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 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 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 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.Item Phenotypic characterization and genome analysis of a novel Salmonella Typhimurium phage having unique tail fiber genes.(Springer Nature Limited, 2022-04-06) Sattar S; Ullah I; Khanum S; Bailie M; Shamsi B; Ahmed I; Shah STA; Javed S; Ghafoor A; Pervaiz A; Sohail F; Shah NA; Imdad K; Bostan N; Altermann ESalmonella enterica serovar Typhimurium is a foodborne pathogen causing occasional outbreaks of enteric infections in humans. Salmonella has one of the largest pools of temperate phages in its genome that possess evolutionary significance for pathogen. In this study, we characterized a novel temperate phage Salmonella phage BIS20 (BIS20) with unique tail fiber genes. It belongs to the subfamily Peduovirinae genus Eganvirus and infects Salmonella Typhimurium strain (SE-BS17; Acc. NO MZ503545) of poultry origin. Phage BIS20 was viable only at biological pH and temperature ranges (pH7 and 37 °C). Despite being temperate BIS20 significantly slowed down the growth of host strain for 24 h as compared to control (P < 0.009). Phage BIS20 features 29,477-base pair (bp) linear DNA genome with 53% GC content and encodes for 37 putative ORFs. These ORFs have mosaic arrangement as indicated by its ORF similarity to various phages and prophages in NCBI. Genome analysis indicates its similarity to Salmonella enterica serovar Senftenberg prophage (SEStP) sequence (Nucleotide similarity 87.7%) and Escherichia virus 186 (~ 82.4% nucleotide similarity). Capsid genes were conserved however those associated with tail fiber formation and assembly were unique to all members of genus Eganvirus. We found strong evidence of recombination hotspot in tail fiber gene. Our study identifies BIS20 as a new species of genus Eganvirus temperate phages as its maximum nucleotide similarity is 82.4% with any phage in NCBI. Our findings may contribute to understanding of origin of new temperate phages.Item Nourishing the Infant Gut Microbiome to Support Immune Health: Protocol of SUN (Seeding Through Feeding) Randomized Controlled Trial.(JMIR Publications, 2024-09-02) Wall CR; Roy NC; Mullaney JA; McNabb WC; Gasser O; Fraser K; Altermann E; Young W; Cooney J; Lawrence R; Jiang Y; Galland BC; Fu X; Tonkie JN; Mahawar N; Lovell AL; Ma SBackground: The introduction of complementary foods during the first year of life influences the diversity of the gut microbiome. How this diversity affects immune development and health is unclear. Objective: This study evaluates the effect of consuming kūmara or kūmara with added banana powder (resistant starch) compared to a reference control at 4 months post randomization on the prevalence of respiratory tract infections and the development of the gut microbiome. Methods: This study is a double-blind, randomized controlled trial of mothers and their 6-month-old infants (up to n=300) who have not yet started solids. Infants are randomized into one of 3 groups: control arm (C), standard kūmara intervention (K), and a kūmara intervention with added banana powder product (K+) to be consumed daily for 4 months until the infant is approximately 10 months old. Infants are matched for sex using stratified randomization. Data are collected at baseline (prior to commencing solid food) and at 2 and 4 months after commencing solid food (at around 8 and 10 months of age). Data and samples collected at each timepoint include weight and length, intervention adherence (months 2 and 4), illness and medication history, dietary intake (months 2 and 4), sleep (diary and actigraphy), maternal dietary intake, breast milk, feces (baseline and 4 months), and blood samples (baseline and 4 months). Results: The trial was approved by the Health and Disability Ethics Committee of the Ministry of Health, New Zealand (reference 20/NTA/9). Recruitment and data collection did not commence until January 2022 due to the COVID-19 pandemic. Data collection and analyses are expected to conclude in January 2024 and early 2025, respectively. Results are to be published in 2024 and 2025. Conclusions: The results of this study will help us understand how the introduction of a specific prebiotic complementary food affects the microbiota and relative abundances of the microbial species, the modulation of immune development, and infant health. It will contribute to the expanding body of research that aims to deepen our understanding of the connections between nutrition, gut microbiota, and early-life postnatal health. Trial Registration: Australian New Zealand Clinical Trials Registry ACTRN12620000026921; https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=378654 International Registered Report Identifier (IRRID): DERR1-10.2196/56772 JMIR Res Protoc 2024;13:e56772Item PLAN-M; Mycobacteriophage Endolysins Fused to Biodegradable Nanobeads Mitigate Mycobacterial Growth in Liquid and on Surfaces.(Frontiers Media S.A., 2021-04-26) Davies CG; Reilly K; Altermann E; Hendrickson HL; Butaye PRThe Mycobacteria are a genus of Actinobacteria that include human pathogens such as Mycobacterium tuberculosis (TB). Active TB disease can spread by airborne transmission to healthcare workers and to their community. The HHMI SEA-PHAGES program has contributed to discovering bacteriophages that are able to infect M. smegmatis MC2 155, a close relative of M. tuberculosis. This collection of diverse Mycobacteriophages is an excellent resource for trialling bacteriophage-sourced enzymes in novel applications. Herein we measured the ability Mycobacteriophage endolysins to lyse their host strain when functionally fused to biodegradable polyhydroxyalkanoate (PHA) nanobeads. PHA nanobeads facilitate both the expression and the application of enzymes to surfaces and have been demonstrated to stabilize a wide array of proteins for practical applications whilst eliminating the challenges of traditional protein purification. We selected two Lysin A and six Lysin B homologs to be functionally fused to the polyhydroxyalkanoate synthase C (PhaC). Expression of these constructs resulted in functional lysins displayed on the surface of PHA nanobeads. The lysins thus directionally displayed on nanobeads lysed up to 79% of the M. smegmatis MC2 155 population using 80 mg/mL of nanobeads in pure culture. In order to determine whether the nanobeads would be effective as a protective layer in PPE we adapted a fabric-based test and observed a maximum of 1 log loss of the cell population after 5 h of exposure on a textile (91% cell lysis). Lysin B enzymes performed better than the Lysin A enzymes as a protective barrier on textiles surface assays. These results suggest that bacterial endolysins are efficient in their action when displayed on PHA nanobeads and can cause significant population mortality in as little as 45 min. Our results provide the proof-of-principle that Mycobacteriophage endolysins can be used on functionalized nanobeads where they can protect surfaces such as personal protective equipment (PPE) that routinely come into contact with aerosolised bacteria.