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Objectives: Antimicrobial drugs are frequently administered in veal calves, but investigations on associations with antimicrobial susceptibility of bacteria are scarce and convey partly contradictory findings. The aim of this study was to investigate associations of antimicrobial use (AMU) during the fattening period with antimicrobial susceptibility shortly before slaughter.Methods: Detailed treatment data of 1905 veal calves from 38 farms were collected prospectively during monthly farm visits for 1 year (n = 1864 treatments, n = 535 visits); 1582 Escherichia coli, 1059 Pasteurella multocida and 315 Mannheimia haemolytica were isolated from rectal and nasopharyngeal swabs collected before slaughter and subjected to antimicrobial susceptibility testing by microdilution. Associations of antimicrobial treatments with resistant isolates were investigated at the calf level.Results: Associations of AMU with antimicrobial resistance were observed using generalized linear models. For E. coli, the odds of being resistant were increased with increased AMU (OR 1.36 when number of treatments >1, P = 0.066). Use of tetracyclines was associated with resistance to tetracycline (OR 1.86, P < 0.001) and use of penicillins was associated with resistance to ampicillin (OR 1.66, P = 0.014). No significant associations were observed for P. multocida (use of aminoglycosides: OR 3.66 for resistance to spectinomycin, P = 0.074). For M. haemolytica, the odds of being resistant were increased with increased AMU (OR 4.63, P < 0.001), and use of tetracyclines was associated with resistance to tetracycline (OR 6.49, P < 0.001).Conclusions: Occurrence of resistant bacteria shortly before slaughter was associated with AMU in veal calves. Prudent and appropriate use may contribute to limit the selection of resistant bacteria on veal farms. [ABSTRACT FROM AUTHOR]

This study aimed to determine the taxonomic status of a new group of bovine strains of the genus Acinetobacter characterized by the rare ability to grow at temperatures above 44 °C. Initially, 24 strains were isolated from cattle feces collected at 11 farms in Czechia in 2022, representing a tentative new species based on preliminary whole-cell MALDI-TOF MS identification and rpoB gene sequencing. Twelve strains encompassing the within-group diversity were studied in detail, including whole genome de novo sequencing. Core genome-based phylogenetic analysis revealed that the 12 strains form a distinct clade within the genus. The genomic average nucleotide identity based on BLAST (ANIb) values within the clade were ≥ 98.2%, whereas the ANIb values between the clade and the known Acinetobacter species were < 83%. Each of the 12 genomes consisted of a circular chromosome (3.05-3.28 Mb) and 1-6 extrachromosomal elements (1.43-122.5 kb). All strains were non-glucose oxidizing, non-hemolytic, non-proteolytic, and prototrophic, and used acetate, ethanol, and DL-lactate as sole carbon and energy sources. Unrestricted growth at 47 °C was their unique diagnostic characteristic in a genus-wide comparative analysis and their growth kinetics at 37-46 °C differed from that of Acinetobacter baumannii. The studied strains were susceptible to 18 antibiotics except for sporadic resistance to streptomycin, tetracycline, and sulfonamides associated with the presence of strA/strB, tet(Y), and sul2 genes, respectively. We conclude that the studied strains represent a new species, for which we propose the name Acinetobacter thermotolerans sp. nov. The type strain is ANC 7454 T (= CCM 9356 T  = CCUG 77195 T  = CNCTC 8200 T )., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier GmbH. All rights reserved.)

Background: The addition of wine lees to diets can make up for the deficiencies caused by traditional forages in beef cattle farming. However, the effects of different wine lees ratios on average daily weight, gastrointestinal microbial community structure and metabolites in Guanling crossbred cattle have been rarely studied. This study assessed the effects of feeds containing wine lees on weight gain, gastrointestinal microbial community structure, and metabolites in Guanling crossbred cattle and elucidated the metabolic responses induced by wine lees. Eighteen cows were randomly assigned to receive fed concentrate (C group), feed containing 15% wine lees (group A), or feed containing 30% wine lees (group B) for 60 days., Results: The average daily weight gain of group A and group B increased by 76.75% and 57.65%, respectively, compared with group C. Microbial community analysis showed that wine lees increased the abundance of Prevotella&#95;1 in the rumen, decreased the abundance of Ruminococcaceae UCG 011 and Lachnospiraceae&#95;FCS020&#95;group in the rumen, and increased the abundance of Tyzzerella&#95;4, Family&#95;Xlll&#95;AD3011&#95;group, Granulicella, and Eisenbergiella in the cecum. Metabolomics analyses showed that wine lees decreased the concentrations of indole-3-ethanol in the rumen, and complexity cecal metabolism. Notably, linoleic acid metabolism was significantly enriched in both the rumen and cecum. Mantel test analyses indicated that the adverse effects of WL were reduced by stimulating the metabolism of linoleic acid, α-linolenic acid, and tryptophan, and these changes were mediated by intestinal microorganisms. The Guanling cattle cecum was enriched for several unfavorable metabolic pathways when wine lees concentrations reached 30%, which increased the likelihood of intestinal lesions., Conclusion: This study shows that WL supplementation alters gut microbiota and metabolic pathways, improving cattle growth and health. Moderate WL levels (15%) enhance gut health and beneficial pathways (e.g., linoleic and alpha-linolenic acid metabolism). However, higher WL inclusion (30%) may activate adverse pathways, raising the risk of intestinal damage. To maximize benefits and minimize risks, WL levels should be carefully managed., (© 2024. The Author(s).)

Ruminants play an important part in the food supply chain, and manipulating rumen microbiota is important to maximising ruminants' production. Rumen microbiota through rumen fermentation produces as major end products volatile fatty acids that provide animal's energy requirements, and microbial CP. Diet is a key factor that can manipulate rumen microbiota, and each variation of the physical and chemical composition creates a specific niche that selects specific microbes. Alteration in the chemical composition of forage, the addition of concentrates in the diet, or the inclusion of plant extract and probiotics, can induce a change in rumen microbiota. High-throughput sequencing technologies are the approaches utilised to investigate the microbial system. Also, the application of omics technologies allows us to understand rumen microbiota composition and these approaches are useful to improve selection programmes. The aim of this review was to summarise the knowledge about rumen microbiota, its role in nutrient metabolism, and how diet can influence its composition., (Copyright © 2024 The Author(s). Published by Elsevier B.V. All rights reserved.)

