Background Ear and tail lesions are prevalent indicators of impaired welfare observed in pig production with different multifactorial causes. Understanding the progression of ear and tail lesions over time is important to implement preventative strategies on commercial pig farms. Therefore, this case study aimed to provide a detailed account of patterns of ear and tail lesions in pigs on a single commercial farm during the grower-finisher period. Case presentation A total of 1,676 12-week old pigs (n = 773 females and n = 903 males, all tail docked) were followed from arrival to the grower facilities until transferred to the finisher stage on a commercial pig farm in Ireland. Pigs were individually weighed and inspected for the severity of fresh ear and tail lesions (score 0–4) on transfer to the first grower (24.9 ± 5.33 kg, 12 weeks of age, n = 1,676 pigs), second grower (33.3 ± 7.04 kg, 14 weeks of age, n = 1,641 pigs), and finisher stage (60.2 ± 7.74 kg, 18 weeks of age, n = 1,626 pigs). Due to the low number of pigs with high scores, ear lesions were classified as no (score 0), mild (score 1), moderate (score 2) and severe (score ≥ 3) and tail lesions were classified as no (score 0), mild (score 1), and moderate-to-severe (score ≥ 2). Ear lesions were more prevalent than tail lesions at each inspection. There were approx. 19% of pigs with ear lesions at all three inspections but no pigs presented with tail lesions at all three inspections. When considering the specific severity categories, we observed 32 different ear lesion score combinations and 15 different tail lesion score combinations across the three inspections. Conclusion The high number of observed patterns of ear and tail lesions suggest large individual variability in lesion progression. Ear lesions were more of an issue than tail lesions and little is known about this health and welfare problem indicating that further research into causes and management strategies is needed.

The production of milk must be balanced with the sustainable consumption of water resources to ensure the future sustainability of the global dairy industry. Thus, this review article aimed to collate and summarize the literature in the dairy water-usage domain. While green water use (e.g., rainfall) was found to be largest category of water use on both stall and pasture-based dairy farms, on-farm blue water (i.e., freshwater) may be much more susceptible to local water shortages due to the nature of its localized supply through rivers, lakes, or groundwater aquifers. Research related to freshwater use on dairy farms has focused on monitoring, modeling, and analyzing the parlor water use and free water intake of dairy cows. Parlor water use depends upon factors related to milk precooling, farm size, milking systems, farming systems, and washing practices. Dry matter intake is a prominent variable in explaining free water intake variability; however, due to the unavailability of accurate data, some studies have reported moving away from dry matter intake at the expense of prediction accuracy. Machine-learning algorithms have been shown to improve dairy water-prediction accuracy by 23%, which may allow for coarse model inputs without reducing accuracy. Accurate models of on-farm water use allow for an increased number of dairy farms to be used in water footprinting studies, as the need for physical metering equipment is mitigated.

The objective of this study was to compare the grazing efficiency of 30 perennial ryegrass varieties, differing in ploidy and heading date. Plots were grazed by lactating dairy cows and managed under a rotational grazing system with 19 grazing events occurring over two years. Pre-grazing and post-grazing compressed sward heights were measured with a rising plate meter. A mixed model was used to predict the post-grazing sward height of each variety based on year, grazing event, block and pre-grazing sward height. Residual grazed height (RGH) was derived as the difference between the actual and predicted post-grazing sward height and was used as the measure of grazing efficiency. Negative RGH values indicated that the actual herbage removed was greater than that predicted and so indicated a superior grazing efficiency. Varieties differed in their level of grazing efficiency (p < .001), with RGH values ranging from −0.38 to +0.34 cm. Tetraploid varieties exhibited significantly greater grazing efficiency performance than diploids (p < .001), with average RGH values of −0.13 and +0.13 cm respectively. A significant difference in grazing efficiency was found among recommended perennial ryegrass varieties that are not being recorded by mechanically harvested simulated grazing protocols. A variety reappraisal that included grazing efficiency could identify varieties capable of improving on-farm livestock productivity from grass.

