Institut für Nutztierwissenschaften

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Mendelian randomisation to uncover causal associations between conformation, metabolism, and production as potential exposure to reproduction in German Holstein dairy cattle
(2025) Schwarz, Leopold; Heise, Johannes; Liu, Zengting; Bennewitz, Jörn; Thaller, Georg; Tetens, Jens; Schwarz, Leopold; Department of Animal Sciences, Georg-August-University, 37077, Göttingen, Germany; Heise, Johannes; Vereinigte Informationssysteme Tierhaltung w.V. (VIT), 27283, Verden, Germany; Liu, Zengting; Vereinigte Informationssysteme Tierhaltung w.V. (VIT), 27283, Verden, Germany; Bennewitz, Jörn; Institute of Animal Science, University of Hohenheim, 70599, Stuttgart, Germany; Thaller, Georg; Institute of Animal Breeding and Husbandry, Christian-Albrechts-University, 24118, Kiel, Germany; Tetens, Jens; Department of Animal Sciences, Georg-August-University, 37077, Göttingen, Germany
Background: Reproduction is vital to welfare, health, and economics in animal husbandry and breeding. Health and reproduction are increasingly being considered because of the observed genetic correlations between reproduction, health, conformation, and performance traits in dairy cattle. Understanding the detailed genetic architecture underlying these traits would represent a major step in comprehending their interplay. Identifying known, putative or novel associations in genomics could improve animal health, welfare, and performance while allowing further adjustments in animal breeding. Results: We conducted genome-wide association studies for 25 different traits belonging to four different complexes, namely reproduction (n = 13), conformation (n = 6), production (n = 3), and metabolism (n = 3), using a cohort of over 235,000 dairy cows. As a result, we identified genome-wide significant signals for all the studied traits. The obtained summary statistics collected served as the input for a Mendelian randomisation approach (GSMR) to infer causal associations between putative exposure and reproduction traits. The study considered conformation, production, and metabolism as exposure and reproduction as outcome. A range of 139 to 252 genome-wide significant SNPs per combination were identified as instrumental variables (IVs). Out of 156 trait combinations, 135 demonstrated statistically significant effects, thereby enabling the identification of the responsible IVs. Combinations of traits related to metabolism (38 out of 39), conformation (68 out of 78), or production (29 out of 39) were found to have significant effects on reproduction. These relationships were partially non-linear. Moreover, a separate variance component estimation supported these findings, strongly correlating with the GSMR results and offering suggestions for improvement. Downstream analyses of selected representative traits per complex resulted in identifying and investigating potential physiological mechanisms. Notably, we identified both trait-specific SNPs and genes that appeared to influence specific traits per complex, as well as more general SNPs that were common between exposure and outcome traits. Conclusions: Our study confirms the known genetic associations between reproduction traits and the three complexes tested. It provides new insights into causality, indicating a non-linear relationship between conformation and reproduction. In addition, the downstream analyses have identified several clustered genes that may mediate this association.
Weaning age influences indicators of rumen function and development in female Holstein calves
(2022) Schwarzkopf, Sarah; Kinoshita, Asako; Hüther, Liane; Salm, Laurenz; Kehraus, Saskia; Südekum, Karl-Heinz; Huber, Korinna; Dänicke, Sven; Frahm, Jana; Schwarzkopf, Sarah; Department of Functional Anatomy of Livestock, Institute of Animal Science, University of Hohenheim, Stuttgart, Germany; Kinoshita, Asako; Department of Functional Anatomy of Livestock, Institute of Animal Science, University of Hohenheim, Stuttgart, Germany; Hüther, Liane; Institute of Animal Nutrition, Friedrich-Loeffler-Institute, Braunschweig, Germany; Salm, Laurenz; Institute of Animal Nutrition, Friedrich-Loeffler-Institute, Braunschweig, Germany; Kehraus, Saskia; Institute of Animal Science, University of Bonn, Bonn, Germany; Südekum, Karl-Heinz; Institute of Animal Science, University of Bonn, Bonn, Germany; Huber, Korinna; Department of Functional Anatomy of Livestock, Institute of Animal Science, University of Hohenheim, Stuttgart, Germany; Dänicke, Sven; Institute of Animal Nutrition, Friedrich-Loeffler-Institute, Braunschweig, Germany; Frahm, Jana; Institute of Animal Nutrition, Friedrich-Loeffler-Institute, Braunschweig, Germany
Background: Prenatal and postnatal conditions are crucial for the development of calves. Primiparous cows are still maturing during pregnancy, thus competing with the nutritional needs of their offspring. Therefore, mature cows might provide a superior intrauterine condition. Furthermore, weaning calves at an older age might affect them positively as well by reducing stress and offering time for various organs and their functions to develop. We aimed to evaluate effects of mothers’ parity and calves’ weaning age on gastrointestinal development and corresponding acid–base balance. Fifty-nine female German Holstein calves (about 8 days old) were investigated in a 2 × 2 factorial experiment with factors weaning age (7 vs. 17 weeks) and parity of mother (primiparous vs. multiparous). Calves were randomly assigned to one of these four groups. Animal behavior that was observed included resting, chewing and active behavior. Results: Behavioral patterns were interactively affected by time and weaning age. Rumen sounds per 2 min increased in early-weaned calves during their weaning period. In late-weaned calves a consistently increase in rumen sounds was already recorded before their weaning period. Urinary N-containing compounds (creatinine, hippuric acid, uric acid, urea, allantoin) were interactively affected by time and weaning age. Concentrations of all measured compounds except urea increased during early weaning. All except hippuric acid concentration decreased in early-weaned calves after weaning. In late-weaned calves allantoin and uric acid increased before weaning and did not change during weaning. Conclusion: These results suggest that late-weaned calves developed adequate rumen functions and acid–base balance, whereas early-weaned calves might have suffered from ruminal acidosis and catabolism. Weaning calves at 7 weeks of age might be too early for an adequate rumen development.
