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.

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

Anaerobic fungi (AF) play an essential role in feed conversion due to their potent fiber degrading enzymes and invasive growth. Much has been learned about this unusual fungal phylum since the paradigm shifting work of Colin Orpin in the 1970s, when he characterized the first AF. Molecular approaches targeting specific phylogenetic marker genes have facilitated taxonomic classification of AF, which had been previously been complicated by the complex life cycles and associated morphologies. Although we now have a much better understanding of their diversity, it is believed that there are still numerous genera of AF that remain to be described in gut ecosystems. Recent marker-gene based studies have shown that fungal diversity in the herbivore gut is much like the bacterial population, driven by host phylogeny, host genetics and diet. Since AF are major contributors to the degradation of plant material ingested by the host animal, it is understandable that there has been great interest in exploring the enzymatic repertoire of these microorganisms in order to establish a better understanding of how AF, and their enzymes, can be used to improve host health and performance, while simultaneously reducing the ecological footprint of the livestock industry. A detailed understanding of AF and their interaction with other gut microbes as well as the host animal is essential, especially when production of affordable high-quality protein and other animal-based products needs to meet the demands of an increasing human population. Such a mechanistic understanding, leading to more sustainable livestock practices, will be possible with recently developed -omics technologies that have already provided first insights into the different contributions of the fungal and bacterial population in the rumen during plant cell wall hydrolysis.

/pdf/anaerobic-fungi-past-present-and-future-y6vgpkw2o0.pdf

Anaerobic Fungi: Past, Present, and Future.

The anaerobic rumen fungal community play a critical role in fibrous material degradation. However, there is a lack of data describing the composition of anaerobic rumen fungal community of full grazing ruminants in the Qinghai-Tibetan Plateau. For this reason, we employed the next-generation sequencing technique to elucidate the rumen fungal structure composition and evaluate the effects of host species on fungal communities. Community comparisons (Bray-Curtis index) between yak and Tibetan sheep revealed that the rumen fungal community was affected by host species (p < 0.05). The alpha diversity indices in the yak were significantly higher than in the Tibetan sheep and Small Tail Han sheep. Neocallimastigomycota was predominant regardless of host species. Within this phylum, unidentified genus of Neocallimastigaceae was the most dominant in all samples, followed by Piromyces and Orpinomyces. Moreover, the shared and unique OTUs in the rumen were identified and most of them belonged to the Orpinomyces. Co-occurrence network analysis identified that each animal species had their own keystone species and most of them were non-dominant flora. Our data indicate that host breeds override living environment as the key factor that determines fungal community in the rumen of grazing ruminants in the Qinghai-Tibetan Plateau.

Characterization of Anaerobic Rumen Fungal Community Composition in Yak, Tibetan Sheep and Small Tail Han Sheep Grazing on the Qinghai-Tibetan Plateau.

Effect of dietary corn gluten inclusion on rumen fermentation, microbiota and methane emissions in goats

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

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

Calcium propionate is a safe and reliable food and feed additive. It can be metabolized and absorbed by humans and animals as a precursor for glucose synthesis. In addition, calcium propionate provides essential calcium to mammals. In the perinatal period of dairy cows, many cows cannot adjust to the tremendous metabolic, endocrine, and physiological changes, resulting in ketosis and fatty liver due to a negative energy balance (NEB) or milk fever induced by hypocalcemia. On hot weather days, cow feed (TMR or silage) is susceptible to mildew, which produces mycotoxins. These two issues are closely related to dairy health and performance. Perinatal period metabolic disease significantly reduces cow production and increases the elimination rate because it causes major glucose and calcium deficiencies. Feeding a diet contaminated with mycotoxin leads to rumen metabolic disorders, a reduced reproductive rate (increased abortion rate), an increased number of milk somatic cells, and decreased milk production, as well as an increased occurrence of mastitis and hoof disease. Propionic acid is the primary gluconeogenic precursor in dairy cows and one of the safest mold inhibitors. Therefore, calcium propionate, which can be hydrolyzed into propionic acid and Ca2+ in the rumen, may be a good feed additive for alleviating NEB and milk fever in the perinatal period of dairy cows. It can also be used to inhibit TMR or silage deterioration in hot weather and regulate rumen development in calves. This paper reviews the application of calcium propionate in dairy cows.

