Qualified presumption of safety (QPS) was developed to provide a generic safety evaluation for biological agents to support EFSA's Scientific Panels. The taxonomic identity, body of knowledge, safety concerns and antimicrobial resistance are assessed. Safety concerns identified for a taxonomic unit (TU) are where possible to be confirmed at strain or product level, reflected by 'qualifications'. No new information was found that would change the previously recommended QPS TUs and their qualifications. The list of microorganisms notified to EFSA was updated with 54 biological agents, received between April and September 2019; 23 already had QPS status, 14 were excluded from the QPS exercise (7 filamentous fungi, 6 Escherichia coli, Sphingomonas paucimobilis which was already evaluated). Seventeen, corresponding to 16 TUs, were evaluated for possible QPS status, fourteen of these for the first time, and Protaminobacter rubrum, evaluated previously, was excluded because it is not a valid species. Eight TUs are recommended for QPS status. Lactobacillus parafarraginis and Zygosaccharomyces rouxii are recommended to be included in the QPS list. Parageobacillus thermoglucosidasius and Paenibacillus illinoisensis can be recommended for the QPS list with the qualification 'for production purposes only' and absence of toxigenic potential. Bacillus velezensis can be recommended for the QPS list with the qualification 'absence of toxigenic potential and the absence of aminoglycoside production ability'. Cupriavidus necator, Aurantiochytrium limacinum and Tetraselmis chuii can be recommended for the QPS list with the qualification 'production purposes only'. Pantoea ananatis is not recommended for the QPS list due to lack of body of knowledge in relation to its pathogenicity potential for plants. Corynebacterium stationis, Hamamotoa singularis, Rhodococcus aetherivorans and Rhodococcus ruber cannot be recommended for the QPS list due to lack of body of knowledge. Kodamaea ohmeri cannot be recommended for the QPS list due to safety concerns.

https://efsa.onlinelibrary.wiley.com/doi/pdf/10.2903/j.efsa.2020.5965

Update of the list of QPS-recommended biological agents intentionally added to food or feed as notified to EFSA 13: suitability of taxonomic units notified to EFSA until September 2020.

Introduction and Historical Considerations. Vitamin A. Vitamin D. Vitamin E. Vitamin K. Thiamin. Riboflavin. Niacin. Vitamin B6. Pantothenic Acid. Biotin. Folacin. Vitamin B12. Choline. Vitamin C. Vitamin-Like Substances. Essential Fatty Acids. Vitamin Supplementation. Bibliography. Appendix. Index.

Vitamin Source@@@Vitamins in Animal Nutrition: Comparative Aspects to Human Nutrition

Blackening and odorization of urban rivers: a bio-geochemical process

The purpose of this study was to examine the effects of two pasture feeding systems—perennial ryegrass (GRS) and perennial ryegrass and white clover (CLV)—and an indoor total mixed ration (TMR) system on the (a) rumen microbiome; (b) rumen fluid and milk metabolome; and (c) to assess the potential to distinguish milk from different feeding systems by their respective metabolomes. Rumen fluid was collected from nine rumen cannulated cows under the different feeding systems in early, mid and late lactation, and raw milk samples were collected from ten non-cannulated cows in mid-lactation from each of the feeding systems. The microbiota present in rumen liquid and solid portions were analysed using 16S rRNA gene sequencing, while 1H-NMR untargeted metabolomic analysis was performed on rumen fluid and raw milk samples. The rumen microbiota composition was not found to be significantly altered by any feeding system in this study, likely as a result of a shortened adaptation period (two weeks’ exposure time). In contrast, feeding system had a significant effect on both the rumen and milk metabolome. Increased concentrations of volatile fatty acids including acetic acid, an important source of energy for the cow, were detected in the rumen of TMR and CLV-fed cows. Pasture feeding resulted in significantly higher concentrations of isoacids in the rumen. The ruminal fluids of both CLV and GRS-fed cows were found to have increased concentrations of p-cresol, a product of microbiome metabolism. CLV feeding resulted in increased rumen concentrations of formate, a substrate compound for methanogenesis. The TMR feeding resulted in significantly higher rumen choline content, which contributes to animal health and milk production, and succinate, a product of carbohydrate metabolism. Milk and rumen-fluids were shown to have varying levels of dimethyl sulfone in each feeding system, which was found to be an important compound for distinguishing between the diets. CLV feeding resulted in increased concentrations of milk urea. Milk from pasture-based feeding systems was shown to have significantly higher concentrations of hippuric acid, a potential biomarker of pasture-derived milk. This study has demonstrated that 1H-NMR metabolomics coupled with multivariate analysis is capable of distinguishing both rumen-fluid and milk derived from cows on different feeding systems, specifically between indoor TMR and pasture-based diets used in this study.