Unraveling the role of shrimp hydrolysate as a food supplement in the immune function and fecal microbiota of beagle dogs
(2025) Guilherme-Fernandes, Joana; Barroso, Carolina; Correia, Alexandra; Aires, Tiago; Yergaliyev, Timur; Camarinha-Silva, Amélia; Vilanova, Manuel; Fonseca, António J. M.; Lima, Sofia A. C.; Maia, Margarida R. G.; Cabrita, Ana R. J.; Guilherme-Fernandes, Joana; REQUIMTE, LAQV, ICBAS, School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal; Barroso, Carolina; REQUIMTE, LAQV, ICBAS, School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal; Correia, Alexandra; i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal; Aires, Tiago; SORGAL, Sociedade de Óleos e Rações S.A. S. João Ovar, Portugal; Yergaliyev, Timur; Hohenheim Center for Livestock Microbiome Research, HoLMiR, University of Hohenheim, Stuttgart, Germany; Camarinha-Silva, Amélia; Hohenheim Center for Livestock Microbiome Research, HoLMiR, University of Hohenheim, Stuttgart, Germany; Vilanova, Manuel; i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal; Fonseca, António J. M.; REQUIMTE, LAQV, ICBAS, School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal; Lima, Sofia A. C.; REQUIMTE, LAQV, ICBAS, School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal; Maia, Margarida R. G.; REQUIMTE, LAQV, ICBAS, School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal; Cabrita, Ana R. J.; REQUIMTE, LAQV, ICBAS, School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
The inclusion of protein hydrolysates from animal by-products in petfood may enhance the industry’s sustainability, while contributing to dogs’ health due to their nutritional and functional properties. However, inconsistent results of protein hydrolysates on gut microbiota, immune responses, among other health parameters, have been observed in dogs. This study aimed to evaluate the effects of diets supplemented with 5% shrimp hydrolysate, compared to non-supplemented diets, on hematological parameters, serum chemistry profile, innate and adaptive immune function, and fecal microbiota composition in adult Beagle dogs during a 12-week feeding trial. Dietary inclusion of shrimp hydrolysate decreased blood eosinophils ( P = 0.017) and glucose levels ( P = 0.023), while increasing levels of white blood cells ( P = 0.002), platelets ( P = 0.038), neutrophils ( P = 0.036), and CD4 + ( P < 0.001) and CD8 + T cells ( P < 0.001) single producers of tumor necrosis factor-alpha. It also led to a more extensive proliferation of CD4 + T cells in response to LipL32 antigen ( P = 0.020) and to a decrease in superoxide production in stimulated cells ( P = 0.002). Additionally, supplemented diets increased Oscillospiraceae ( P-adj = 0.005) and Clostridia ( P-adj = 0.017) abundance, and decreased such of Sellimonas ( P-adj = 0.025). Overall, the results indicate that diet supplementation with shrimp hydrolysate at 5% modulates the immune response and fecal microbiota, highlighting its potential to be included in hypoallergenic and gastrointestinal diets, and in diets for diabetic dogs.
Fecal cortisol metabolites indicate increased stress levels in horses during breaking-in: a pilot study
(2025) Krieber, Julia; Nowak, Aurelia C.; Geissberger, Jakob; Illichmann, Oliver; Macho-Maschler, Sabine; Palme, Rupert; Dengler, Franziska; Krieber, Julia; Institute of Physiology and Pathophysiology, Department of Biological Sciences and Pathobiology, University of Veterinary Medicine Vienna, 1210 Vienna, Austria, (A.C.N.);; Nowak, Aurelia C.; Institute of Physiology and Pathophysiology, Department of Biological Sciences and Pathobiology, University of Veterinary Medicine Vienna, 1210 Vienna, Austria, (A.C.N.);; Geissberger, Jakob; Institute of Physiology and Pathophysiology, Department of Biological Sciences and Pathobiology, University of Veterinary Medicine Vienna, 1210 Vienna, Austria, (A.C.N.);; Illichmann, Oliver; Institute of Physiology and Pathophysiology, Department of Biological Sciences and Pathobiology, University of Veterinary Medicine Vienna, 1210 Vienna, Austria, (A.C.N.);; Macho-Maschler, Sabine; Experimental Endocrinology, Department of Biological Sciences and Pathobiology, University of Veterinary Medicine Vienna, 1210 Vienna, Austria;; Palme, Rupert; Experimental Endocrinology, Department of Biological Sciences and Pathobiology, University of Veterinary Medicine Vienna, 1210 Vienna, Austria;; Dengler, Franziska; Institute of Physiology and Pathophysiology, Department of Biological Sciences and Pathobiology, University of Veterinary Medicine Vienna, 1210 Vienna, Austria, (A.C.N.);; Madigan, John
Sport horses are frequently exposed to situations that were identified as stressors, indicated by an increased cortisol release, which might impair animal welfare. However, while many studies deal with the impact of exercise, transport, and competition on stress in horses, little is known about the early phase of a horse’s sports career and studies investigating the stress level of young horses during breaking-in are limited. To compare stress levels in unridden horses, horses during breaking-in, and horses in training we collected fecal samples of young, unridden horses ( n = 28) and of horses in different training stages ( n = 13) and measured fecal cortisol metabolite (FCM) concentrations. Our preliminary results showed that FCM concentrations of unridden horses were significantly lower than those of horses in training (Mann–Whitney rank sum test, p < 0.001). Particularly in the first year under the saddle FCMs were significantly higher than in unridden horses (one way ANOVA + post hoc Holm–Sidak test, p < 0.05), with a tendency for FCM levels to decrease with time in training. Furthermore, we observed that within the group of ridden horses there was a larger range of variability in FCM levels, suggesting individual variations regarding their ability to deal with (training-induced) stress. These results indicate that breaking-in is a stressful time for young horses, underlining the importance of carrying out the initial training as carefully as possible.
