Journal Articles
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Item The Host Adaptation of Staphylococcus aureus to Farmed Ruminants in New Zealand, With Special Reference to Clonal Complex 1(John Wiley and Sons Ltd, 2025-06) Nesaraj J; Grinberg A; Laven R; Chanyi R; Altermann E; Bandi C; Biggs PJGenetic features of host adaptation of S. aureus to ruminants have been extensively studied, but the extent to which this adaptation occurs in nature remains unknown. In New Zealand, clonal complex 1 (CC1) is among the most common lineages in humans and the dominant lineage in cattle, enabling between-, and within-CC genomic comparisons of epidemiologically cohesive samples of isolates. We assessed the following genomic benchmarks of host adaptation to ruminants in 277 S. aureus from cattle, small ruminants, humans, and pets: 1, phylogenetic clustering of ruminant strains; 2, abundance of homo-specific ruminant-adaptive factors, and 3, scarcity of heterospecific factors. The genomic comparisons were complemented by comparative analyses of the metabolism of carbon sources that abound in ruminant milk. We identified features fulfilling the three benchmarks in virtually all ruminant isolates, including CC1. Data suggest the virulomes adapt to the ruminant niche sensu lato accross CCs. CC1 forms a ruminant-adapted clade that appears better equipped to utilise milk carbon sources than human CC1. Strain flow across the human–ruminant interface appears to only occur occasionally. Taken together, the results suggest a specialisation, rather than mere adaptation, clarifying why zoonotic and zoo-anthroponotic S. aureus transmission between ruminants and humans has hardly ever been reported.Item Genetic regulation of antibody responsiveness to immunization in substrains of BALB/c mice.(John Wiley and Sons Inc., 2019-01-01) Poyntz HC; Jones A; Jauregui R; Young W; Gestin A; Mooney A; Lamiable O; Altermann E; Schmidt A; Gasser O; Weyrich L; Jolly CJ; Linterman MA; Gros GL; Hawkins ED; Forbes-Blom EAntibody-mediated immunity is highly protective against disease. The majority of current vaccines confer protection through humoral immunity, but there is high variability in responsiveness across populations. Identifying immune mechanisms that mediate low antibody responsiveness may provide potential strategies to boost vaccine efficacy. Here, we report diverse antibody responsiveness to unadjuvanted as well as adjuvanted immunization in substrains of BALB/c mice, resulting in high and low antibody response phenotypes. Furthermore, these antibody phenotypes were not affected by changes in environmental factors such as the gut microbiota composition. Antigen-specific B cells following immunization had a marked difference in capability to class switch, resulting in perturbed IgG isotype antibody production. In vitro, a B-cell intrinsic defect in the regulation of class-switch recombination was identified in mice with low IgG antibody production. Whole genome sequencing identified polymorphisms associated with the magnitude of antibody produced, and we propose candidate genes that may regulate isotype class-switching capability. This study highlights that mice sourced from different vendors can have significantly altered humoral immune response profiles, and provides a resource to interrogate genetic regulators of antibody responsiveness. Together these results further our understanding of immune heterogeneity and suggest additional research on the genetic influences of adjuvanted vaccine strategies is warranted for enhancing vaccine efficacy.Item Editorial: Mobile DNA element-driven evolution of bacterial pathogens(Frontiers Media S A, 2025-03-19) Cloeckaert A; Zygmunt MS; Vale FF; Altermann E; Li TItem Isolation and characterization of Methanosphaera sp. ISO3-F5, a member of a novel and widespread species of rumen methanogens growing with methanol plus hydrogen(The Microbes, 2024-12-03) Jeyanathan J; Palevich N; Reilly K; Palevich FP; Maclean PH; Li D; Altermann E; Kim CC; van Scheepstal IM; Hoskin SO; Kelly WJ; Leahy SC; Attwood GT; Ronimus RS; Henderson G; Janssen PHRumen methanogens predominantly fall into two physiological groups: hydrogenotrophs which use hydrogen (H2) to reduce carbon dioxide (CO2) to methane (CH4), and methylotrophs which use H2 to reduce methanol and methylamines as substrates for methanogenesis. We used a dilution to extinction approach to isolate two hydrogenotrophic Methanocatella spp. and four cultures of methylotrophic methanogens from sheep rumen contents. Three of the methylotrophs were stable mixed cultures containing methanogens belonging to different lineages of the order Methanomassiliicoccales and one was a pure Methanosphaera culture. Methanosphaera sp. ISO3-F5 has a comparatively large genome (2.68 Mb) comprised of two replicons, a chromosome and a megaplasmid. The genome has an average G + C content of 30.5 % and encodes 2360 putative protein-coding genes. Cells of ISO3-F5 have a spherical shape, 