Pasture Feeding Changes the Bovine Rumen and Milk Metabolome

Enteric methane emissions are the single largest source of direct greenhouse gas emissions (GHG) in beef and dairy value chains and a substantial contributor to anthropogenic methane emissions globally. In late 2019, the World Wildlife Fund (WWF), the Advanced Research Projects Agency-Energy (ARPA-E) and the Foundation for Food and Agriculture Research (FFAR) convened approximately 50 stakeholders representing research and production of seaweeds, animal feeds, dairy cattle, and beef and dairy foods to discuss challenges and opportunities associated with the use of seaweed-based ingredients to reduce enteric methane emissions. This Perspective article describes the considerations identified by the workshop participants and suggests next steps for the further development and evaluation of seaweed-based feed ingredients as enteric methane mitigants. Although numerous compounds derived from sources other than seaweed have been identified as having enteric methane mitigation potential, these mitigants are outside the scope of this article.

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Key Considerations for the Use of Seaweed to Reduce Enteric Methane Emissions From Cattle

The requirements of thiamine in adult ruminants are mainly met by ruminal bacterial synthesis, and thiamine deficiencies will occur when dairy cows overfed with high grain diet. However, there is limited knowledge with regard to the ruminal thiamine synthesis bacteria, and whether thiamine deficiency is related to the altered bacterial community by high grain diet is still unclear. To explore thiamine synthesis bacteria and the response of ruminal microbiota to high grain feeding and thiamine supplementation, six rumen-cannulated Holstein cows were randomly assigned into a replicated 3×3 Latin square design trial. Three treatments were control diet (CON, 20% dietary starch, DM basis), high grain diet (HG, 33.2% dietary starch, DM basis) and high grain diet supplemented with 180 mg thiamine/kg DMI (HG+T). On day 21 of each period, rumen content samples were collected at 3 h postfeeding. Ruminal thiamine concentration was detected by high performance liquid chromatography. The microbiota composition was determined using Illumina MiSeq sequencing of 16S rRNA gene. Cows receiving thiamine supplementation had greater ruminal pH value, acetate and thiamine content in the rumen. Principal coordinate analysis and similarity analysis indicated that HG feeding and thiamine supplementation caused a strong shift in bacterial composition and structure in the rumen. At the genus level, compared with CON group, the relative abundances of 19 genera were significantly changed by HG feeding. Thiamine supplementation increased the abundance of cellulolytic bacteria including Bacteroides, Ruminococcus 1, Pyramidobacter, Succinivibrio and Ruminobacter, and their increases enhanced the fiber degradation and ruminal acetate production in HG+T group. Christensenellaceae R7, Lachnospira, Succiniclasticum, and Ruminococcaceae NK4A214 exhibited a negative response to thiamine supplementation. Moreover, correlation analysis revealed that ruminal thiamine concentration was positively correlated with Bacteroides, Ruminococcus 1, Ruminobacter, Pyramidobacter and Fibrobacter. Taken together, we concluded that Bacteroides, Ruminococcus 1, Ruminobacter, Pyramidobacter and Fibrobacter in rumen content may be associated with thiamine synthesis or thiamine is required for their growth and metabolism. In addition, thiamine supplementation can potentially improve rumen function, as indicated by greater numbers of cellulolytic bacteria within the rumen. These findings facilitate understanding of bacterial thiamine synthesis within rumen and thiamine’s function in dairy cows.