Achromobacter marplatensis strain YKS2 isolated from the yak rumen has the feature of producing cellulose. This study aims to analyze the genome and safety of strain YKS2 in vivo, considering its future research and application prospects. The genome of strain YKS2 was sequenced and used for genomic in silico studies. The administration of strain YKS2 in three doses was carried out on mice for 3 days of oral and 7 days of clinical observation tests. The BW, FI, organ indices, gut microbiota, and histological appearances of organs and intestines, along with hematological parameters and serum biochemistry, were measured in mice. The chromosome size of strain YKS2 was 6,588,568 bp, with a GC content of 65.27%. The 6058 coding sequences of strain YKS2 without plasmid were predicted and annotated and have multiple functions. The mice in all groups were alive, with good mental states and functional activities. Compared with the control group, there was no significant difference in the three dose groups on BW, FI, hematological parameters (WBC, LYM, etc.), and serum biochemistry (ALB, ALT, etc.). No abnormalities were observed in the main visceral organs, intestinal tissue, and V/C value in groups. However, the IEL number of duodenum and gut microbiota diversity (Shannon's index) in the high-dose group was significantly higher than in the control group (p < 0.05). Besides, the low dose of strain YKS2 also significantly affected the bacterial abundance of Firmicutes, Actinobacteria, and desulphurizing Bacteroidetes at the phylum level. There was no significant effect at genus levels in groups. In conclusion, the study revealed the genome and potential functional genes of strain YKS2, which is beneficial to understanding the features of the A. marplatensis strain and proved strain YKS2 to be without acute toxicity to mice. However, a long-term feeding toxicity experiment in vivo should be performed to further ensure its potential application value strain in the animal industry., (© 2023. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

Toxoplasma gondii is the agent of toxoplasmosis, which is common to both humans and cattle. That is why the goal of work was to study the spreading of the agent of toxoplasmosis among cattle in certain regions of Ukraine, which in turn will make it possible to predict the appearance of the disease among people and prevent the development of its clinical signs. Whole blood or serum samples of cattle of different ages and sexes from farms in Kyiv, Zhytomyr, Khmelnytskyi and Lviv regions of Ukraine were sent to the laboratory for research. The presence of total antibodies to T. gondii was determined in the serum of the animals. To do this, we used the method of enzyme-linked immunosorbent assay using test kits from different manufacturers in accordance with the guidelines. In general, the prevalence of T. gondii among cattle in Kyiv, Zhytomyr, Khmelnytskyi and Lviv regions of Ukraine according to the results of studies was 10.3% (95% confidence interval: 6.7-15.1). At the same time, the study of animals was carried out in two stages, in 2014 and 2018, and the prevalence did not differ significantly. Thus, in 2014, according to the results of research, a positive reaction to the agent of toxoplasmosis was detected in 10 samples or 13.9% (95% confidence interval: 7.3-23.4), while in 2018 this figure was 11 samples or 8.4% (95% confidence interval: 4.5-14.1) of the studied animals. Also, in 2014 and 2018 studies found that the highest level of seroprevalence of the agent of toxoplasmosis in both years of research was registered in cattle from farms of Zhytomyr and Kyiv regions was 11.9% (95% confidence interval: 4.5-24.4) and 11% (95% confidence interval: 5.9-18.3), respectively. During the conducted research, an increase in the prevalence of T. gondii with the age of animals was statistically significant. Among animals under six months of age, of the 65 serum samples tested, 3 tested positively to the agent (4.6; 95% confidence interval: 1.2-12.1), while in the group of animals older than three years (49 cows) 10 samples were positively responded (20.4; 95% confidence interval: 10.9-33.4) compared to the previous group of animals, the P-value was 0.0114. So, the data obtained indicate the presence of the agent of toxoplasmosis among cattle in Ukraine, which requires further study and development of approaches to prevent human infection when eating meat and dairy products of positively reacting animals [ABSTRACT FROM AUTHOR]

Bovine brucellosis caused by the organism Brucella abortus is a chronic infectious disease of public health and economic significance. Studies on prevalence of bovine brucellosis in Abia State are scarce. Therefore, a cross-sectional study was conducted to determine the prevalence of bovine brucellosis in the State. Blood samples were collected from 212 cattle from various parts of the State and sera subjected to Rose Bengal Plate Test (RBPT) to detect antibodies against Brucella. Overall sero-prevalence of 13.7% was reported. The prevalence was higher in female cattle (24.2%) than in males (11%). Red Bororo showed higher seropositivity (26.7%) than other breeds screened. Sero-prevalence was higher in the semi-intensively managed animals (27.8%) than in extensively reared cattle. Similarly, cattle aged 2 to 3 years recorded a higher prevalence (25%) than others. However, there was no statistically significant association between the seroprevalence of brucellosis and sex (P= 0.05), age (P=0.82), breed (P=0.25), and management system (P=0.07 ). The detection of brucellosis in cattle poses a very significant public health risk in Abia state, and so it is important to carry out awareness campaigns to enlighten cattle handlers and the general public of its public health significance. [ABSTRACT FROM AUTHOR]