The potential of gene editing and genomic selection in improving quantitative traits: A simulation study regarding dual-purpose chicken
(2024) Chuang, Edward; Bennewitz, Jörn
The practice of chick culling is the killing of day-old chicks of the layer line chicken. Because of their inability to lay eggs and inefficiency to grow meat, killing them instead of raising them is more economically efficient. In recent years, this practice has raised ethical concerns and led to the ban of this practice in several countries, including Germany and France. One of the several possible solutions is the use of dual-purpose chicken. Unlike the commercial layers, the dual-purpose chicken has abilities in both egg laying and meat production. Even though dual-purpose chicken has better meat growth performance compared to the commercial layers, the use of dual-purpose chicken is still challenging. One of the major challenges to improve dual-purpose chicken is the negative correlation between egg production and meat production. To cope with this negative correlation, some have proposed that gene editing could be a helpful tool to mitigate the problem. The aim of this simulation study is to explore the potential of gene editing to improve negatively correlated quantitative traits. To be more specific, given the aforementioned reasons, the negative correlation between the meat and egg production traits in chicken was chosen as the topic of this study. That is, chicken breeding programs that develop and improve dual-purpose chicken were simulated to discuss the potential of gene editing in animal breeding programs. Chapter 1 begins this thesis with a general introduction of the background to the problem of chick culling, the challenge of developing dual-purpose chicken, and the use of gene editing. Some previous simulation studies on the use of gene editing to improve quantitative traits in animal breeding programs is also introduced in this chapter. Chapter 2 presents a literature review that discusses how gene editing technologies could change the breeding and production of farm animals. In accordance with this thesis's aim, a specific focus was placed on improving quantitative traits. By reviewing the technical and social limitations of gene editing, this review provides a basis for further discussion of the feasibility of the gene-editing implementation as presented in the next chapters. Chapter 3 introduces the simulation framework to explore the potential of gene editing in chicken breeding programs. This framework first simulates two divergently selected lines that reflect the commercial layers and broilers. Based on these two lines, two alternative breeding programs were simulated. One is to develop a dual-purpose line from a layer line (the L-Pure Scenario), while the other selects and improves a synthetic line obtained from a cross between a layer line and a broiler line (the L-B cross scenario). In both breeding schemes, gene editing was integrated into the genomic selection scheme applying optimal contribution selection. The simulation presented in Chapter 4 considers multiplex genome editing that could edit five to one hundred single nucleotide variants at a time. These variants include the causal variants and other falsely edited variants. The results suggest that multiplex gene editing is beneficial in both the L-Pure and the L-B cross scenarios. It also demonstrated that when the risk of negative off-target effect exists, editing more nucleotides does not guarantee extra genetic gain. The simulation presented in Chapter 5 considers the introduction of major genes that would have larger effects on meat production. Here, only the L-Pure scenario is considered. Different to Chapter 4, in this chapter, editing is only possible with only one gene at a time. This chapter aims to study the effects of the numbers of major genes and the pleiotropy (on egg production and meat production). The results suggest that gene editing would be beneficial in dual-purpose chicken breeding programs when the gene is mildly pleiotropic. Chapter 6 ends the thesis with a general discussion that covers the limitations of this study and the possibilities to further expand the simulation study.
An evaluation of the lineage of Brucella isolates in turkey by a whole-genome single-nucleotide polymorphism analysis
(2024) Akar, Kadir; Holzer, Katharina; Hoelzle, Ludwig E.; Yıldız Öz, Gülseren; Abdelmegid, Shaimaa; Baklan, Emin Ayhan; Eroğlu, Buket; Atıl, Eray; Moustafa, Shawky A.; Wareth, Gamal; Elkhayat, Manar; Akar, Kadir; Faculty of Veterinary Medicine, Van Yuzuncu Yıl University, 65090 Van, Turkey; Holzer, Katharina; Department of Livestock Infectiology and Environmental Hygiene, Institute of Animal Science, University of Hohenheim, 70599 Stuttgart, Germany;; Hoelzle, Ludwig E.; Department of Livestock Infectiology and Environmental Hygiene, Institute of Animal Science, University of Hohenheim, 70599 Stuttgart, Germany;; Yıldız Öz, Gülseren; NRL for Brucellosis, Pendik Veterinary Control Institute, 34890 Istanbul, Turkey; (G.Y.Ö.); (E.A.B.); (B.E.); (E.A.); Abdelmegid, Shaimaa; Faculty of Veterinary Medicine, Assiut University, Assiut 71515, Egypt;; Baklan, Emin Ayhan; NRL for Brucellosis, Pendik Veterinary Control Institute, 34890 Istanbul, Turkey; (G.Y.Ö.); (E.A.B.); (B.E.); (E.A.); Eroğlu, Buket; NRL for Brucellosis, Pendik Veterinary Control Institute, 34890 Istanbul, Turkey; (G.Y.Ö.); (E.A.B.); (B.E.); (E.A.); Atıl, Eray; NRL for Brucellosis, Pendik Veterinary Control Institute, 34890 Istanbul, Turkey; (G.Y.Ö.); (E.A.B.); (B.E.); (E.A.); Moustafa, Shawky A.; Faculty of Veterinary Medicine, Benha University, Toukh 13736, Egypt; (S.A.M.); (M.E.); Wareth, Gamal; Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institute, 07743 Jena, Germany;; Elkhayat, Manar; Faculty of Veterinary Medicine, Benha University, Toukh 13736, Egypt; (S.A.M.); (M.E.); Pedersen, Karl
Brucellosis is a disease caused by the Brucella ( B. ) species. It is a zoonotic disease that affects farm animals and causes economic losses in many countries worldwide. Brucella has the ability to persist in the environment and infect the host at low doses. Thus, it is more important to trace brucellosis outbreaks, identify their sources of infection, and interrupt their transmission. Some countries already have initial data, but most of these data are based on a Multiple-Locus Variable-Number Tandem-Repeat Analysis (MLVA), which is completely unsuitable for studying the Brucella genome. Since brucellosis is an endemic disease in Turkey, this study aimed to examine the genome of Turkish Brucella isolates collected between 2018 and 2020, except for one isolate, which was from 2012. A total of 28 strains of B. melitensis ( n = 15) and B. abortus ( n = 13) were analyzed using a core-genome single-nucleotide polymorphism (cgSNP) analysis. A potential connection between the Turkish isolates and entries from Sweden, Israel, Syria, Austria, and India for B. melitensis was detected. For B. abortus , there may be potential associations with entries from China. This explains the tight ties found between Brucella strains from neighboring countries and isolates from Turkey. Therefore, it is recommended that strict measures be taken and the possible effects of uncontrolled animal introduction are emphasized.