/pdf/illumina-sequencing-approach-to-characterize-thiamine-3v4dz1tqwk.pdf

Illumina Sequencing Approach to Characterize Thiamine Metabolism Related Bacteria and the Impacts of Thiamine Supplementation on Ruminal Microbiota in Dairy Cows Fed High-Grain Diets

The rumen microbial complex adaptive mechanism invalidates various methane (CH4) mitigation strategies. Shifting the hydrogen flow towards alternative electron acceptors, such as propionate, was considered to be a meaningful mitigation strategy. A completely randomized design was applied in in vitro incubation to investigate the effects of replacing forage fiber with nonforage fiber sources (NFFS) in diets on methanogenesis, hydrogen metabolism, propionate production and the methanogenic and bacterial community. There are two treatments in the current study, CON (a basic total mixed ration) and TRT (a modified total mixed ration). The dietary treatments were achieved by partly replacing forage fiber with NFFS (wheat bran and soybean hull) to decrease forage neutral detergent fiber (fNDF) content from 24.0% to 15.8%, with the composition and inclusion rate of other dietary ingredients remaining the same in total mixed rations. The concentrations of CH4, hydrogen (H2) and volatile fatty acids were determined using a gas chromatograph. The archaeal and bacterial 16S rRNA genes were sequenced by Miseq high-throughput sequencing and used to reveal relative the abundance of methanogenic and bacterial communities. The results revealed that the concentration of propionate was significantly increased, while the concentration of acetate and the acetate to propionate ratio were not affected by treatments. Compared with CON, the production of H2 increased by 8.45% and the production of CH4 decreased by 14.06%. The relative abundance of Methanomassiliicoccus was significantly increased, but the relative abundance of Methanobrevibacter tended to decrease in TRT group. At the bacterial phylum level, the TRT group significantly decreased the relative abundance of Firmicutes and tended to increase the relative abundance of Bacteroidetes. The replacement of forage fiber with NFFS in diets can affect methanogenesis by shifting the hydrogen flow towards propionate, and part is directed to H2 in vitro. The shift was achieved by a substitution of Firmicutes by Bacteroidetes, another substitution of Methanobrevibacter by Methanomassiliicoccus. Theoretical predictions of displacements of H2 metabolism from methanogenesis to propionate production was supported by the dietary intervention in vitro.

Shifts of Hydrogen Metabolism From Methanogenesis to Propionate Production in Response to Replacement of Forage Fiber With Non-forage Fiber Sources in Diets in vitro.

As the co-enzyme of pyruvate dehydrogenase and α-ketoglutarate dehydrogenase, thiamine plays a critical role in carbohydrate metabolism in dairy cows. Apart from feedstuff, microbial thiamine synthesis in the rumen is the main source for dairy cows. However, the amount of ruminal thiamine synthesis, which is influenced by dietary N levels and forage to concentrate ratio, varies greatly. Notably, when dairy cows are overfed high-grain diets, subacute ruminal acidosis (SARA) occurs and results in thiamine deficiency. Thiamine deficiency is characterised by decreased ruminal and blood thiamine concentrations and an increased blood thiamine pyrophosphate effect to >45 %. Thiamine deficiency caused by SARA is mainly related to the increased thiamine requirement during high grain feeding, decreased bacterial thiamine synthesis in the rumen, increased thiamine degradation by thiaminase, and decreased thiamine absorption by transporters. Interestingly, thiamine deficiency can be reversed by exogenous thiamine supplementation in the diet. Besides, thiamine supplementation has beneficial effects in dairy cows, such as increased milk and component production and attenuated SARA by improving rumen fermentation, balancing bacterial community and alleviating inflammatory response in the ruminal epithelium. However, there is no conclusive dietary thiamine recommendation for dairy cows, and the impacts of thiamine supplementation on protozoa, solid-attached bacteria, rumen wall-adherent bacteria and nutrient metabolism in dairy cows are still unclear. This knowledge is critical to understand thiamine status and function in dairy cows. Overall, the present review described the current state of knowledge on thiamine nutrition in dairy cows and the major problems that must be addressed in future research.

/pdf/thiamine-status-metabolism-and-application-in-dairy-cows-a-1rm74e2a12.pdf

Thiamine status, metabolism and application in dairy cows: a review.