Ruminant livestock are major contributors to anthropogenic methane emissions in the United States and worldwide. Enteric methane is generated by methanogenic archaea residing in ruminant digestive tracts. Information on when methanogens colonize the gut and when they begin to interact with bacteria during the early phases of the ruminant life cycle is less explored. The objectives of this study were (i) to investigate the composition of the methanogenic archaeal community at birth and through the weaning transition and (ii) to determine if and when the methanogenic archaea begin to interact with bacteria in the lower gut of neonatal dairy calves. Ten female Holstein calves (approximately 45kg birth weight) were enrolled in the study. Fecal samples were collected every two weeks (Wk 2, 4, 6, 8, 10, and 12) between birth and weaning and analyzed for methanogenic archaeal diversity via 16S rRNA amplicon sequencing and quantitative real-time PCR (RT-qPCR). Estimates of alpha diversity (Observed species, and Shannon diversity index) and beta diversity (weighted and unweighted UniFrac distances) showed significant differences (P < 0.05) between archaeal communities across timepoints. Both 16S rRNA amplicon sequencing and RT-qPCR analyses revealed Methanobrevibacter was the most prevalent genus at Wk2, Wk4, and Wk6, whereas Methanosphaera gradually increased with time and was most abundant at Wk10 and Wk12. Correlation analysis revealed that Methanobrevibacter and Methanosphaera were inversely correlated with each other and formed distinct cohorts with specific bacterial lineages similar to those reported in the mature rumen, thus revealing that these associations are established during the preweaning period. Therefore, the preweaning period presents a window of opportunity to interfere with early-life methanogenic colonization with the ultimate goal of reducing enteric methane emissions without perturbing ruminal function later in the life of dairy cattle., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Indugu et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Background: Along bacteria, yeasts are common in forages and forage fermentations as spoilage microbes or as additives, yet few studies exist with species-level data on these fungi's occurrence in feedstuff. Active dry yeast and other yeast-based products are also common feed additives in animal husbandry. Here, we aimed to characterize both fermented and non-fermented milking cow feedstuff samples from Hungary to assess their microbial diversity in the first such study from Central Europe., Results: We applied long-read bacterial metabarcoding to 10 fermented and 25 non-fermented types of samples to assess bacterial communities and their characteristics, surveyed culturable mold and yeast abundance, and identified culturable yeast species. Fermented forages showed the abundance of Aerococcaceae, Bacillaceae, Brucellaceae, Lactobacillaceae, Staphylococcaceae, and Thermoactinomycetaceae, non-fermented ones had Cyanothecaceae, Enterobacteriaceae, Erwiniaceae, Gomontiellaceae, Oxalobacteraceae, Rhodobiaceae, Rickettsiaceae, and Staphylococcaceae. Abundances of bacterial families showed mostly weak correlation with yeast CFU numbers, only Microcoleaceae (positive) and Enterococcaceae and Alcaligenaceae (negative correlation) showed moderate correlation. We identified 14 yeast species, most commonly Diutina rugosa, Pichia fermentans, P. kudriavzevii, and Wickerhahomyces anomalus. We recorded S. cerevisiae isolates only from animal feed mixes with added active dry yeast, while the species was completely absent from fermented forages. The S. cerevisiae isolates showed high genetic uniformity., Conclusion: Our results show that both fermented and non-fermented forages harbor diverse bacterial microbiota, with higher alpha diversity in the latter. The bacterial microbiome had an overall weak correlation with yeast abundance, but yeasts were present in the majority of the samples, including four new records for forages as a habitat for yeasts. Yeasts in forages mostly represented common species including opportunistic pathogens, along with a single strain of Saccharomyces used as a feed mix additive., (© 2024. The Author(s).)

The rumen microbiome is the focus of a growing body of research, mostly based on investigation of rumen fluid samples collected once from each animal. Exploring the temporal stability of rumen microbiome profiles is imperative, as it enables evaluating the reliability of findings obtained through single-timepoint sampling. We explored the temporal stability of rumen microbiomes considering taxonomic and functional aspects across the 7-month growing-finishing phase spanning 6 timepoints. We identified a temporally stable core microbiome, encompassing 515 microbial genera (e.g., Methanobacterium) and 417 microbial KEGG genes (e.g., K00856-adenosine kinase). The temporally stable core microbiome profiles collected from all timepoints were strongly associated with production traits with substantial economic and environmental impact (e.g., average daily gain, daily feed intake, and methane emissions); 515 microbial genera explained 45-83%, and 417 microbial genes explained 44-83% of their phenotypic variation. Microbiome profiles influenced by the bovine genome explained 54-87% of the genetic variation of bovine traits. Overall, our results provide evidence that the temporally stable core microbiome identified can accurately predict host performance traits at phenotypic and genetic level based on a single timepoint sample taken as early as 7 months prior to slaughter., (© 2024. The Author(s).)

This study provides an emended description of Acinetobacter faecalis, a species previously described based on a single isolate (YIM 103518 T ) from elephant feces in China. Our emended description is based on 15 novel isolates conspecific with the A. faecalis type strain, obtained from eight cattle farms in the Czech Republic. The A. faecalis strains have relatively small genomes (≈2.5-2.7 Mbp), with a GC content of 36.3-36.7 mol%. Core genome-based phylogenetic analysis showed that the 15 strains, together with the type strain of A. faecalis, form a distinct and internally coherent phylogroup within the genus. Pairwise genomic ANIb values for the 16 A. faecalis strains were 97.32-99.04 %, while ANIb values between the genomes of the 16 strains and those of the other Acinetobacter spp. were ≤ 86.2 %. Analysis of whole-cell MALDI-TOF mass spectra supported the distinctness and cohesiveness of the taxon. The A. faecalis strains could be differentiated from the other validly named Acinetobacter spp. by the absence of hemolytic activity along with their ability to grow at 37 °C and on L-aspartate, ethanol, and L-glutamate but not at 41 °C or on adipate or 2,3-butanediol. Reduced susceptibility to sulfamethoxazole, trimethoprim and/or streptomycin was shown in eight strains, along with the presence of corresponding antibiotic resistance genes. In conclusion, this study provides a comprehensive description of A. faecalis and demonstrates its occurrence in cattle feces. Though the ecological role of A. faecalis remains unknown, our results show its ability to acquire antibiotic resistance genes, likely as an adaptation to antibiotic selection pressure in livestock farms., (Copyright © 2024 Elsevier GmbH. All rights reserved.)