0.6–1.2 µm in diameter, usually occurring in pairs or loose clumps, and have no flagellum. Cells stain Gram positive, have a single thick cell wall and divide by the formation of a cross wall. The optimum temperature for growth was 39°C to 42°C and the optimum pH was 6.7–6.8. Acetate was required for growth, but CH4 was not produced from acetate, formate, ethanol, methylamine, or isopropanol with or without H2/CO2. Volatile fatty acids and rumen fluid were also found to enhance the growth of ISO3-F5, while coenzyme M did not. ISO3-F5 produced CH4 from methanol in the presence of H2 and the genes encoding the necessary methanogenesis pathway have been identified. Based on morphological, physiological, and genomic characteristics, ISO3-F5 is a new species of the genus Methanosphaera. Our study shows that simple isolation methods allowed us to culture diverse and significant members of the rumen methanogen community.Item The Classification and Evolution of Bacterial Cross-Feeding(Frontiers Media S.A., 2019-05-14) Smith NW; Shorten PR; Altermann E; Roy NC; McNabb WC; Harcombe WBacterial feeding has evolved toward specific evolutionary niches and the sources of energy differ between species and strains. Although bacteria fundamentally compete for nutrients, the excreted products from one strain may be the preferred energy source or a source of essential nutrients for another strain. The large variability in feeding preferences between bacterial strains often provides for complex cross-feeding relationships between bacteria, particularly in complex environments such as the human lower gut, which impacts on the host's digestion and nutrition. Although a large amount of information is available on cross-feeding between bacterial strains, it is important to consider the evolution of cross-feeding. Adaptation to environmental stimuli is a continuous process, thus understanding the evolution of microbial cross-feeding interactions allows us to determine the resilience of microbial populations to changes to this environment, such as changes in nutrient supply, and how new interactions might emerge in the future. In this review, we provide a framework of terminology dividing bacterial cross-feeding into four forms that can be used for the classification and analysis of cross-feeding dynamics. Under the proposed framework, we discuss the evolutionary origins for the four forms of cross-feeding and factors such as spatial structure that influence their emergence and subsequent persistence. This review draws from both the theoretical and experimental evolutionary literature to provide a cross-disciplinary perspective on the evolution of different types of cross-feeding.Item Sustainable Management of Medicago sativa for Future Climates: Insect Pests, Endophytes and Multitrophic Interactions in a Complex Environment(Frontiers Media S.A., 2022-04-26) McNeill MR; Tu X; Altermann E; Beilei W; Shi S; Stout MJMedicago sativa L. (alfalfa, syn. lucerne) is an important forage crop for livestock, which is subject to attack from a range of insect pests and susceptible to diseases that can reduce production and persistence. This review considers the main insect pests affecting M. sativa in China and New Zealand as well as the wider plant resistance mechanisms and multitrophic interaction that occur between plants, insect pests, entomopathogens, endophytes, the environment, and climate change. This is with a view to identifying new research opportunities applicable to M. sativa that can be applied to improving production and persistence of this important agricultural crop. These opportunities include identification and activity of entomopathogens/endophytes (e.g., Bacillus and Pseudomonas spp., Metarhizium spp.) and plant growth enhancers (Trichoderma), as well as multitrophic plant-insect-microbial interactions.Item The Effects of Unfermented and Fermented Cow and Sheep Milk on the Gut Microbiota.(Frontiers Media S.A., 2019-03-06) Rettedal EA; Altermann E; Roy NC; Dalziel JE; Mayo BA variety of fermented foods have been linked to improved human health, but their impacts on the gut microbiome have not been well characterized. Dairy products are one of the most popular fermented foods and are commonly consumed worldwide. One area we currently lack data on is how the process of fermentation changes the gut microbiota upon digestion. What is even less well characterized are the possible differences between cow and other mammals' milks. Our aim was to compare the impact of unfermented skim milk and fermented skim milk products (milk/yogurt) originating from two species (cow/sheep) on the gut microbiome using a rat model. Male Sprague-Dawley rats were fed a dairy-free diet supplemented with one of four treatment dairy drinks (cow milk, cow yogurt, sheep milk, sheep yogurt) for 2 weeks. The viable starter culture bacteria in the yogurts were depleted in this study to reduce their potential influence on gut bacterial communities. At the end of the