Ruminal thiamine deficiencies occur when dairy cows are overfed with high-concentrate diet, and thiamine supplementation has been proved to attenuate high-concentrate diet induced SARA. However, there is limited knowledge of the relationship between thiamine supplementation in high-concentrate diets and ruminal fungi. In order to investigate the impacts of thiamine supplementation on ruminal fungi, twelve Chinese Holstein dairy cows were randomly assigned into three treatments: control diet (CON; 20% starch, dry matter basis), high-concentrate diet (HC; 33.2% starch, dry matter basis) and high-concentrate diet supplemented with 180 mg thiamine/kg dry matter intake. Dry matter intake and milk production were recorded during the experimental periods. On day 21, rumen fluid samples were collected at 3 h postfeeding and ruminal pH, thiamine concentration and volatile fatty acids were measured. Metagenome sequencing method was conducted to detect ruminal fungi composition. Feeding HC significantly decreased dry matter intake, milk production, ruminal pH, ruminal acetate and thiamine concentration, however, significantly increased propionate and isovalerate (P < 0.05). These changes were inversed by thiamine supplementation (P < 0.05). Totally, seven phyla and almost 1050 species of rumen fungi were identified across all samples in which especially, 3 genera and 10 species of strictly anaerobic fungi phylum Neocallimastigomycota was found. Principal coordinate analysis indicated that feeding HC and thiamine supplementation caused a significant inverse in ruminal fungi composition. Feeding HC significantly decreased the abundance of fungi compared with CON (P < 0.05) while thiamine supplementation significantly increased the abundance of ruminal fungi (P < 0.05). These results indicated that thiamine supplementation may effectively attenuate rumen metabolic disorder caused by HC diet through buffering the ruminal pH, shifting the rumen fermentation pattern and increasing the abundance of ruminal fungi. The findings in this study could therefore contribute to the further understanding of the mechanism of thiamine’s function in dairy cows.

/pdf/metagenome-sequencing-to-analyze-the-impacts-of-thiamine-3a8hwljua1.pdf

Metagenome sequencing to analyze the impacts of thiamine supplementation on ruminal fungi in dairy cows fed high-concentrate diets.

With the improvement in the intense genetic selection of dairy cows, advanced management strategies, and improved feed quality and disease control, milk production level has been greatly improved. However, the negative energy balance (NEB) is increasingly serious at the postpartum stage because the intake of nutrients cannot meet the demand of quickly improved milk production. The NEB leads to a large amount of body fat mobilization and consequently the elevated production of ketones, which causes metabolic diseases such as ketosis and fatty liver. The high milk production of dairy cows in early lactation aggravates NEB. The metabolic diseases lead to metabolic disorders, a decrease in reproductive performance, and lactation performance decline, seriously affecting the health and production of cows. Propylene glycol (PG) can alleviate NEB through gluconeogenesis and inhibit the synthesis of ketone bodies. In addition, PG improves milk yield, reproduction, and immune performance by improving plasma glucose and liver function in ketosis cows, and reduces milk fat percentage. However, a large dose of PG (above 500 g/d) has toxic and side effects in cows. The feeding method used was an oral drench. The combination of PG with some other additives can improve the effects in preventing ketosis. Overall, the present review summarizes the recent research progress in the impacts of NEB in dairy cows and the properties of PG in alleviating NEB and reducing the risk of ketosis.

https://www.mdpi.com/2076-2615/10/9/1526/pdf

Xuemei Nan

Papers

Illumina Sequencing Approach to Characterize Thiamine Metabolism Related Bacteria and the Impacts of Thiamine Supplementation on Ruminal Microbiota in Dairy Cows Fed High-Grain Diets

Shifts of Hydrogen Metabolism From Methanogenesis to Propionate Production in Response to Replacement of Forage Fiber With Non-forage Fiber Sources in Diets in vitro.

Thiamine status, metabolism and application in dairy cows: a review.

Metagenome sequencing to analyze the impacts of thiamine supplementation on ruminal fungi in dairy cows fed high-concentrate diets.

Effects of Propylene Glycol on Negative Energy Balance of Postpartum Dairy Cows