In ruminants, the rumen is a specialized stomach that is adapted to the breakdown of plant-derived complex polysaccharides through the coordinated activities of a diverse microbial community. Bacteroidota is a major phylum in this bovine rumen microbiota. They contain several clusters of genes called polysaccharide utilization loci (PULs) that encode proteins working in concert to capture, degrade, and transport polysaccharides. Despite the critical role of SusD-like proteins for efficient substrate transport, they remain largely unexplored. Here, we present the biochemical characterization of a SusD-like protein encoded by a β-glucan utilization locus from an Escherichia coli metagenomic clone previously isolated by functional screening of the bovine rumen microbiome. In this study, we show that clone 41O1 can grow on laminaritriose, cellotriose, and a mixture of cellobiosyl-cellobiose and glucosyl-cellotriose as sole carbon sources. Based on this, we used various in vitro analyses to investigate the binding ability of 41O1&#95;SusD-like towards these oligosaccharides and the corresponding polysaccharides. We observed a clear binding affinity for β-1,6 branched β-1,3-glucans (laminarins, yeast β-glucan) and laminaritriose. Comparison of the AlphaFold2 model of 41O1&#95;SusD-like with its closest structural homologs highlights a similar pattern of substrate recognition. In particular, three tryptophan residues are shown to be crucial for laminarin recognition. In the context of the cow rumen, we discuss the possible substrates targeted by the 41O1&#95;PUL, such as the (1,3;1,4)-β-d-glucans present in cereal grains or the β-1,3- and (1,3;1,6)-β-d-glucans that are components of the cell wall of ruminal yeasts.IMPORTANCEThe rumen microbiota can majorly impact overall animal health, feed efficiency, and release of harmful substances into the environment. This microbiota is involved in the fermentation of organic matter to provide the host with valuable and assimilable nutrients. Bacteroidota efficiently captures, breaks down, and imports complex polysaccharides through the concerted action of proteins encoded by polysaccharide utilization loci (PULs). Within this system, SusD-like protein has proven necessary for the active internalization of the substrate. Nevertheless, the vast majority of SusD-like proteins characterized to date originate from cultured bacteria. With regard to the diversity and importance of uncultured bacteria in the rumen, further studies are required to better understand the role of polysaccharide utilization loci in ruminal polysaccharide degradation. Our detailed characterization of the 41O1&#95;SusD-like therefore contributes to a better understanding of the carbohydrate metabolism of an uncultured Bacteroides from the cow rumen., Competing Interests: The authors declare no conflict of interest.

Microbiota analyses are key to understanding the bacterial communities within dairy cattle, but the impact of different storage conditions on these analyses remains unclear. This study sought to examine the effects of freezing at -80°C immediately after collection, refrigeration at 4°C for three days and seven days and absolute ethanol preservation on the microbiota diversity of pooled fecal samples from dairy cattle. Examining 16S rRNA gene sequences, alpha (Shannon, Pielou evenness, observed features and Faith PD indices) and beta (Bray-Curtis, βw and Weighted UniFrac) diversity were assessed. The effects of storage conditions on these metrics were evaluated using linear mixed models and PERMANOVA, incorporating the farm as a random effect. Our findings reveal that 7d and E significantly altered the Shannon index, suggesting a change in community composition. Changes in Pielou evenness for 3d and 7d storage when compared to 0d were found, indicating a shift in species evenness. Ethanol preservation impacted both observed features and Faith PD indices. Storage conditions significantly influenced Bray-Curtis, βw, and Weighted UniFrac metrics, indicating changes in community structure. PERMANOVA analysis showed that these storage conditions significantly contributed to microbiota differences compared to immediate freezing. In conclusion, our results demonstrate that while refrigeration for three days had minimal impact, seven days of refrigeration and ethanol preservation significantly altered microbiota analyses. These findings highlight the importance of sample storage considerations in microbiota research., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Jaramillo-Jaramillo et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

The performance of dairy cows is influenced by the microbial communities hosted within their digestive tract. While the rumen microbiota has long been associated with host phenotypes, the impact of the faecal microbiota remains elusive. In this study, we collected 697 faecal samples from commercial Holstein cows and analysed them with 16S rRNA gene analyses. For each animal, routinely recorded data, i.e., milk yield, fat yield, protein yield, fat content, protein content, and an aggregate production trait (pINEL) based on the French economic dairy index, were available to assess the links between the faecal microbiota and host production. Our findings revealed a strong and significant association between the structure of the bacterial and prokaryote community (β-diversity) and dairy production. In addition, differential abundance analyses identified 48 genera whose abundances were significantly associated with pINEL, milk, fat and protein yield. Among these genera, the increased abundance of Bifidobacterium, and particularly an amplicon sequence variant with a 16S rRNA V3-V4 gene region identical to B. globosum and B. pseudolongum, was found to be the most important for high-yielding animals. Bifidobacterium seemed to be a potential key member of the bovine faecal microbiota that should be further investigated. Conversely, the p-1088-a5 gut group genus was found more abundant in low-productive cows. In conclusion, this study demonstrates significant associations between the faecal microbiota and the performance of dairy cows at the whole lactation scale. A better understanding of the physiology of the gut microbiota could help to improve dairy cow production., (Copyright © 2024 The Author(s). Published by Elsevier B.V. All rights reserved.)