The aim of this study was to assess the effect of tail lesion severity on skin temperature of slaughter pigs measured at the base of the tail and the ear by infrared thermography camera and to evaluate the association between the temperature measurements. Pigs were randomly selected in the lairage, containing ~200 pigs/pen. Tail lesions were scored according to severity, using a 0-4 scale. Tail lesion scores 0 and 1 were summed as it was difficult to distinguish healed lesions from mild lesions due to animal dirtiness. In total, 269 study pigs were imaged at the two locations. The effect of tail lesion score and sex of the pig on the highest temperature of the infrared image areas were analyzed using linear mixed models. Association between the tail base and ear base temperatures was evaluated using Pearson correlation. Skin temperature measured at the base of the tail was significantly lower for tails scored 0–1 than for all other tail lesion scores (P < 0.05). Pigs with tail lesion scored 2 had significantly lower skin temperatures at the base of the tail than pigs with tail lesion scored 3 or 4 (P < 0.05) while there was no difference in skin temperature at the base of the tail between pigs with tail lesion scored 3 and 4 (P > 0.05). Skin temperature measured at the ear base was significantly lower for pigs with tail lesion scored 0–1 than pigs of all other tail lesion scores (P < 0.05) with no difference between the other scores (P > 0.05). Furthermore, there was an association between the two measurements (r = 0.50; P < 0.001). The findings suggest that even pigs with moderate tail lesions (score 2) may have general inflammation and infection, evidenced by the elevated systemic temperature compared to pigs with none or mild tail lesion (score 0–1).

In spite of many initiatives to set up community or farmer-group-based seed production, there is little empirical evidence about the group functioning in producing and marketing quality seed. This article therefore aims to contribute to better understanding of the process and practice of seed potato cooperatives’ formation and operation in Chencha, Ethiopia. Our study specifically focused on why and how farmer groups organize, produce and market quality seed potato. We collected primary data from two seed potato cooperatives in three phases through interviews, focus group discussions, and field assessment and store inventories on bacterial wilt incidence. We found that the support to the establishing of the two seed potato cooperatives focused more on improving the members’ seed potato production capacity and less on building good governance in the seed chain. The experiences showed the tensions between prescriptive rules, collective action and individual interests which made it very hard to maintain quality seed standards and friendship at the same time. In general, the root of having weak seed cooperatives may not be the lack of intent towards building durable farmer groups. Rather, development practitioners did not take the set-up of strong farmer groups as an evolving process, which continually engages in diagnosis and responds to the emerging social as well as material challenges. The set-up of farmer-group-based seed production, therefore, needs to shift from ‘standard production models’ to an evolving model: an open and flexible model guided by trials, challenges and existing socio-technical and institutional realities.

Background Brown seaweeds are known to be a rich source of fiber with the presence of several non-digestible polysaccharides including laminarin, fucoidan and alginate. These individual polysaccharides have previously been shown to favorably alter the gut microbiota composition and activity albeit the effect of the collective brown seaweed fiber component on the microbiota remains to be determined. Methods This study investigated the effect of a crude polysaccharide-rich extract obtained from Laminaria digitata (CE) and a depolymerized CE extract (DE) on the gut microbiota composition and metabolism using an in vitro fecal batch culture model though metagenomic compositional analysis using 16S rRNA FLX amplicon pyrosequencing and short-chain fatty acid (SCFA) analysis using GC-FID. Results Selective culture analysis showed no significant changes in cultured lactobacilli or bifidobacteria between the CE or DE and the cellulose-negative control at any time point measured (0, 5, 10, 24, 36, 48 h). Following metagenomic analysis, the CE and DE significantly altered the relative abundance of several families including Lachnospiraceae and genera including Streptococcus, Ruminococcus and Parabacteroides of human fecal bacterial populations in comparison to cellulose after 24 h. The concentrations of acetic acid, propionic acid, butyric acid and total SCFA were significantly higher for both the CE and DE compared to cellulose after 10, 24, 36 and 48 h fermentation (p < 0.05). Furthermore, the acetate:propionate ratio was significantly reduced (p < 0.05) for both CD and DE following 24, 36 and 48 h fermentation. Conclusion The microbiota-associated metabolic and compositional changes noted provide initial indication of putative beneficial health benefits of L. digitata in vitro; however, research is needed to clarify if L. digitata-derived fiber can favorably alter the gut microbiota and confer health benefits in vivo.