Subconjunctival bleedings in neonatal calves: a case series report
(2022) Steffl, Martin; Nautscher, Nadine; Steffl, Martin; Faculty of Agricultural Sciences, Institute of Animal Science, University of Hohenheim, Stuttgart, Germany; Nautscher, Nadine; Faculty of Agricultural Sciences, Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
Background: In animals, only few reports exist about the occurrence and causes of subconjunctival bleedings, especially in newborn calves. Most case reports and studies showed that the major risk factors for subconjunctival bleedings in animals are traumatic events such as birth trauma and traffic accidents, respectively. In neonatal babies, it is suggested that compression of the thorax and abdomen during delivery or forces generated in utero during labor may raise venous pressure to conjunctival vessels and can cause subconjunctival bleedings. Results: The incidence of bleedings in neonatal Holstein–Friesian calves was 2.4 per cent of 289 neonatal calves examined over a six-year period. In general, two types of subconjunctival bleedings were seen. One was usually in a semilunar fashion immediately outside the limbus of the eye. The other type was a stripe or macule of variable size at different positions of the sclera. The subconjunctival bleedings were not related to gestational time. In all cases, affected calves were born without assistance. Multiparous cows were more often involved in the calves with subconjunctival bleedings. Two calves examined haematologically did not show signs of anemia or thrombocytopenia. Conclusions: Subconjunctival bleedings in neonatal calves appear not to be incidental findings. Main causes or associated conditions of subconjunctival bleedings were not found.
Endogenous mucosal phosphatases characterization in duodenum brush border membrane of laying hens
(2025) Hanauska, Anna; Sommerfeld, Vera; Schollenberger, Margit; Huber, Korinna; Rodehutscord, Markus
Chicken mucosal phosphatases can partially degrade phytate contained in the feed. Little is known about the characteristics and degradation products of such mucosal phosphatases and the effects of age and genetic strain of the chicken. The objective of this study was to characterize endogenous mucosal phosphatases of two laying hen strains fed diets with or without mineral phosphorus (P) before and after the onset of egg laying. Hens of the strains Lohmann Brown-classic (LB) and Lohmann LSL-classic (LSL) were sacrificed in weeks 19 and 24 of age after 4 weeks of feeding one of two diets with (P+) or without (P-) mineral P supplement. Mucosa of the duodenum was collected, and the brush border membrane (BBM) of enterocytes was enriched and used for phosphatase activity determination. Additionally, the BBM was used in a modified three-step in vitro assay to study the InsP6 degradation products. The results of both in vitro assays were not significantly affected by hen strain and diet. The activity of mucosal phosphatase in 19-week-old hens was, on average, 0.8 µmol Pi/g BBM protein/min lower than in 24-week-old hens (P < 0.002). Consistently, the InsP6 concentration in the incubation residue was significantly higher in 19-week-old hens than in 24-week-old hens (P < 0.001). In the incubation residue, the concentrations of Ins(1,2,3,4,5)P5, Ins(1,2,3,4,6)P5, and Ins(1,2,3,4)P4 were significantly lower (P ≤ 0.002), and those of InsP3 and InsP2 were significantly higher (P ≤ 0.027) when BBM of 24-week-old hens was used compared to 19-week-old hens. The InsP6 degradation products suggest the activity primarily of a 6- and secondarily of a 5-phytase in the duodenal mucosa. The consistent results from both in vitro assays provide a comprehensive characterization of these enzymes. Under the conditions of this study, small intestine calcium concentration appeared to influence mucosal enzyme activity more than dietary mineral P supplementation.
Composition of the ileum microbiota is a mediator between the host genome and phosphorus utilization and other efficiency traits in Japanese quail (Coturnix japonica)
(2022) Haas, Valentin; Vollmar, Solveig; Preuß, Siegfried; Rodehutscord, Markus; Camarinha-Silva, Amélia; Bennewitz, Jörn; Haas, Valentin; Institute of Animal Science, University of Hohenheim, Stuttgart, Germany; Vollmar, Solveig; Institute of Animal Science, University of Hohenheim, Stuttgart, Germany; Preuß, Siegfried; Institute of Animal Science, University of Hohenheim, Stuttgart, Germany; Rodehutscord, Markus; Institute of Animal Science, University of Hohenheim, Stuttgart, Germany; Camarinha-Silva, Amélia; Institute of Animal Science, University of Hohenheim, Stuttgart, Germany; Bennewitz, Jörn; Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
Background: Phosphorus is an essential nutrient in all living organisms and, currently, it is the focus of much attention due to its global scarcity, the environmental impact of phosphorus from excreta, and its low digestibility due to its storage in the form of phytates in plants. In poultry, phosphorus utilization is influenced by composition of the ileum microbiota and host genetics. In our study, we analyzed the impact of host genetics on composition of the ileum microbiota and the relationship of the relative abundance of ileal bacterial genera with phosphorus utilization and related quantitative traits in Japanese quail. An F2 cross of 758 quails was genotyped with 4k genome-wide single nucleotide polymorphisms (SNPs) and composition of the ileum microbiota was characterized using target amplicon sequencing. Heritabilities of the relative abundance of bacterial genera were estimated and quantitative trait locus (QTL) linkage mapping for the host was conducted for the heritable genera. Phenotypic and genetic correlations and recursive relationships between bacterial genera and quantitative traits were estimated using structural equation models. A genomic best linear unbiased prediction (GBLUP) and microbial (M)BLUP hologenomic selection approach was applied to assess the feasibility of breeding for improved phosphorus utilization based on the host genome and the heritable part of composition of the ileum microbiota. Results: Among the 59 bacterial genera examined, 24 showed a significant heritability (nominal p ≤ 0.05), ranging from 0.04 to 0.17. For these genera, six genome-wide significant QTL were mapped. Significant recursive effects were found, which support the indirect host genetic effects on the host’s quantitative traits via microbiota composition in the ileum of quail. Cross-validated microbial and genomic prediction accuracies confirmed the strong impact of microbial composition and host genetics on the host’s quantitative traits, as the GBLUP accuracies based on the heritable microbiota-mediated components of the traits were similar to the accuracies of conventional GBLUP based on genome-wide SNPs. Conclusions: Our results revealed a significant effect of host genetics on composition of the ileal microbiota and confirmed that host genetics and composition of the ileum microbiota have an impact on the host’s quantitative traits. This offers the possibility to breed for improved phosphorus utilization based on the host genome and the heritable part of composition of the ileum microbiota.