The development and growth of animals coincide with the establishment and maturation of their microbiotas. To evaluate the respiratory and fecal microbiotas of beef calves from birth to weaning, a total of 30 pregnant cows, and their calves at birth, were enrolled in this study. Deep nasal swabs and feces were collected from calves longitudinally, starting on the day of birth and ending on the day of weaning. Nasopharyngeal, vaginal, and fecal samples were also collected from cows, and the microbiotas of all samples were analyzed. The fecal microbiota of calves was enriched with Lactobacillus during the first 8 weeks of life, before being displaced by genera associated with fiber digestion, and then increasing in diversity across time. In contrast, the diversity of calf respiratory microbiota generally decreased with age. At birth, the calf and cow nasal microbiotas were highly similar, indicating colonization from dam contact. This was supported by microbial source-tracking analysis. The structure of the calf nasal microbiota remained similar to that of the cows, until weaning, when it diverged. The changes were driven by a decrease in Lactobacillus and an increase in genera typically associated with bovine respiratory disease, including Mannheimia , Pasteurella , and Mycoplasma . These three genera colonized calves early in life, though Mannheimia was initially transferred from the cow reproductive tract. Path analysis was used to model the interrelationships of calf respiratory and fecal microbiotas. It was observed that respiratory Lactobacillus and fecal Oscillospiraceae UCG-005 negatively affected the abundance of Mannheimia or Pasteurella .IMPORTANCEIn beef cattle production, bovine respiratory disease (BRD) accounts for most of the feedlot morbidities and mortalities. Metaphylaxis is a common management tool to mitigate BRD, however its use has led to increased antimicrobial resistance. Novel methods to mitigate BRD are needed, including microbiota-based strategies. However, information on the respiratory bacteria of beef calves prior to weaning was limited. In this study, it was shown that the microbiota of cows influenced the initial composition of both respiratory and fecal microbiotas in calves. While colonization of the respiratory tract of calves by BRD-associated genera occurred early in life, their relative abundances increased at weaning, and were negatively correlated with respiratory and gut bacteria. Thus, microbiotas of both the respiratory and gastrointestinal tracts have important roles in antagonism of respiratory pathogens and are potential targets for enhancing calf respiratory health. Modulation may be most beneficial, if done prior to weaning, before opportunistic pathogens establish colonization., Competing Interests: The authors declare no conflict of interest.

Deciphering the activity of individual microbes within complex communities and environments remains a challenge. Here we describe the development of microbiome single-cell transcriptomics using droplet-based single-cell RNA sequencing and pangenome-based computational analysis to characterize the functional heterogeneity of the rumen microbiome. We generated a microbial genome database (the Bovine Gastro Microbial Genome Map) as a functional reference map for the construction of a single-cell transcriptomic atlas of the rumen microbiome. The atlas includes 174,531 microbial cells and 2,534 species, of which 172 are core active species grouped into 12 functional clusters. We detected single-cell-level functional roles, including a key role for Basfia succiniciproducens in the carbohydrate metabolic niche of the rumen microbiome. Furthermore, we explored functional heterogeneity and reveal metabolic niche trajectories driven by biofilm formation pathway genes within B. succiniciproducens. Our results provide a resource for studying the rumen microbiome and illustrate the diverse functions of individual microbial cells that drive their ecological niche stability or adaptation within the ecosystem., (© 2024. The Author(s), under exclusive licence to Springer Nature Limited.)

Researchers have extensively studied the effect of oxygen on the growth and survival of bacteria. However, the impact of oxygen on bacterial community structure, particularly its ability to select for taxa within the context of a complex microbial community, is still unclear. In a 21-day microcosm experiment, we investigated the effect of aerobic exposure on the fecal community structure and succession pattern in broiler, calf, and piglet feces ( n = 10 for each feces type). Bacterial diversity decreased and community structure changed rapidly in the broiler microbiome ( P < 0.001), while the fecal community of calves and piglets, which have higher initial diversity, was stable after initial exposure but decreased in diversity after 3 days ( P < 0.001). The response to aerobic exposure was host animal specific, but in all three animals, the change in community structure was driven by a decrease in anaerobic species, primarily belonging to Firmicutes and Bacteroidetes (except in broilers where Bacteroidetes increased), along with an increase in aerobic species belonging to Proteobacteria and Actinobacteria. Using random forest regression, we identified microbial features that predict aerobic exposure. In all three animals, host-beneficial Prevotella -related ASVs decreased after exposure, while ASVs belonging to Acinetobacter , Corynbacterium, and Tissierella were increased. The decrease of Prevotella was rapid in broilers but delayed in calves and piglets. Knowing when these pathobionts increase in abundance after aerobic exposure could inform farm sanitation practices and could be important in designing animal experiments that modulate the microbiome.IMPORTANCEThe fecal microbial community is contained within a dynamic ecosystem of interacting microbes that varies in biotic and abiotic components across different animal species. Although oxygen affects bacterial growth, its specific impact on the structure of complex communities, such as those found in feces, and how these effects vary between different animal species are poorly understood. In this study, we demonstrate that the effect of aerobic exposure on the fecal microbiota was host-animal-specific, primarily driven by a decrease in Firmicutes and Bacteroidetes, but accompanied by an increase in Actinobacteria, Proteobacteria, and other pathobionts. Interestingly, we observed that more complex communities from pig and cattle exhibited initial resilience, while a less diverse community from broilers displayed a rapid response to aerobic exposure. Our findings offer insights that can inform farm sanitation practices, as well as experimental design, sample collection, and processing protocols for microbiome studies across various animal species., Competing Interests: The authors declare no conflict of interest.

The importance of ruminal microbiota in ruminants is emphasized, not only as a special symbiotic relationship with ruminants but also as an interactive and dynamic ecosystem established by the metabolites of various rumen microorganisms. Rumen microbial community is essential for life maintenance and production as they help decompose and utilize fiber that is difficult to digest, supplying about 70% of the energy needed by the host and 60-85% of the amino acids that reach the small intestine. Bacteria are the most abundant in the rumen, but protozoa, which are relatively large, account for 40-50% of the total microorganisms. However, the composition of these ruminal microbiota is not conserved or constant throughout life and is greatly influenced by the host. It is known that the initial colonization of calves immediately after birth is mainly influenced by the mother, and later changes depending on various factors such as diet, age, gender and breed. The initial rumen microbial community contains aerobic and facultative anaerobic bacteria due to the presence of oxygen, but as age increases, a hypoxic environment is created inside the rumen, and anaerobic bacteria become dominant in the rumen microbial community. As calves grow, taxonomic diversity increases, especially as they begin to consume solid food. Understanding the factors affecting the rumen microbial community and their effects and changes can lead to the early development and stabilization of the microbial community through the control of rumen microorganisms, and is expected to ultimately help improve host productivity and efficiency., (© 2024. The Author(s), under exclusive licence to Microbiological Society of Korea.)