study, cecal samples were collected and the bacterial community profiles determined via 16S rRNA high-throughput sequencing. Fermentation status drove the composition of the bacterial communities to a greater extent than their animal origin. While overall community alpha diversity did not change among treatment groups, the abundance of a number of taxa differed. The cow milk supplemented treatment group was distinct, with a higher intragroup variability and a distinctive taxonomic composition. Collinsella aerofaciens was of particularly high abundance (9%) for this group. Taxa such as Firmicutes and Lactobacillus were found in higher abundance in communities of rats fed with milk, while Proteobacteria, Bacteroidetes, and Parabacteroides were higher in yogurt fed rats. Collinsella was also found to be of higher abundance in both milk (vs. yogurt) and cows (vs. sheep). This research provides new insight into the effects of unfermented vs. fermented milk (yogurt) and animal origin on gut microbial composition in a healthy host. A number of differences in taxonomic abundance between treatment groups were observed. Most were associated with the effects of fermentation, but others the origin species, or in the case of cow milk, unique to the treatment group. Future studies focusing on understanding microbial metabolism and interactions, should help unravel what drives these differences.Item Editorial: Recent advances and perspectives on the gastrointestinal microbiota of small ruminants.(Frontiers Media S.A., 2024-09-09) Vargas-Bello-Pérez E; Altermann E; Tudisco R; Zhang Q; Puniya AK; Cherdthong A; Knut RRecent research on the gastrointestinal (GI) microbiota of small ruminants such as goats and sheep have provided fascinating insights into their microbial ecology and its impact on health and productivity. Some key advances and perspectives in this field relate to microbial diversity and composition, revealing a diverse array of microbial species inhabiting the GI tract of small ruminants. Members of these microbiomes include bacteria, fungi, protozoa, and archaea, each playing unique roles in the nutrient digestion, immune modulation, and overall gut health. It has been demonstrated that the functional capabilities of GI microbiota, include the fermentation of dietary substrates, synthesis of vitamins, and metabolite production (e.g., short-chain fatty acids). These metabolites influence host physiology, including energy metabolism and immune function.Item Whole-Genome Sequencing of Clostridium sp. Strain FP2, Isolated from Spoiled Venison.(American Society for Microbiology, 2020-04-30) Palevich N; Palevich FP; Maclean PH; Jauregui R; Altermann E; Mills J; Brightwell G; Cuomo CAClostridium sp. strain FP2 was isolated from vacuum-packaged refrigerated spoiled venison in New Zealand. This report describes the generation and annotation of the 5.6-Mb draft genome sequence of Clostridium sp. FP2, which will facilitate future functional genomic studies to improve our understanding of premature spoilage of red meats.Item The Role of Segmented Filamentous Bacteria in Immune Barrier Maturation of the Small Intestine at Weaning.(Frontiers Media S.A., 2021-11-18) Oemcke LA; Anderson RC; Altermann E; Roy NC; McNabb WC; De Los Reyes-Gavilan CGThe microbiological, physical, chemical, and immunological barriers of the gastrointestinal tract (GIT) begin developing in utero and finish maturing postnatally. Maturation of these barriers is essential for the proper functioning of the GIT. Maturation, particularly of the immunological barrier, involves stimulation by bacteria. Segmented filamentous bacteria (SFB) which are anaerobic, spore-forming commensals have been linked to immune activation. The presence and changes in SFB abundance have been positively correlated to immune markers (cytokines and immunoglobulins) in the rat ileum and stool samples, pre- and post-weaning. The abundance of SFB in infant stool increases from 6 months, peaks around 12 months and plateaus 25 months post-weaning. Changes in SFB abundance at these times correlate positively and negatively with the production of interleukin 17 (IL 17) and immunoglobulin A (IgA), respectively, indicating involvement in immune function and maturation. Additionally, the peak in SFB abundance when a human milk diet was complemented by solid foods hints at a diet effect. SFB genome analysis revealed enzymes involved in metabolic pathways for survival, growth and development, host mucosal attachment and substrate acquisition. This narrative review discusses the current knowledge of SFB and their suggested effects on the small intestine immune system. Referencing the published genomes of rat and mouse SFB, the use of food substrates to modulate SFB abundance is proposed while considering their effects on other microbes. Changes in the immune response caused by the interaction of food substrate with SFB may provide insight into their role in infant immunological barrier maturation.