Browsing by Author "Altermann E"

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    A Mathematical Model for the Hydrogenotrophic Metabolism of Sulphate-Reducing Bacteria.
    (Frontiers Media S.A., 2019-07-17) Smith NW; Shorten PR; Altermann E; Roy NC; McNabb WC; Greening C
    Sulphate-reducing bacteria (SRB) are studied across a range of scientific fields due to their characteristic ability to metabolise sulphate and produce hydrogen sulphide, which can lead to significant consequences for human activities. Importantly, they are members of the human gastrointestinal microbial population, contributing to the metabolism of dietary and host secreted molecules found in this environment. The role of the microbiota in host digestion is well studied, but the full role of SRB in this process has not been established. Moreover, from a human health perspective, SRB have been implicated in a number of functional gastrointestinal disorders such as Irritable Bowel Syndrome and the development of colorectal cancer. To assist with the study of SRB, we present a mathematical model for the growth and metabolism of the well-studied SRB, Desulfovibrio vulgaris in a closed system. Previous attempts to model SRB have resulted in complex or highly specific models that are not easily adapted to the study of SRB in different environments, such as the gastrointestinal tract. We propose a simpler, Monod-based model that allows for easy alteration of both key parameter values and the governing equations to enable model adaptation. To prevent any incorrect assumptions about the nature of SRB metabolic pathways, we structure the model to consider only the concentrations of initial and final metabolites in a pathway, which circumvents the current uncertainty around hydrogen cycling by SRB. We parameterise our model using experiments with varied initial substrate conditions, obtaining parameter values that compare well with experimental estimates in the literature. We then validate our model against four independent experiments involving D. vulgaris with further variations to substrate availability. Further use of the model will be possible in a number of settings, notably as part of larger models studying the metabolic interactions between SRB and other hydrogenotrophic microbes in the human gastrointestinal tract and how this relates to functional disorders.
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    Characterization of two novel lytic bacteriophages having lysis potential against MDR avian pathogenic Escherichia coli strains of zoonotic potential.
    (Springer Nature Limited, 2023-06-20) Sattar S; Bailie M; Yaqoob A; Khanum S; Fatima K; Altaf AURB; Ahmed I; Shah STA; Munawar J; Zehra QA; Daud S; Arshad A; Imdad K; Javed S; Tariq A; Bostan N; Altermann E
    Avian pathogenic E. coli (APEC) is associated with local and systemic infections in poultry, ducks, turkeys, and many other avian species, leading to heavy economical losses. These APEC strains are presumed to possess zoonotic potential due to common virulence markers that can cause urinary tract infections in humans. The prophylactic use of antibiotics in the poultry sector has led to the rapid emergence of Multiple Drug Resistant (MDR) APEC strains that act as reservoirs and put human populations at risk. This calls for consideration of alternative strategies to decrease the bacterial load. Here, we report isolation, preliminary characterization, and genome analysis of two novel lytic phage species (Escherichia phage SKA49 and Escherichia phage SKA64) against MDR strain of APEC, QZJM25. Both phages were able to keep QZJM25 growth significantly less than the untreated bacterial control for approximately 18 h. The host range was tested against Escherichia coli strains of poultry and human UTI infections. SKA49 had a broader host range in contrast to SKA64. Both phages were stable at 37 °C only. Their genome analysis indicated their safety as no recombination, integration and host virulence genes were identified. Both these phages can be good candidates for control of APEC strains based on their lysis potential.
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    Competition for Hydrogen Prevents Coexistence of Human Gastrointestinal Hydrogenotrophs in Continuous Culture.
    (Frontiers Media S.A., 2020-05-29) Smith NW; Shorten PR; Altermann E; Roy NC; McNabb WC; Kappler U
    Understanding the metabolic dynamics of the human gastrointestinal tract (GIT) microbiota is of growing importance as research continues to link the microbiome to host health status. Microbial strains that metabolize hydrogen have been associated with a variety of both positive and negative host nutritional and health outcomes, but limited data exists for their competition in the GIT. To enable greater insight into the behaviour of these microbes, a mathematical model was developed for the metabolism and growth of the three major hydrogenotrophic groups: sulphate-reducing bacteria (SRB), methanogens and reductive acetogens. In batch culture simulations with abundant sulphate and hydrogen, the SRB outcompeted the methanogen for hydrogen due to having a half-saturation constant 106 times lower than that of the methanogen. The acetogen, with a high model threshold for hydrogen uptake of around 70 mM, was the least competitive. Under high lactate and zero sulphate conditions, hydrogen exchange between the SRB and the methanogen was the dominant interaction. The methanogen grew at 70% the rate of the SRB, with negligible acetogen growth. In continuous culture simulations, both the SRB and the methanogen were washed out at dilution rates above 0.15 h-1 regardless of substrate availability, whereas the acetogen could survive under abundant hydrogen conditions. Specific combinations of conditions were required for survival of more than one hydrogenotroph in continuous culture, and survival of all three was not possible. The stringency of these requirements and the inability of the model to simulate survival of all three hydrogenotrophs in continuous culture demonstrates that factors outside of those modelled are vital to allow hydrogenotroph coexistence in the GIT.