The diverse rumen microbiome converts lowquality feedstuffs into usable energy and provides approximately 70% of the energy required by its ruminant host through fermentation byproducts. Due to microbial impacts on host health and productivity, numerous studies have associated rumen microbiome variation with important sustainability phenotypes, such as feed efficiency and methane emissions. Although diet, genetics, and environment contribute to variation in feed efficiency, selection for feed-efficient beef cattle using genetic improvement technologies has helped to understand and improve the persistence and longevity of such phenotypes within the herd. While diet has been considered to be the primary driver for the composition and structure of the rumen microbiome, recent studies have indicated the microbial communities present in the rumen are under low-to-moderate host genetic control. The mutualistic, commensal, and parasitic microorganisms that reside in the rumen and lower gastrointestinal tract of cattle and other ruminants exert enormous influence over animal physiology and performance. The ability to interrogate these systems at great depth has permitted a greater understanding of the microbiological and molecular mechanisms involved in ruminant nutrition and health. The work in our group in the field of beef cattle gut microbiology, as it relates to feed efficiency, permits the exploration of these critical microbial community networks. This knowledge will aid researchers seeking to address the grand challenge of maintaining host-efficient gut microbiomes throughout cattle production operations. This work is supported by the Agriculture and Food Research Initiative grant no. 2020-67015-30832 from the USDA National Institute of Food and Agriculture. [ABSTRACT FROM AUTHOR]

Background: In order to verify the existence of an anthrax outbreak, determine its scope, grasp the epidemiological characteristics and find out the cause of the outbreak and recommend preventive and control measures., Methods: Etiological hypothesis was developed through descriptive epidemiological methods. Hypotheses were tested by analyzing epidemiological methods by comparing the differences in the incidence of different exposure types. Nucleic acid detection and bacterial isolation and culture in the BSL-2 laboratories. SPSS 21 was used to conduct statistical analysis., Results: A total of 126 family, workshop, shop environment samples and meat samples were collected, and 6 samples were collected from skin lesions of suspected cutaneous anthrax cases. 41 samples were positive by rPCR and 8 strains of Bacillus anthracis were cultivated. Participated in slaughtering, cutting beef of sick cattles was significantly associated with cutaneous anthrax (RR 3.75, 95% CI 1.08-13.07), this behavior is extremely dangerous., Conclusions: Comprehensive analysis of laboratory results and epidemiological survey results and environmental assessments, we judge this epidemic to be an outbreak of cutaneous anthrax, associated with slaughtering and other processes from infected cattle imported from other province., (© 2022. The Author(s).)

Antimicrobials have been widely used in dairy farms to prevent and control dairy cattle diseases since 1960s. This led to the emergence of antimicrobial resistant bacteria (ARB) that, along with their antimicrobial resistance genes (ARGs), can spread from dairy farms to humans. Therefore, regular antimicrobial resistance (AMR) monitoring is important to implement proper mitigation measures. The objective of this study was to determine the prevalence of AMR and extended-spectrum beta-lactamases (ESBLs)-producing Escherichia coli in dairy cattle. A cross-sectional study was conducted in four dairy cattle farms (A-D) in East Tennessee. A total of 80 samples consisting of 20 samples each of bulk tank milk, feces, dairy cattle manure-amended soil, and prairie soil adjacent to the farms were collected and cultured for the isolation of E. coli . Tetracycline (TET r )-, third-generation cephalosporin (TGC r )- and nalidixic acid (NAL r )-resistant E. coli ( n  = 88) were isolated and identified on agar media supplemented with TET, cefotaxime, and NAL, respectively. TGC r E. coli were tested for ESBLs and other coselected ARGs. TET r (74%, n  = 88) was the most common, followed by TGC r (20%) and NAL r (8%). Farms had significant ( p  < 0.001) differences: the highest prevalence of TGC r (55%) and TET r (100%) were observed in farm D, while all NAL r isolates were from farm C. Over 83% of TGC r isolates ( n  = 18) harbored ESBL gene bla CTX-M . Majority (78%) of the E. coli isolates were multidrug-resistant (MDR), being positive for beta-lactams ( bla CTX-M ), TETs tet ( A ), tet ( B ), tet ( M )), sulfonamides ( sul 2), aminoglycosides ( strA ), and phenicols ( floR ). This study indicated the widespread occurrence of MDR ESBLs- E. coli in dairy cattle farms. AMR surveillance of more dairy farms and identification of farm-level risk factors are important to mitigate the occurrence and spread of ARB of significant public health importance, such as ESBLs- E. coli .

The increasing number of diversified small-scale farms (DSSF) that raise outdoor-based livestock in the USA reflects growing consumer demand for sustainably produced food. Diversified farms are small scale and raise a combination of multiple livestock species and numerous produce varieties. This 2015-2016 cross-sectional study aimed to describe the unique characteristics of DSSF in California, estimate the prevalence of Shiga toxin-producing Escherichia coli (STEC) in livestock and evaluate the association between risk factors and the presence of STEC in livestock, using generalised linear mixed models. STEC prevalence was 13.62% (76/558). Significant variables in the mixed-effect logistic regression model included daily maximum temperature (OR 0.95; CI 95% 0.91-0.98), livestock sample source (cattle (OR 4.61; CI 95% 1.64-12.96) and sheep (OR 5.29; CI 95% 1.80-15.51)), multiple species sharing the same barn (OR 6.23; CI 95% 1.84-21.15) and livestock having contact with wild areas (OR 3.63; CI 95% 1.37-9.62). Identification of STEC serogroups of public health concern (e.g. O157:H7, O26, O103) in this study indicated the need for mitigation strategies to ensure food safety by evaluating risk factors and management practices that contribute to the spread and prevalence of foodborne pathogens in a pre-harvest environment on DSSF.