Occurrence of ‘Candidatus Mycoplasma haemosuis’ in fattening pigs, sows and piglets in Germany using a novel gap-based quantitative real-time PCR assay
(2022) Ade, Julia; Stadler, Julia; Ritzmann, Mathias; Zübert, Christina; Hoelzle, Katharina; Hoelzle, Ludwig E.; Ade, Julia; Institute of Animal Science, Department of Livestock Infectiology and Environmental Hygiene, University of Hohenheim, Stuttgart, Germany; Stadler, Julia; Clinic for Swine, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-Universität Munich, Oberschleissheim, Germany; Ritzmann, Mathias; Clinic for Swine, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-Universität Munich, Oberschleissheim, Germany; Zübert, Christina; Institute of Animal Science, Department of Livestock Infectiology and Environmental Hygiene, University of Hohenheim, Stuttgart, Germany; Hoelzle, Katharina; Institute of Animal Science, Department of Livestock Infectiology and Environmental Hygiene, University of Hohenheim, Stuttgart, Germany; Hoelzle, Ludwig E.; Institute of Animal Science, Department of Livestock Infectiology and Environmental Hygiene, University of Hohenheim, Stuttgart, Germany
Background: The appearance of the novel porcine haemotrophic mycoplasma (HM) species ‘Candidatus Mycoplasma haemosuis’ was reported in apparently healthy but also in clinically sick animals in China, Korea and in a case report from Germany. Outside of Asia, however, nothing further is known about the frequency of ‘Ca. M. haemosuis’ in pigs to date. To investigate the distribution of this novel HM species in Germany, fattening pigs, sows and pre-suckling piglets were examined using a herein developed quantitative real-time PCR assay (qPCR). Because the piglets were sampled before the first colostrum uptake, additional information on a possible vertical transmission from dams to their offspring was obtained. Results: Our novel qPCR assay successfully detected ‘Ca. M. haemosuis’ in all blood samples from the ‘Ca. M. haemosuis’-infected pigs. No cross-reactivity was detected when DNA from non-target Mycoplasma spp. and other bacterial species representing 105 bacteria/reaction were used as a template. The lower limit of detection of the qPCR was thus 10 gap gene copies per reaction and 2.5 x 103 genome equivalents (GE) per mL blood. ‘Candidatus M. haemosuis’ was detected by this qPCR in blood samples from a total out of 6.25% sows (13/208), 4.50% pre-suckling piglets (28/622) and 17.50% fattening pigs (35/200). On farm level, 3 out of 21 piglet producing farms (14.28%) and 9 out of 20 fattening farms (45.00%) were positive for ‘Ca. M. haemosuis’. Co-infections with M. suis were evident in all age groups. Conclusion: ‘Candidatus M. haemosuis’ infection is present in German pig farms and the detection of the novel porcine HM species in piglets immediately after birth before colostrum intake indicates vertical transmission. The novel qPCR assay specific for ‘Ca. M. haemosuis’ described herein will be a prerequisite for future studies on the prevalence, epidemiology as well as the clinical and economic impact of ‘Ca. M. haemosuis’ infections.
Structural variants and tandem repeats in the founder individuals of four F2 pig crosses and implications to F2 GWAS results
(2022) Blaj, Iulia; Tetens, Jens; Bennewitz, Jörn; Thaller, Georg; Falker-Gieske, Clemens; Blaj, Iulia; Institute of Animal Breeding and Husbandry, Kiel University, Kiel, Germany; Tetens, Jens; Center for Integrated Breeding Research, Georg-August-University, Göttingen, Germany; Bennewitz, Jörn; Institute of Animal Husbandry and Breeding, University of Hohenheim, Stuttgart, Germany; Thaller, Georg; Institute of Animal Breeding and Husbandry, Kiel University, Kiel, Germany; Falker-Gieske, Clemens; Department of Animal Sciences, Georg-August-University, Göttingen, Germany
Background: Structural variants and tandem repeats are relevant sources of genomic variation that are not routinely analyzed in genome wide association studies mainly due to challenging identification and genotyping. Here, we profiled these variants via state-of-the-art strategies in the founder animals of four F2 pig crosses using whole-genome sequence data (20x coverage). The variants were compared at a founder level with the commonly screened SNPs and small indels. At the F2 level, we carried out an association study using imputed structural variants and tandem repeats with four growth and carcass traits followed by a comparison with a previously conducted SNPs and small indels based association study. Results: A total of 13,201 high confidence structural variants and 103,730 polymorphic tandem repeats (with a repeat length of 2-20 bp) were profiled in the founders. We observed a moderate to high (r from 0.48 to 0.57) level of co-localization between SNPs or small indels and structural variants or tandem repeats. In the association step 56.56% of the significant variants were not in high LD with significantly associated SNPs and small indels identified for the same traits in the earlier study and thus presumably not tagged in case of a standard association study. For the four growth and carcass traits investigated, many of the already proposed candidate genes in our previous studies were confirmed and additional ones were identified. Interestingly, a common pattern on how structural variants or tandem repeats regulate the phenotypic traits emerged. Many of the significant variants were embedded or nearby long non-coding RNAs drawing attention to their functional importance. Through which specific mechanisms the identified long non-coding RNAs and their associated structural variants or tandem repeats contribute to quantitative trait variation will need further investigation. Conclusions: The current study provides insights into the characteristics of structural variants and tandem repeats and their role in association studies. A systematic incorporation of these variants into genome wide association studies is advised. While not of immediate interest for genomic prediction purposes, this will be particularly beneficial for elucidating biological mechanisms driving the complex trait variation.