The opportunities in the fields of probiotics and prebiotics to a great degree stem from what we can learn about how they influence the microbiota and interact with the host. We discuss recent insights, cutting-edge technologies and controversial results from the perspective of early career researchers innovating in these areas. This perspective emerged from the 2019 meeting of the International Scientific Association for Probiotics and Prebiotics - Student and Fellows Association (ISAPP-SFA). Probiotic and prebiotic research is being driven by genetic characterization and modification of strains, state-of-the-art in vitro, in vivo, and in silico techniques designed to uncover the effects of probiotics and prebiotics on their targets, and metabolomic tools to identify key molecules that mediate benefits on the host. These research tools offer unprecedented insights into the functionality of probiotics and prebiotics in the host ecosystem. Young scientists need to acquire these diverse toolsets, or form inter-connected teams to perform comprehensive experiments and systematic analysis of data. This will be critical to identify microbial structure and co-dependencies at body sites and determine how administered probiotic strains and prebiotic substances influence the host. This and other strategies proposed in this review will pave the way for translating the health benefits observed during research into real-life outcomes. Probiotic strains and prebiotic products can contribute greatly to the amelioration of global issues threatening society. The intent of this article is to provide an early career researcher’s perspective on where the biggest opportunities lie to advance science and impact human health.

Abstract Background The objective of this study was to examine the inter-relationships between pig farm management and facilities (as assessed by questionnaire) and post-mortem lung lesion (lung score assesment), which are the result of respiratory infections. The relationships between carcass characteristics and post-mortem lung lesion scores were also investigated. Results Questionnaire responses were collected from 22 self-selecting pig farmers about their farm facilities/management and health condition of the respiratory system of pigs, including the occurrence of clinical respiratory signs, results of laboratory testing for respiratory pathogens, and the use of respiratory vaccines. When fatteners were sent to the abattoir, their carcasses (n = 1,976) were examined for evidence of respiratory disease by lung lesion (pleuritis pneumonia-like (PP-like) and enzootic pneumonia-like (EP-like) lesions) scoring and the Actinobacillus pleuropneumoniae Index (APPI) was calculated. Carcass characteristics were recorded and, retrospectively, the prevalence of cachectic pigs was calculated. Using these variables, the relationships between farm facilities/management and lung lesions scores and the relationships between the latter and carcass characteristics and cachexia were explored. The key findings relating farm facilities and management to lung lesions were: slatted floors were associated with significantly higher EP-like lesions scores than litter bedding in weaners, single-stage fattening in the same building was associated with significantly higher EP-like lesions scores than two-stage fattening, but herd size, stocking density, use of all-in/all-out (AIAO) rule, technological break duration and variation in daily temperature did not affect lung lesions scores. The key findings relating lung lesion scores to carcass characteristics were: a significant, negative correlation between EP-like scores and carcass weight but not with other carcass characteristics, a significant positive correlation between PP-like scores and carcass meat content and prevalence of cachectic carcasses and a significant positive correlation between lung APPI and prevalence of cachectic carcasses. Conclusions It can be concluded that both farm facilities and management affect lung lesions scores and that the latter affect carcass characteristics. Lung lesion scoring is an inexpensive technique suitable for rapid monitoring of large numbers of carcasses that can be performed after animal slaughter. It provides useful information to inform producers about possible deficits in farm facilities or management and is a predictor of economic loss due to poorer quality carcasses.