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    Complete Annotated Genome Sequence of Limosilactobacillus fermentum AGR1487.
    (American Society for Microbiology, 2021-01-07) Bailie MA; Altermann E; Young W; Roy NC; McNabb WC; Putonti C
    Limosilactobacillus fermentum is a probiotic species; however, L. fermentum AGR1487 increases colon inflammation in germfree mice and decreases barrier integrity in Caco-2 cells. The AGR1487 genome was sequenced to explore these phenotypes. The genome is a single, circular, 1,939,032-bp chromosome with a G+C content of 52.17% and no plasmids.
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    Complete Genome Sequence of Lactobacillus fermentum Strain AGR1485, a Human Oral Isolate.
    (American Society for Microbiology, 2020-09-03) Bailie MA; Altermann E; Young W; Roy NC; McNabb WC; Gill SR
    Lactobacillus fermentum is found in food products and is generally considered safe. L. fermentum AGR1485 promotes barrier integrity in Caco-2 cells and has genetic similarities to other known probiotic L. fermentum strains. L. fermentum AGR1485 has potential as a probiotic and was sequenced to explore these probiotic properties. The genome is a 2.2-Mbp circular chromosome with no plasmids and a GC content of 51.15%.
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    Complete genome sequence of Methanosphaera sp. ISO3-F5, a rumen methylotrophic methanogen.
    (American Society for Microbiology, 2024-04-11) Palevich N; Jeyanathan J; Reilly K; Palevich FP; Maclean PH; Li D; Altermann E; Kelly WJ; Leahy SC; Attwood GT; Ronimus RS; Henderson G; Janssen PH; Stedman KM
    Methanosphaera spp. are methylotrophic methanogenic archaea and members of the order Methanobacteriales with few cultured representatives. Methanosphaera sp. ISO3-F5 was isolated from sheep rumen contents in New Zealand. Here, we report its complete genome, consisting of a large chromosome and a megaplasmid (GenBank accession numbers CP118753 and CP118754, respectively).
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    Complete Genome Sequence of Paenibacillus sp. Strain E222, a Bacterial Symbiont of an Epichloë Fungal Endophyte of Ryegrass.
    (American Society for Microbiology, 2020-10-08) Bastías DA; Jauregui R; Applegate ER; Altermann E; Card SD; Johnson LJ; Stajich JE
    We report on the whole-genome sequence of Paenibacillus sp. strain E222, a bacterium isolated from a fresh culture of Epichloë festucae var. lolii, a mutualistic fungal endophyte of perennial ryegrass. The genome has a size of 7.8 Mb and a G+C content of 46% and encodes 6,796 putative protein-coding genes.
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    Complete Genome Sequences of Eight Faecalibacterium sp. Strains Isolated from Healthy Human Stool
    (American Society for Microbiology, 2023-01-24) Fraccascia D; Chanyi RM; Altermann E; Roy NC; Flint SH; McNabb WC; Dunning Hotopp JC
    Eight Faecalibacterium sp. strains were isolated from feces of healthy human volunteers. Here, we describe their genome sequences. The genome sizes ranged from 2.78 Mbp to 3.23 Mbp, with an average GC content of 56.6% and encoding 2,795 protein-coding genes on average.