Determination of optimal phage load and administration time for antibacterial treatment
(2024) Plunder, Steffen; Burkard, Markus; Helling, Thomas; Lauer, Ulrich M.; Hoelzle, Ludwig E.; Marongiu, Luigi
Using phages as antibacterials is becoming a customary practice in Western countries. Nonetheless, successful treatments must consider the growth rate of the bacterial host and the degradation of the virions. Therefore, successful treatments require administering the right amount of phage (viral load, Vφ) at the right moment (administration time, Tφ). The present protocols implement a machine learning approach to determine the best combination of Vφ and Tφ to obtain the elimination of the target bacterium from a system. Basic Protocol 1: One bacterium, one phage. Alternate Protocol 1: One bacterium, one phage (wrapping function). Alternate Protocol 2: One bacterium, one phage (wrapping function, alternative growing model). Basic Protocol 2: Two bacteria, one phage. Alternate Protocol 3: Two bacteria, one phage (launch from terminal).
Impact of added phytase and different dietary InsP6 levels on the structure and core microbiota of the digestive tract in broiler chickens
(2025) Rubio-Cervantes, Ismael; Wolfrum, Stephanie; Rodehutscord, Markus; Camarinha-Silva, Amélia
The main objective of this research was to investigate the composition and shifts of the gut microbiota of broiler chickens in response to varying exogenous phytase combined with increasing levels of myo-inositol (1,2,3,4,5,6) hexakis (dihydrogen phosphate) (InsP6) in the feed. The InsP6 level was adjusted with the addition of oilseed meals (OSM) at the expense of maize starch. A secondary objective was to assess the existence of a core microbiota across the feed, litter and gastrointestinal tract (GIT). A total of 840 Ross 308 broiler chickens were raised in 84 elevated pens in groups of 10. The treatments consisted of four feed mixtures (FM) designed to achieve 1.4 (FM1.4), 1.9 (FM1.9), 2.4 (FM2.4), and, 3.0 (FM3.0) g InsP6-P/kg, each combined with 500, 1500 or 3000 FTU phytase/kg. In the crop and the ileum, Lactobacillus relative abundance decreased when OSM and phytase increased (p < 0.05), while FM2.4 and FM3.0 were associated with increased Ligilactobacillus abundance across the GIT (p < 0.05). No interaction effects were found across the studied sections (p = 0.22). Four amplicon sequence variants (ASV), identified within the genera Lactobacillus, Ligilactobacillus, and Limosilactobacillus were consistently found across the intestine sections. These four ASVs represented 58.9 % of the relative abundance in the crop, 72.9 % in the ileum and 29.7 % in the ceca. The results demonstrated that higher levels of OSM in the feed and exogenous phytase significantly affected these bacterial populations, decreasing Lactobacillus while increasing Ligilactobacillus, indicating independent effects of FM and phytase supplementation.
Assessing functional properties of diet protein hydrolysate and oil from fish waste on canine immune parameters, cardiac biomarkers, and fecal microbiota
(2024) Cabrita, Ana R. J.; Barroso, Carolina; Fontes-Sousa, Ana Patrícia; Correia, Alexandra; Teixeira, Luzia; Maia, Margarida R. G.; Vilanova, Manuel; Yergaliyev, Timur; Camarinha-Silva, Amélia; Fonseca, António J. M.; Cabrita, Ana R. J.; REQUIMTE, Network of Chemistry and Technology, LAQV, Laboratory for Green Chemistry, ICBAS, School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal; Barroso, Carolina; REQUIMTE, Network of Chemistry and Technology, LAQV, Laboratory for Green Chemistry, ICBAS, School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal; Fontes-Sousa, Ana Patrícia; Department of Immuno-Physiology and Pharmacology, Center for Pharmacological Research and Drug Innovation (MedInUP), ICBAS, School of Medicine and Biomedical Sciences, Veterinary Hospital of the University of Porto (UPVET), University of Porto, Porto, Portugal; Correia, Alexandra; ICBAS – School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal; Teixeira, Luzia; ICBAS – School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal; Maia, Margarida R. G.; REQUIMTE, Network of Chemistry and Technology, LAQV, Laboratory for Green Chemistry, ICBAS, School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal; Vilanova, Manuel; ICBAS – School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal; Yergaliyev, Timur; HoLMiR – Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Stuttgart, Germany; Camarinha-Silva, Amélia; HoLMiR – Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Stuttgart, Germany; Fonseca, António J. M.; REQUIMTE, Network of Chemistry and Technology, LAQV, Laboratory for Green Chemistry, ICBAS, School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
Locally produced fish hydrolysate and oil from the agrifood sector comprises a sustainable solution both to the problem of fish waste disposal and to the petfood sector with potential benefits for the animal’s health. This study evaluated the effects of the dietary replacement of mainly imported shrimp hydrolysate (5%) and salmon oil (3%; control diet) with locally produced fish hydrolysate (5%) and oil (3.2%) obtained from fish waste (experimental diet) on systemic inflammation markers, adipokines levels, cardiac function and fecal microbiota of adult dogs. Samples and measurements were taken from a feeding trial conducted according to a crossover design with two diets (control and experimental diets), six adult Beagle dogs per diet and two periods of 6 weeks each. The experimental diet, with higher docosahexaenoic (DHA) and eicosapentaenoic (EPA) acids contents, decreased plasmatic triglycerides and the activity of angiotensin converting enzyme, also tending to decrease total cholesterol. No effects of diet were observed on serum levels of the pro-inflammatory cytokines interleukin (IL)-1β, IL-8, and IL-12/IL-23 p40, and of the serum levels of the anti-inflammatory adipokine adiponectin. Blood pressure, heart rate and echocardiographic measurements were similar between diets with the only exception of left atrial to aorta diameter ratio that was higher in dogs fed the experimental diet, but without clinical relevance. Diet did not significantly affect fecal immunoglobulin A concentration. Regarding fecal microbiome, Megasphaera was the most abundant genus, followed by Bifidobacterium , Fusobacterium , and Prevotella , being the relative abundances of Fusobacterium and Ileibacterium genera positively affected by the experimental diet. Overall, results from the performed short term trial suggest that shrimp hydrolysate and salmon oil can be replaced by protein hydrolysate and oil from fish by-products without affecting systemic inflammatory markers, cardiac structure and function, but potentially benefiting bacterial genera associated with healthy microbiome. Considering the high DHA and EPA contents and the antioxidant properties of fish oil and hydrolysate, it would be worthwhile in the future to assess their long-term effects on inflammatory markers and their role in spontaneous canine cardiac diseases and to perform metabolomic and metagenomics analysis to elucidate the relevance of microbiota changes in the gut.