Abstract Background Artisanal cheeses usually contain a highly diverse microbial community which can significantly impact their quality and safety. Here, we describe a detailed longitudinal study assessing the impact of ripening in three natural caves on the microbiome and resistome succession across three different producers of Cabrales blue-veined cheese. Results Both the producer and cave in which cheeses were ripened significantly influenced the cheese microbiome. Lactococcus and the former Lactobacillus genus, among other taxa, showed high abundance in cheeses at initial stages of ripening, either coming from the raw material, starter culture used, and/or the environment of processing plants. Along cheese ripening in caves, these taxa were displaced by other bacteria, such as Tetragenococcus, Corynebacterium, Brevibacterium, Yaniella, and Staphylococcus, predominantly originating from cave environments (mainly food contact surfaces), as demonstrated by source-tracking analysis, strain analysis at read level, and the characterization of 613 metagenome-assembled genomes. The high abundance of Tetragenococcus koreensis and Tetragenococcus halophilus detected in cheese has not been found previously in cheese metagenomes. Furthermore, Tetragenococcus showed a high level of horizontal gene transfer with other members of the cheese microbiome, mainly with Lactococcus and Staphylococcus, involving genes related to carbohydrate metabolism functions. The resistome analysis revealed that raw milk and the associated processing environments are a rich reservoir of antimicrobial resistance determinants, mainly associated with resistance to aminoglycosides, tetracyclines, and β-lactam antibiotics and harbored by aerobic gram-negative bacteria of high relevance from a safety point of view, such as Escherichia coli, Salmonella enterica, Acinetobacter, and Klebsiella pneumoniae, and that the displacement of most raw milk-associated taxa by cave-associated taxa during ripening gave rise to a significant decrease in the load of ARGs and, therefore, to a safer end product. Conclusion Overall, the cave environments represented an important source of non-starter microorganisms which may play a relevant role in the quality and safety of the end products. Among them, we have identified novel taxa and taxa not previously regarded as being dominant components of the cheese microbiome (Tetragenococcus spp.), providing very valuable information for the authentication of this protected designation of origin artisanal cheese. Video Abstract

Abstract Background Recent endeavours in metagenomics, exemplified by projects such as the human microbiome project and TARA Oceans, have illuminated the complexities of microbial biomes. A robust bioinformatic pipeline and meticulous evaluation of their methodology have contributed to the success of these projects. The soil environment, however, with its unique challenges, requires a specialized methodological exploration to maximize microbial insights. A notable limitation in soil microbiome studies is the dearth of soil-specific reference databases available to classifiers that emulate the complexity of soil communities. There is also a lack of in-vitro mock communities derived from soil strains that can be assessed for taxonomic classification accuracy. Results In this study, we generated a custom in-silico mock community containing microbial genomes commonly observed in the soil microbiome. Using this mock community, we simulated shotgun sequencing data to evaluate the performance of three leading metagenomic classifiers: Kraken2 (supplemented with Bracken, using a custom database derived from GTDB-TK genomes along with its own default database), Kaiju, and MetaPhlAn, utilizing their respective default databases for a robust analysis. Our results highlight the importance of optimizing taxonomic classification parameters, database selection, as well as analysing trimmed reads and contigs. Our study showed that classifiers tailored to the specific taxa present in our samples led to fewer errors compared to broader databases including microbial eukaryotes, protozoa, or human genomes, highlighting the effectiveness of targeted taxonomic classification. Notably, an optimal classifier performance was achieved when applying a relative abundance threshold of 0.001% or 0.005%. The Kraken2 supplemented with bracken, with a custom database demonstrated superior precision, sensitivity, F1 score, and overall sequence classification. Using a custom database, this classifier classified 99% of in-silico reads and 58% of real-world soil shotgun reads, with the latter identifying previously overlooked phyla using a custom database. Conclusion This study underscores the potential advantages of in-silico methodological optimization in metagenomic analyses, especially when deciphering the complexities of soil microbiomes. We demonstrate that the choice of classifier and database significantly impacts microbial taxonomic profiling. Our findings suggest that employing Kraken2 with Bracken, coupled with a custom database of GTDB-TK genomes and fungal genomes at a relative abundance threshold of 0.001% provides optimal accuracy in soil shotgun metagenome analysis.