptible to the antibiotics levofloxacin and teicoplanin when compared with non-adapted cells.

Microbiota and Particulate Matter Assessment in Portuguese Optical Shops Providing Contact Lens Services

The aim of this work was to assess the microbiota (fungi and bacteria) and particulate matter in optical shops, contributing to a specific protocol to ensure a proper assessment. Air samples were collected through an impaction method. Surface and equipment swab samples were also collected side-by-side. Measurements of particulate matter were performed using portable direct-reading equipment. A walkthrough survey and checklist was also applied in each shop. Regarding air sampling, eight of the 13 shops analysed were above the legal requirement and 10 from the 26 surfaces samples were overloaded. In three out of the 13 shops fungal contamination in the analysed equipment was not detected. The bacteria air load was above the threshold in one of the 13 analysed shops. However, bacterial counts were detected in all sampled equipment. Fungi and bacteria air load suggested to be influencing all of the other surface and equipment samples. These results reinforce the need to improve air quality, not only to comply with the legal requirements, but also to ensure proper hygienic conditions. Public health intervention is needed to assure the quality and safety of the rooms and equipment in optical shops that perform health interventions in patients.

Cytotoxic and Inflammatory Potential of Air Samples from Occupational Settings with Exposure to Organic Dust

Organic dust and related microbial exposures are the main inducers of several respiratory symptoms. Occupational exposure to organic dust is very common and has been reported in diverse settings. In vitro tests using relevant cell cultures can be very useful for characterizing the toxicity of complex mixtures present in the air of occupational environments such as organic dust. In this study, the cell viability and the inflammatory response, as measured by the production of pro-inflammatory cytokines tumor necrosis factor-α (TNFα) and interleukin-1 β (IL-1β), were determined in human macrophages derived from THP-1 monocytic cells. These cells were exposed to air samples from five occupational settings known to possess high levels of contamination of organic dust: poultry and swine feed industries, waste sorting, poultry production and slaughterhouses. Additionally, fungi and particle contamination of those settings was studied to better characterize the organic dust composition. All air samples collected from the assessed workplaces caused both cytotoxic and pro-inflammatory effects. The highest responses were observed in the feed industry, particularly in swine feed production. This study emphasizes the importance of measuring the organic dust/mixture effects in occupational settings and suggests that differences in the organic dust content may result in differences in health effects for exposed workers.

Fungal contamination in green coffee beans samples: A public health concern

Studies on the microbiology of coffee cherries and beans have shown that the predominant toxigenic fungal genera (Aspergillus and Penicillium) are natural coffee contaminants. The aim of this study was to investigate the distribution of fungi in Coffea arabica L. (Arabica coffee) and Coffea canephora L. var. robusta (Robusta coffee) green coffee samples obtained from different sources at the pre-roasting stage. Twenty-eight green coffee samples from different countries of origin (Brazil, Timor, Honduras, Angola, Vietnam, Costa Rica, Colombia, Guatemala, Nicaragua, India, and Uganda) were evaluated. The fungal load in the contaminated samples ranged from 0 to 12330 colony forming units (CFU)/g, of which approximately 67% presented contamination levels below 1500 CFU/g, while 11% exhibited intermediate contamination levels between 1500 and 3000 CFU/g. Contamination levels higher than 3000 CFU/g were found in 22% of contaminated coffee samples. Fifteen different fungi were isolated by culture-based methods and Aspergillus species belonging to different sections (complexes). The predominant Aspergillus section detected was Nigri (39%), followed by Aspergillus section Circumdati (29%). Molecular analysis detected the presence of Aspergillus sections Fumigati and Circumdati. The% coffee samples where Aspergillus species were identified by culture-based methods were 96%. Data demonstrated that green coffee beans samples were contaminated with toxigenic fungal species. Since mycotoxins may be resistant to the roasting process, this suggests possible exposure to mycotoxins through consumption of coffee. Further studies need to be conducted to provide information on critical points of coffee processing, such that fungal contamination may be reduced or eliminated and thus exposure to fungi and mycotoxins through coffee handling and consumption be prevented.