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    Culture and genome-based analysis of four soil Clostridium isolates reveal their potential for antimicrobial production
    (BioMed Central Ltd, 2021-12) Pahalagedara ASNW; Jauregui R; Maclean P; Altermann E; Flint S; Palmer J; Brightwell G; Gupta TB
    BACKGROUND: Soil bacteria are a major source of specialized metabolites including antimicrobial compounds. Yet, one of the most diverse genera of bacteria ubiquitously present in soil, Clostridium, has been largely overlooked in bioactive compound discovery. As Clostridium spp. thrive in extreme environments with their metabolic mechanisms adapted to the harsh conditions, they are likely to synthesize molecules with unknown structures, properties, and functions. Therefore, their potential to synthesize small molecules with biological activities should be of great interest in the search for novel antimicrobial compounds. The current study focused on investigating the antimicrobial potential of four soil Clostridium isolates, FS01, FS2.2 FS03, and FS04, using a genome-led approach, validated by culture-based methods. RESULTS: Conditioned/spent media from all four Clostridium isolates showed varying levels of antimicrobial activity against indicator microorganism; all four isolates significantly inhibited the growth of Pseudomonas aeruginosa. FS01, FS2.2, and FS04 were active against Bacillus mycoides and FS03 reduced the growth of Bacillus cereus. Phylogenetic analysis together with DNA-DNA hybridization (dDDH), average nucleotide identity (ANI), and functional genome distribution (FGD) analyses confirmed that FS01, FS2.2, and FS04 belong to the species Paraclostridium bifermentans, Clostridium cadaveris, and Clostridium senegalense respectively, while FS03 may represent a novel species of the genus Clostridium. Bioinformatics analysis using antiSMASH 5.0 predicted the presence of eight biosynthetic gene clusters (BGCs) encoding for the synthesis of ribosomally synthesized post-translationally modified peptides (RiPPs) and non-ribosomal peptides (NRPs) in four genomes. All predicted BGCs showed no similarity with any known BGCs suggesting novelty of the molecules from those predicted gene clusters. In addition, the analysis of genomes for putative virulence factors revealed the presence of four putative Clostridium toxin related genes in FS01 and FS2.2 genomes. No genes associated with the main Clostridium toxins were identified in the FS03 and FS04 genomes. CONCLUSIONS: The presence of BGCs encoding for uncharacterized RiPPs and NRPSs in the genomes of antagonistic Clostridium spp. isolated from farm soil indicated their potential to produce novel secondary metabolites. This study serves as a basis for the identification and characterization of potent antimicrobials from these soil Clostridium spp. and expands the current knowledge base, encouraging future research into bioactive compound production in members of the genus Clostridium.
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    Differences in Aroma Metabolite Profile, Microstructure, and Rheological Properties of Fermented Milk Using Different Cultures
    (MDPI (Basel, Switzerland), 2023-05-02) Nguyen HTH; Gomes Reis M; Wa Y; Alfante R; Chanyi RM; Altermann E; Day L; Božani´c R
    Texture and flavour are the key attributes determining sensory quality and are highly affected by starter cultures. A selection of phenotypic strains is needed to create diverse texture and flavour to meet consumers' preferences. In this study, the use of five lactic acid bacteria strains in the production of fermented milk, along with the metabolite profiles, microstructure, and rheological properties of the fermented milk samples, was investigated. Our results showed that Lactobacillus helveticus (LH) and Streptococcus thermophilus (ST) had a stronger acidification during fermentation but resulted in products with a coarser protein network compared to Lactococcus lactis (BL1) and Leuconostoc mesenteroides (CL3). Milk fermented by LH had the highest viscosity and exopolysaccharide concentration, while milk fermented by ST had the highest concentration of diacetyl. Although Leuconostoc pseudomesenteroides (CL3ST) had a minimal acidification capability, it produced high levels of ethyl-derived compounds associated with sweet, fruity, and floral fragrances. The results demonstrated that LH and ST could be used as starter cultures targeting fermented milks with different viscosities, while BL1, CL3, and CL3ST are suitable as adjunct cultures to impact different acidic sharpness and flavour notes.
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    Draft Genome Sequence of Clostridium bowmanii DSM 14206T, Isolated from an Antarctic Microbial Mat.
    (American Society for Microbiology, 2022-01-20) Palevich FP; Palevich N; Maclean PH; Altermann E; Mills J; Brightwell G; Gill SR
    Clostridium bowmanii type strain DSM 14206 (ATCC BAA-581) was isolated from a microbial mat sample retrieved from Lake Fryxell, Antarctica. This report describes the generation and annotation of the 4.9-Mb draft genome sequence of C. bowmanii DSM 14206T.
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    Draft Genome Sequence of Clostridium estertheticum subsp. laramiense DSM 14864T, Isolated from Spoiled Uncooked Beef.
    (American Society for Microbiology, 2019-11-21) Palevich N; Palevich FP; Maclean PH; Jauregui R; Altermann E; Mills J; Brightwell G; Newton ILG
    Clostridium estertheticum subsp. laramiense type strain DSM 14864 (ATCC 51254) was isolated from vacuum-packaged refrigerated spoiled beef. This report describes the generation and annotation of the 5.0-Mb draft genome sequence of C. estertheticum subsp. laramiense DSM 14864T.
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    Draft Genome Sequence of Clostridium estertheticum-Like Strain FP3, Isolated from Spoiled Uncooked Lamb.