https://www.mdpi.com/2076-2615/10/8/1336/pdf

Research on the Applications of Calcium Propionate in Dairy Cows: A Review

Overfeeding of high-concentrate diet (HC) frequently leads to subacute ruminal acidosis (SARA) in modern dairy cows’ production. Thiamine supplementation has been confirmed to attenuate HC induced SARA by increasing ruminal pH and ratio of acetate to propionate, and decreasing rumen lactate, biogenic amines and lipopolysaccharide (LPS). The effects of thiamine supplementation in HC on rumen bacteria and fungi profile had been detected in our previous studies, however, effects of thiamine supplementation in HC on rumen non-methanogen archaea is still unclear. The objective of the present study was therefore to investigate the effects of thiamine supplementation on ruminal archaea, especially non-methanogens in HC induced SARA cows. HC feeding significantly decreased dry matter intake, milk production, milk fat content, ruminal pH and the concentrations of thiamine and acetate in rumen fluid compared with control diet (CON) (P < 0.05), while the concentrations of propionate and ammonia-nitrogen (NH3-N) were significantly increased compared with CON (P < 0.05). These changes caused by HC were inversed by thiamine supplementation (P < 0.05). The taxonomy results showed that ruminal archaea ranged from 0.37 to 0.47% of the whole microbiota. Four characterized phyla, a number of Candidatus archaea and almost 660 species were identified in the present study. In which Euryarchaeota occupied the largest proportion of the whole archaea. Furthermore, thiamine supplementation treatment significantly increased the relative abundance of non-methanogens compared with CON and HC treatments. Thaumarchaeota was increased in HC compared with CON. Thiamine supplementation significantly increased Crenarchaeota, Nanoarchaeota and the Candidatus phyla, however decreased Thaumarchaeota compared with HC treatment. HC feeding significantly decreased ruminal pH and increased the content of NH3-N which led to N loss and the increase of the relative abundance of Thaumarchaeota. Thiamine supplementation increased ruminal pH, improved the activity of ammonia utilizing bacteria, and decreased Thaumarchaeota abundance to reduce the ruminal NH3 content and finally reduced N loss. Overall, these findings contributed to the understanding of thiamine’s function in dairy cows and provided new strategies to improve dairy cows’ health under high-concentrate feeding regime.

/pdf/metagenomic-insights-into-effects-of-thiamine-3tdcqyy4tr.pdf

Metagenomic insights into effects of thiamine supplementation on ruminal non-methanogen archaea in high-concentrate diets feeding dairy cows.

Estimating the feed intake of grazing herbivores is critical for determining their nutrition, overall productivity and utilization of grassland resources. A 17-day indoor feeding experiment was conducted to evaluate the potential use of Medicago sativa as a natural supplement for estimating the total feed intake of sheep. A total of 16 sheep were randomly assigned to four diets (four sheep per diet) containing a known amount of M. sativa together with up to seven forages common to typical steppes. The diets were: diet 1, M. sativa + Leymus chinensis + Puccinellia distans; diet 2, species in diet 1 + Phragmites australis; diet 3, species in diet 2 + Chenopodium album + Elymus sibiricus; and diet 4, species in diet 3 + Artemisia scoparia + Artemisia tanacetifolia. After faecal marker concentrations were corrected by individual sheep recovery, treatment mean recovery or overall recovery, the proportions of M. sativa and other dietary forages were estimated from a combination of alkanes and long-chain alcohols using a least-square procedure. Total intake was the ratio of the known intake of M. sativa to its estimated dietary proportion. Each dietary component intake was obtained using total intake and the corresponding dietary proportions. The estimated values were compared with actual values to assess the estimation accuracy. The results showed that M. sativa exhibited a distinguishable marker pattern in comparison to the other dietary forage species. The accuracy of the dietary composition estimates was significantly (P < 0.001) affected by both diet diversity and the faecal recovery method. The proportion of M. sativa and total intake across all diets could be accurately estimated using the individual sheep or the treatment mean recovery methods. The largest differences between the estimated and observed total intake were 2.6 g and 19.2 g, respectively, representing only 0.4% and 2.6% of the total intake. However, they were significantly (P < 0.05) biased for most diets when using the overall recovery method. Due to the difficulty in obtaining individual sheep recovery under field conditions, treatment mean recovery is recommended. This study suggests that M. sativa, a natural roughage instead of a labelled concentrate, can be utilized as a dietary supplement to accurately estimate the total feed intake of sheep indoors and further indicates that it has potential to be used in steppe grassland of northern China, where the marker patterns of M. sativa differ markedly from commonly occurring plant species.

Yuming Guo

Papers

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

Research on the Applications of Calcium Propionate in Dairy Cows: A Review

Metagenomic insights into effects of thiamine supplementation on ruminal non-methanogen archaea in high-concentrate diets feeding dairy cows.

The potential application of plant wax markers from alfalfa for estimating the total feed intake of sheep.