The 16SrXII-P phytoplasma GOE is separated from other stolbur phytoplasmas by key genomic features
(2025) Toth, Rafael; Huettel, Bruno; Varrelmann, Mark; Kube, Michael; Toth, Rafael; Department of Integrative Infection Biology Crops-Livestock, University of Hohenheim, 70599 Stuttgart, Germany;; Huettel, Bruno; Max Planck-Genome-Center Cologne, 50829 Cologne, Germany;; Varrelmann, Mark; Institute of Sugar Beet Research (IfZ), 37079 Göttingen, Germany;; Kube, Michael; Department of Integrative Infection Biology Crops-Livestock, University of Hohenheim, 70599 Stuttgart, Germany;; Kizheva, Yoana; Hristova, Petya
The syndrome “bassess richesses” is a vector-borne disease of sugar beet in Germany. The gammaproteobacterium ‘ Candidatus Arsenophonus phytopathogenicus’ causes reduced sugar content and biomass, growth abnormalities, and yellowing. Co-infection with the 16SrXII-P stolbur phytoplasmas often leads to more severe symptoms and a risk of complete economic loss. This yellowing agent of the Mollicutes class had not been described before, so its differences from other stolbur phytoplasmas remained unanswered. The genome of strain GOE was sequenced, providing a resource to analyze its characteristics. Phylogenetic position was revised, genome organization was compared, and functional reconstructions of metabolic and virulence factors were performed. Average nucleotide identity analysis indicates that GOE represents a new ‘ Ca. Phytoplasma’ species. Our results show that GOE is also distinct from other stolbur phytoplasmas in terms of smaller genome size and G+C content. Its reductive evolution is reflected in conserved membrane protein repertoire and minimal metabolism. The encoding of a riboflavin kinase indicates a lost pathway of phytoplasmas outside the groups 16SrXII and 16SrXIII. GOE shows a complete tra5 transposon harboring orthologs of SAP11, SAP54, and SAP05 effectors indicating an original phytoplasma pathogenicity island. Our results deepen the understanding of phytoplasma evolution and reaffirm the heterogeneity of stolbur phytoplasmas.
Haemotrophic mycoplasmas infecting pigs: a review of the current knowledge
(2024) Ade, Julia; Eddicks, Matthias; Ritzmann, Mathias; Hoelzle, Katharina; Hoelzle, Ludwig E.; Stadler, Julia; Ade, Julia; Department of Livestock Infectiology and Environmental Hygiene, Institute of Animal Science, University of Hohenheim, 70593 Stuttgart, Germany; Eddicks, Matthias; Clinic for Swine, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-Universität München, 85764 Oberschleissheim, Germany; Ritzmann, Mathias; Clinic for Swine, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-Universität München, 85764 Oberschleissheim, Germany; Hoelzle, Katharina; Department of Livestock Infectiology and Environmental Hygiene, Institute of Animal Science, University of Hohenheim, 70593 Stuttgart, Germany; Hoelzle, Ludwig E.; Department of Livestock Infectiology and Environmental Hygiene, Institute of Animal Science, University of Hohenheim, 70593 Stuttgart, Germany; Stadler, Julia; Clinic for Swine, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-Universität München, 85764 Oberschleissheim, Germany; Highland, Margaret A.
Haemotrophic mycoplasmas (haemoplasmas) are a group of highly specific and adapted bacteria. Three different haemoplasma species in pigs are known to date: Mycoplasma ( M .) suis , M. parvum and ‘ Candidatus ( Ca .) M. haemosuis’. Even though these bacteria have been known in pig farming for a long time, it is difficult to draw general conclusions about the relevance of their infections in pigs. This review summarizes the current knowledge on the three porcine haemoplasma species with regards to clinical and pathological descriptions, pathobiology, epidemiology and diagnostics as well as prevention and therapy. Overall, it is clear that considerably more data are available for M. suis than for the other two species, but generally, porcine haemoplasmas were found to be highly prevalent all over the world. Mycoplasma suis is the most virulent species, causing acute infectious anaemia in pigs (IAP), whereas M. parvum usually results in chronic and subclinical infections associated with performance losses. Little is known about the clinical significance of the recently discovered third porcine species ‘ Ca . M. haemosuis’. So far, the described pathogenic mechanisms mainly include direct destruction of erythrocytes via adhesion, invasion, eryptosis and nutrient scavenging, indirect erythrocyte lysis due to immune-mediated events and immune dysregulation processes. A review of published diagnostic data confirms PCR assays as the current standard method, with various cross-species and species-specific protocols. Overall, there is a need for further examination to obtain valuable insights for practical application, specifically regarding the importance of subclinical infections in naturally infected animals. An essential requirement for this will be to gain a more comprehensive understanding of the mechanisms operating between the host and the pathogen.
Hemotrophic mycoplasmas - vector transmission in livestock
(2024) Arendt, Mareike; Stadler, Julia; Ritzmann, Mathias; Ade, Julia; Hoelzle, Katharina; Hoelzle, Ludwig E.; Arendt, Mareike; Department of Livestock Infectiology and Environmental Hygiene, Institute of Animal Science, University of Hohenheim, 70593 Stuttgart, Germany; (M.A.); (J.A.); (K.H.); Stadler, Julia; Clinic for Swine, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-Universität München, 85764 Oberschleissheim, Germany; (J.S.); (M.R.); Ritzmann, Mathias; Clinic for Swine, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-Universität München, 85764 Oberschleissheim, Germany; (J.S.); (M.R.); Ade, Julia; Department of Livestock Infectiology and Environmental Hygiene, Institute of Animal Science, University of Hohenheim, 70593 Stuttgart, Germany; (M.A.); (J.A.); (K.H.); Hoelzle, Katharina; Department of Livestock Infectiology and Environmental Hygiene, Institute of Animal Science, University of Hohenheim, 70593 Stuttgart, Germany; (M.A.); (J.A.); (K.H.); Hoelzle, Ludwig E.; Department of Livestock Infectiology and Environmental Hygiene, Institute of Animal Science, University of Hohenheim, 70593 Stuttgart, Germany; (M.A.); (J.A.); (K.H.); Dozois, Charles M.