    (American Society for Microbiology, 2020-05-14) Palevich N; Palevich FP; Maclean PH; Jauregui R; Altermann E; Mills J; Brightwell G; Gill SR
    Clostridium estertheticum-like strain FP3 was isolated from vacuum-packaged refrigerated spoiled lamb. This bacterium is psychrotrophic, Gram positive, spore-forming, and a strict anaerobe. Here, we report the generation and annotation of the 5.6-Mb draft genome sequence of C. estertheticum-like strain FP3.
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    Draft Genome Sequence of Clostridium estertheticum-like Strain FP4, Isolated from Spoiled Uncooked Lamb.
    (American Society for Microbiology, 2020-05-07) Palevich N; Palevich FP; Maclean PH; Jauregui R; Altermann E; Mills J; Brightwell G; Rasco D
    In order to improve the phylogenetic resolution of the genus Clostridium and our limited knowledge of meat spoilage caused by Clostridium estertheticum, the genome of C. estertheticum-like strain FP4 was sequenced. Here, we describe the 4.1-Mb draft genome sequence of C. estertheticum-like strain FP4, isolated from vacuum-packaged refrigerated spoiled lamb.
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    Draft Genome Sequence of Clostridium sp. Strain FP1, with Similarity to Clostridium tagluense, Isolated from Spoiled Lamb.
    (American Society for Microbiology, 2020-04-30) Palevich N; Palevich FP; Maclean PH; Jauregui R; Altermann E; Mills J; Brightwell G; Hotopp JCD
    Clostridium sp. strain FP1 was isolated from vacuum-packaged refrigerated spoiled lamb, and this article describes its 5.4-Mb draft genome sequence. The FP1 genome was sequenced to facilitate source tracking and attribution studies, adding to our understanding of the role of Clostridium species in premature spoilage of red meats.
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    Draft Genome Sequence of Psychrotolerant Clostridium sp. Strain M14, Isolated from Spoiled Uncooked Venison.
    (American Society for Microbiology, 2020-04-16) Palevich N; Palevich FP; Maclean PH; Jauregui R; Altermann E; Mills J; Brightwell G; Hotopp JCD
    Clostridium sp. strain M14 was isolated from vacuum-packaged refrigerated spoiled venison, and this report describes the generation and annotation of its 3.9-Mb draft genome sequence.
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    Draft Genome Sequences of Macrococcus caseolyticus, Macrococcus canis, Macrococcus bohemicus, and Macrococcus goetzii.
    (American Society for Microbiology, 2019-05-09) Mazhar S; Altermann E; Hill C; McAuliffe O; Cuomo C
    Here, we present the draft genome sequences of 14 strains of 4 species of the genus Macrococcus These strains were isolated from bovine milk and tongue samples obtained during a screening program.
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    Draft Genome Sequences of the Type Strains of Six Macrococcus Species.
    (American Society for Microbiology, 2019-05-09) Mazhar S; Altermann E; Hill C; McAuliffe O; Cuomo C
    We report here the draft genome sequences of Macrococcus bovicus ATCC 51825T, Macrococcus carouselicus ATCC 51828T, Macrococcus equipercicus ATCC 51831T, Macrococcus brunensis CCM4811T, Macrococcus hajekii CCM4809T, and Macrococcus lamae CCM4815T The availability of the genome sequences of these species will enable cross-species comparison, which could lead to a more comprehensive understanding of organisms of the Macrococcus genus.
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    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 R
    Recent 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.
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    Editors' Prelude to Microbiome Research Reports.
    (OAE Publishing, 2021-07-20) Ventura M; van Sinderen D; Turroni F; Milani C; Munoz J; Haller D; Ross RP; Collado MC; Allen-Vercoe E; Del Rio D; Altermann E; Katayama T; Zoetendal EG; Belzer C; Mena P; Im S-H; Gueimonde M; Margolles A; Ruiz L; Lacroix C; Stanton C; Barbara G; Saminen S; Scott KP; Barrangou R; Bottacini F; Marco ML
    It is our sincere pleasure to introduce a new scientific journal named Microbiome Research Reports (acronym MRR), born out of an ambitious initiative from the Editorial Board of this new journal. Our motivation to initiate a new journal on microbiome research was driven by the importance and impact of the microbiome for human and planetary health, with related research interest and effort driven by the scientific community on the subject. In fact, research findings on this subject represent a Copernican Revolution influencing all research branches of the Life Sciences. For example, vast efforts are currently invested in elucidating potential links between microbiome and disease, which could lead to the discovery of microbial biomarkers for novel therapeutic and preventative strategies. We feel that it is very timely to launch a new journal focusing on Microbiome studies in humans and other animals, i.e., both wild- and domesticated- animals, being convinced that it will be a platform for the dissemination of microbiome discoveries.