Background: Anthrax is a disease that affects humans and animals. In Ethiopia, anthrax is a reportable disease and assumed to be endemic, although laboratory confirmation has not been routinely performed until recently. We describe the findings from the investigation of two outbreaks in Amhara region., Methods: Following reports of suspected outbreaks in Wag Hamra zone (Outbreak 1) and South Gondar zone (Outbreak 2), multi-sectoral teams involving both animal and public health officials were deployed to investigate and establish control programs. A suspect case was defined as: sudden death with rapid bloating or bleeding from orifice(s) with unclotted blood (animals); and signs compatible with cutaneous, ingestion, or inhalation anthrax ≤7 days after exposure to a suspect animal (humans). Suspect human cases were interviewed using a standard questionnaire. Samples were collected from humans with suspected anthrax (Outbreak 1 and Outbreak 2) as well as dried meat of suspect animal cases (Outbreak 2). A case was confirmed if a positive test was returned using real-time polymerase chain reaction (qPCR)., Results: In Outbreak 1, a total of 49 cows died due to suspected anthrax and 22 humans developed symptoms consistent with cutaneous anthrax (40% attack rate), two of whom died due to suspected ingestion anthrax. Three people were confirmed to have anthrax by qPCR. In Outbreak 2, anthrax was suspected to have caused the deaths of two livestock animals and one human. Subsequent investigation revealed 18 suspected cases of cutaneous anthrax in humans (27% attack rate). None of the 12 human samples collected tested positive, however, a swab taken from the dried meat of one animal case (goat) was positive by qPCR., Conclusion: We report the first qPCR-confirmed outbreaks of anthrax in Ethiopia. Both outbreaks were controlled through active case finding, carcass management, ring vaccination of livestock, training of health professionals and outreach with livestock owners. Human and animal health authorities should work together using a One Health approach to improve case reporting and vaccine coverage., Competing Interests: The authors have declared that no competing interests exist.

Three Gram-negative, rod-shaped, oxidase-positive, non-spore-forming, non-motile strains (C130915&#95;07 T , C150915&#95;16 and C150915&#95;17) were isolated from lymph nodes of Algerian cows. On the basis of 16S rRNA gene and whole genome similarities, the isolates were almost identical and clearly grouped in the genus Pseudochrobactrum . This allocation was confirmed by the analysis of fatty acids (C 19:cyclo , C 18 : 1 , C 18 : 0 , C 16 : 1 and C 16 : 0 ) and of polar lipids (major components: phosphatidylethanolamine, ornithine-lipids, phosphatidylglycerol, cardiolipin and phosphatidylcholine, plus moderate amounts of phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine and other aminolipids). Genomic, physiological and biochemical data differentiated these isolates from previously described Pseudochrobactrum species in DNA relatedness, carbon assimilation pattern and growth temperature range. Thus, these organisms represent a novel species of the genus Pseudochrobactrum , for which the name Pseudochrobactrum algeriensis sp. nov. is proposed (type strain C130915&#95;07 T =CECT30232 T =LMG 32378 T ).

Gram-positive coccoid bacteria were isolated from the nasal cavities of pigs and calves as well as from axillar and inguinal skin regions of pigs. Phylogenetic analysis of seven strains based on complete genome, 16S rRNA, hsp60 , dnaJ , rpoB and sodA gene sequences and MALDI-TOF MS profiles revealed that they belonged to the genus Macrococcus with the closest relatedness to Macrococcus canis , Macrococcus caseolyticus subsp. caseolyticus and Macrococcus caseolyticus subsp. hominis . DNA relatedness of the type strain JEK37 T with the type strains of M. canis , M. caseolyticus subsp. caseolyticus and M. caseolyticus subsp. hominis was 23.4, 23.1 and 23.0 % by digital DNA-DNA hybridization and 80.39, 80.45 and 80.87 % by average nucleotide identity (ANI) calculations, confirming that they do not belong to the same species. The DNA G+C content of JEK37 T was 35.65 mol%. The novel strains can be differentiated from M. canis KM 45013 T by the ability to fermentate d-ribose and by the absence of DNAase production and haemolysis, from M. caseolyticus subsp. caseolyticus CCUG 15606 T by the ability to fermentate sucrose and from both species by the inability to grow in 9 and 12% NaCl. They differ from M. caseolyiticus subsp. hominis by the presence of α-glucosidase. The most common fatty acids of JEK37 T were C 14 : 0 , C 18 : 1  ω9 c and C 18 : 0 . Known polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, aminolipid, aminoglycolipid, aminophospholipid, glycolipid and phospholipid. Cell-wall peptidoglycan of JEK37 T was of type A3α l-Lys-Gly 2 -L-Ser-Gly (similar to A11.3) and the respiratory quinolone was menaquinone 6. Based on their genotypic and chemotaxonomic characteristics, these strains represent a novel species of the genus Macrococcus , for which we propose the name Macrococcus armenti sp. nov. The type strain is JEK37 T (=DSM 112712 T =CCOS 1982 T ).

Common bacterial causes of bovine respiratory disease (BRD) include Histophilus somni , Mannheimia haemolytica , and Pasteurella multocida . Within M. haemolytica , two major genotypes are commonly found in cattle (1 and 2); however, genotype 2 strains are isolated from diseased lungs much more frequently than genotype 1 strains. Outer membrane proteins (OMPs) of H. somni , P. multocida , and genotype 2 M. haemolytica may be important factors for acquired host immunity. The predicted OMP differences between genotypes 1 and 2 M. haemolytica have been previously identified. In this study, we expanded the focus to include bovine-isolated strain genomes representing all three species and the two M. haemolytica genotypes. Reported here are the core genomes unique to each of them, core genomes shared between some or all combinations of the three species and two M. haemolytica genotypes, and predicted OMPs within these core genomes. The OMPs identified in this study are potential candidates for further studies and the development of interventions against BRD.