Hemotrophic mycoplasmas (HMs) are highly host-adapted and specialized pathogens infecting a wide range of mammals including farm animals, i.e., pigs, cattle, sheep, and goats. Although HMs have been known for over 90 years, we still do not know much about the natural transmission routes within herds. Recently, it has been repeatedly discussed in publications that arthropod vectors may play a role in the transmission of HMs from animal to animal. This is mainly since several HM species could be detected in different potential arthropod vectors by PCR. This review summarizes the available literature about the transmission of bovine, porcine, ovine, and caprine HM species by different hematophagous arthropod vectors. Since most studies are only based on the detection of HMs in potential vectors, there are rare data about the actual vector competence of arthropods. Furthermore, there is a need for additional studies to investigate, whether there are biological vectors in which HMs can multiply and be delivered to new hosts.
New insights into the phylogeny of the A.Br.161 (“A.Br.Heroin”) clade of Bacillus anthracis
(2024) Antwerpen, Markus; Beyer, Wolfgang; Grass, Gregor; Antwerpen, Markus; Bundeswehr Institute of Microbiology (IMB), 80937 Munich, Germany; Beyer, Wolfgang; Department of Livestock Infectiology and Environmental Hygiene, Institute of Animal Science, University of Hohenheim, 70599 Stuttgart, Germany; Grass, Gregor; Bundeswehr Institute of Microbiology (IMB), 80937 Munich, Germany; Anderson, Deborah
Bacillus anthracis is a rare but highly dangerous zoonotic bacterial pathogen. At the beginning of this century, a new manifestation of the disease, injectional anthrax, emerged as a result of recreational heroin consumption involving contaminated drugs. The organisms associated with this 13-year-lasting outbreak event in European drug consumers were all grouped into the canonical single-nucleotide polymorphism (canSNP) clade A-branch (A.Br.) 161 of B. anthracis . Related clade A.Br.161 strains of B. anthracis not associated with heroin consumption have also been identified from different countries, mostly in Asia. Because of inadvertent spread by anthropogenic activities, other strains of this A.Br.161 lineage were, however, isolated from several countries. Thus, without additional isolates from this clade, its origin of evolution or its autochthonous region remains obscure. Here, we genomically characterized six new A.Br.161 group isolates, some of which were from Iran, with others likely historically introduced into Germany. All the chromosomes of these isolates could be grouped into a distinct sub-clade within the A.Br.161 clade. This sub-clade is separated from the main A.Br.161 lineage by a single SNP. We have developed this SNP into a PCR assay facilitating the future attribution of strains to this group.
Effects of feeding diets without mineral P supplement on intestinal phytate degradation, blood concentrations of Ca and P, and excretion of Ca and P in two laying hen strains before and after onset of laying activity
(2024) Sommerfeld, Vera; Bennewitz, Jörn; Camarinha-Silva, Amélia; Feger, Martina; Föller, Michael; Huber, Korinna; Oster, Michael; Ponsuksili, Siriluck; Schmucker, Sonja; Seifert, Jana; Stefanski, Volker; Wimmers, Klaus; Rodehutscord, Markus
The objective of this study was to characterize intestinal phytate degradation and mineral utilization by 2 laying hen strains before and after the onset of egg laying using diets without or with a mineral phosphorus (P) supplement. One offspring of 10 roosters per strain (Lohmann Brown-classic [LB] and Lohmann LSL-classic [LSL]) was sacrificed before (wk 19) and after (wk 24) the onset of egg-laying activity and following 4 wk placement in a metabolic unit. Diets were corn-soybean meal-based and without supplemented P (P-) or with 1 g/kg supplemented P (P+) from monocalcium phosphate. In wk 19 and 24, the blood plasma and digesta of duodenum+jejunum and distal ileum were collected. The concentration of P in blood plasma was higher in hens fed P+ than P- (P < 0.001). In duodenum + jejunum and ileum content, the concentrations of InsP6, Ins(1,2,4,5,6)P5 and Ins(1,2,3,4,5)P5 were lower in P- than in P+ (P ≤ 0.009). In duodenum+jejunum, the concentrations of InsP6, Ins(1,2,4,5,6)P5 and Ins(1,2,3,4,5)P5 were lower in wk 24 than 19 and lower in LSL than LB hens (P < 0.001). The concentration of myo-inositol (MI) in duodenum + jejunum content was lower in wk 19 than 24 (P < 0.001). Following a 4-d total excreta collection, the retained amount of P was higher in P+ than P- (P < 0.001). Phosphorus retention was lower in LB hens fed P- than in other treatments (P × strain: P = 0.039). In the jejunal tissue, some genes related to intracellular InsP metabolism were higher expressed in LB than LSL hens. The renunciation of mineral P increased endogenous phytate degradation, but more P was retained with supplemented P. Differences in endogenous phytate degradation between the periods before and after the onset of egg laying might be attributed to different Ca concentrations in intestinal digesta caused by different Ca needs in both periods.
Antiviral defense systems in the rumen microbiome
(2025) Sáenz, Johan S.; Rios-Galicia, Bibiana; Seifert, Jana
The continuous interaction between phages and their respective hosts has resulted in the evolution of multiple bacterial immune mechanisms. However, the diversity and prevalence of antiviral defense systems in complex communities are still unknown. We therefore investigated the diversity and abundance of viral defense systems in 3,038 high-quality bacterial and archaeal genomes from the rumen. In total, 14,241 defense systems and 31,948 antiviral-related genes were identified. Those genes represented 114 unique system types grouped into 49 families. We observed a high prevalence of defense systems in the genomes. However, the number of defense systems, defense system families, and system density varied widely from genome to genome. Additionally, the number of defense system per genome correlated positively with the number of defense system families and the genome size. Restriction modification, Abi, and cas system families were the most common, but many rare systems were present in only 1% of the genomes. Antiviral defense systems are prevalent and diverse in the rumen, but only a few are dominant, indicating that most systems are rarely present. However, the collection of systems throughout the rumen may represent a pool of mechanisms that can be shared by different members of the community and modulate the phage–host interaction.

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