Laminitis is the inflammation of the lamella, and it has caused great economic loss to the dairy industry and attracted wide attention around the world. In recent years, microbiota are considered to play a significant role in various diseases processes. Therefore, our study aimed to explore the characteristics of ruminal microbiota in laminitis cows. The serum of bovines with or without laminitis was collected to detect concentrations of lipopolysaccharide (LPS), lactic acid, and histamine, and ruminal fluid was collected for 16S rDNA sequence analysis. The results showed a significant increase in LPS and lactic acid levels in the laminitis group compared to the control group cows. In addition, a higher abundance of Candidatus Saccharimonas , Saccharofermentans , Erysipelotrichaceae UCG-009 genus, Acetobacter pasteurianus , Clostridium papyrosolvens , Ruminococcaceae bacterium AE2021 , Porphyromonas crevioricanis , Pseudomonas boreopolis , Pseudomonas psychrotolerans , Rothia nasimurium , and Rothia pickettii was detected in the rumen fluid of laminitis bovines. In conclusion, this article confirms that there are differences in rumen microbiota between healthy and laminitis bovines. The elevated abundance of bacteria that enrich acid-enhancing metabolites, as well as increase the concentration of lactic acid and LPS, could be harmful factors to bovines and increase the risk of laminitis.

The present study investigated the serum microscopic agglutination test (MAT) among 203 bovine bulls with reproduction by natural means, without apparent signs of orchitis or inflammation of accessory reproductive glands. Simultaneously, the semen of all bulls was subjected to sperm viability analysis and PCR based on the 16S rRNA gene. PCR-positive results of semen samples were confirmed by sequencing. A modified seminal plasma agglutination (MSPA) test, replacing the blood serum of all bulls in the MAT with seminal plasma was performed as well. Eight (8/203 = 3.9%) semen samples from bulls were considered nonviable (necrospermia and azoospermia) without relation to the PCR diagnosis. No agglutinin titers were identified in MSPA test. A high frequency (132/203 = 65%) of leptospiral agglutinin titers was identified in the MAT, particularly for the Sejroe serogroup (Hardjo CTG, 100/203 = 49.3%; Wolffi 74/203 = 36.4%; Guaricura 72/203 = 35.5%; and Hardjoprajitno 56/203 = 27.6%). Three (3/203 = 1.5%) semen samples of bulls were positive in the PCR, but these results were not confirmed by sequencing. The high frequency of serovars from the Sejroe serogroup typically adapted to bovines indicates the need for measures for the prophylaxis/control of the pathogen on the sampled farms. Discrepancies among the MAT, sperm viability, and molecular detection of leptospires in semen highlight the need for a combination of methods to diagnose leptospirosis in bovine bulls. To our knowledge, modified seminal plasma agglutination is described for the first time here to investigate anti-Leptospira antibodies produced locally in the genital tract in the diagnosis of bovine leptospirosis among bulls that reproduce by natural means., (© 2021. Sociedade Brasileira de Microbiologia.)

Shiga toxigenic Escherichia coli (STEC) is one of the most important food-borne zoonotic bacterial pathogens responsible for causing gastrointestinal infections, haemorrhagic colitis and haemolytic uremic syndrome. The present study was aimed to isolate and characterize STEC from neonatal dairy calves, animal handlers and their surrounding environment and to establish the genetic relationship among isolates by multilocus sequence typing (MLST). A total number of 115 samples were collected and processed for the isolation of E. coli. The occurrence rate of E. coli was 92.2% (106/115), of which, 18 were typed as STEC. Antibacterial susceptibility analysis revealed 11 (61.1%) strains as multiple drug-resistant (MDR). MLST analysis has delineated 16 sequence types (STs) including nine novel STs. Among STs, ST58 dominated with three strains and was recovered from the environment and neonatal calves. Strains from neonatal calves and humans showed genetic relatedness with significant bootstrap support values indicative of zoonotic transmission potentiality. Analysis of 211 global isolates belonging to 61 STs indicated predominant STs (ST 21, ST 33 and ST 3416) that can be either host-specific (ST 33 and ST 3416) or can be shared among human and bovine hosts (ST 21). The MLST analysis indicates genetic relatedness among isolates and the results predispose inter-host transmission and zoonotic spread., (© 2021. Sociedade Brasileira de Microbiologia.)

Background: The effect of live yeast Saccharomyces cerevisiae strain CNCM I-1077 (SC) on the ruminal degradability of different forages commonly found in dairy diets in South America was evaluated. We also assessed if SC supplementation interacts with forage group to affect ruminal fiber degradability. Four non-lactating rumen-cannulated Holstein cows were randomly assigned to two treatment sequences: Control-SC-Control or SC-Control-SC, in a switchback design, with three 30-day periods. Cows in the SC treatment were supplied with 1 × 10 10 colony-forming units of yeast daily via rumen cannula. In situ degradability of dry matter (DM) and neutral detergent fiber (aNDF) was measured in 15 forages collected in South America. Forages were assigned to one of three groups: corn silages; tropical grasses (sugarcane silages and tropical grass silages); and temperate grasses and alfalfa (oat silages, ryegrass silages, alfalfa silage, and alfalfa hay)., Results: Cows supplemented with SC had higher (P = 0.05) counts of yeasts and lower (P = 0.03) concentration of lactate in rumen fluid. There was no interaction between forage group and yeast supplementation (P > 0.10) on in situ degradability. The SC increased DM (by 4.6%) and aNDF degradation (by 10.3%) at 24 h of incubation (P < 0.05). Metabolomics revealed that a chemical entity (C 17 H 29 N 6 O 3 , m/z 365.2284 [M + H] + ) from the family of lipids and related molecules was suppressed in the rumen fluid of cows supplemented with SC., Conclusion: The SC supplementation improved DM and aNDF degradability regardless of the forage group. © 2021 Society of Chemical Industry., (© 2021 Society of Chemical Industry.)