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Scientific Reports Jun 2024Anthropological and biophysical processes have shaped livestock genomes over Millenia and can explain their current geographic distribution and genetic divergence. We...
Anthropological and biophysical processes have shaped livestock genomes over Millenia and can explain their current geographic distribution and genetic divergence. We analyzed 57 Ethiopian indigenous domestic goat genomes alongside 67 equivalents of east, west, and north-west African, European, South Asian, Middle East, and wild Bezoar goats. Cluster, ADMIXTURE (K = 4) and phylogenetic analysis revealed four genetic groups comprising African, European, South Asian, and wild Bezoar goats. The Middle Eastern goats had an admixed genome of these four genetic groups. At K = 5, the West African Dwarf and Moroccan goats were separated from East African goats demonstrating a likely historical legacy of goat arrival and dispersal into Africa via the coastal Mediterranean Sea and the Horn of Africa. F, XP-EHH, and Hp analysis revealed signatures of selection in Ethiopian goats overlaying genes for thermo-sensitivity, oxidative stress response, high-altitude hypoxic adaptation, reproductive fitness, pathogen defence, immunity, pigmentation, DNA repair, modulation of renal function and integrated fluid and electrolyte homeostasis. Notable examples include TRPV1 (a nociception gene); PTPMT1 (a critical hypoxia survival gene); RETREG (a regulator of reticulophagy during starvation), and WNK4 (a molecular switch for osmoregulation). These results suggest that human-mediated translocations and adaptation to contrasting environments are shaping indigenous African goat genomes.
Topics: Animals; Goats; Ethiopia; Genome; Phylogeny; Stress, Physiological; Genetic Variation
PubMed: 38942813
DOI: 10.1038/s41598-024-65303-x -
Scientific Reports Jun 2024Mycobacterium avium subspecies paratuberculosis (MAP) is the causative agent of Johne's Disease, a chronic granulomatous enteritis of ruminants. MAP establishes an...
Mycobacterium avium subspecies paratuberculosis (MAP) is the causative agent of Johne's Disease, a chronic granulomatous enteritis of ruminants. MAP establishes an infection in the host via the small intestine. This requires the bacterium to adhere to, and be internalised by, cells of the intestinal tract. The effector molecules expressed by MAP for this purpose remain to be fully identified and understood. Mammalian cell entry (mce) proteins have been shown to enable other Mycobacterial species to attach to and invade host epithelial cells. Here, we have expressed Mce1A, Mce1D, Mce3C and Mce4A proteins derived from MAP on the surface of a non-invasive Escherichia coli to characterise their role in the initial interaction between MAP and the host. To this end, expression of mce1A was found to significantly increase the ability of the E. coli to attach and survive intracellularly in human monocyte-like THP-1 cells, whereas expression of mce1D was found to significantly increase attachment and invasion of E. coli to bovine epithelial cell-like MDBK cells, implying cell-type specificity. Furthermore, expression of Mce1A and Mce1D on the surface of a previously non-invasive E. coli enhanced the ability of the bacterium to infect 3D bovine basal-out enteroids. Together, our data contributes to our understanding of the effector molecules utilised by MAP in the initial interaction with the host, and may provide potential targets for therapeutic intervention.
Topics: Mycobacterium avium subsp. paratuberculosis; Paratuberculosis; Animals; Humans; Cattle; Bacterial Proteins; Bacterial Adhesion; Epithelial Cells; Escherichia coli; Cell Line; THP-1 Cells
PubMed: 38942800
DOI: 10.1038/s41598-024-65592-2 -
Scientific Reports Jun 2024Methicillin-resistant Staphylococcus (MRS) has been associated with neonatal infections, with colonization of the anovaginal tract being the main source of vertical...
Methicillin-resistant Staphylococcus (MRS) has been associated with neonatal infections, with colonization of the anovaginal tract being the main source of vertical transmission. The COVID-19 pandemic has altered the frequency of antibiotic usage, potentially contributing to changes in the dynamics of bacterial agents colonizing humans. Here we determined MRS colonization rates among pregnant individuals attending a single maternity in Rio de Janeiro, Brazil before (January 2019-March 2020) and during (May 2020-March 2021) the COVID-19 pandemic. Anovaginal samples (n = 806 [521 samples before and 285 during the pandemic]) were streaked onto chromogenic media. Colonies were identified by MALDI-TOF MS. Detection of mecA gene and SCCmec typing were assessed by PCR and antimicrobial susceptibility testing was done according to CLSI guidelines. After the onset of the pandemic, MRS colonization rates increased significantly (p < 0.05) from 8.6% (45) to 54.7% (156). Overall, 215 (26.6%) MRS isolates were detected, of which S. haemolyticus was the most prevalent species (MRSH, 84.2%; 181 isolates). SCCmec type V was the most frequent among MRS (63.3%; 136), and 31.6% (68) of MRS strains had a non-typeable SCCmec, due to new combinations of ccr and mecA complexes. Among MRS strains, 41.9% (90) were resistant to at least 3 different classes of antimicrobial agents, and 60% (54) of them were S. haemolyticus harboring SCCmec V. MRS colonization rates and the emergence of multidrug-resistant variants detected in this study indicate the need for continuing surveillance of this important pathogen within maternal and child populations.
Topics: Humans; Female; Pregnancy; COVID-19; Staphylococcal Infections; Methicillin-Resistant Staphylococcus aureus; Adult; Brazil; Pregnancy Complications, Infectious; Anti-Bacterial Agents; SARS-CoV-2; Microbial Sensitivity Tests; Pandemics; Vagina
PubMed: 38942787
DOI: 10.1038/s41598-024-64422-9 -
Scientific Reports Jun 2024Improved and contemporary agriculture relies heavily on pesticides, yet some can be quite persistent and have a stable chemical composition, posing a significant threat...
Improved and contemporary agriculture relies heavily on pesticides, yet some can be quite persistent and have a stable chemical composition, posing a significant threat to the ecology. Removing harmful effects is upon their degradability. Biodegradation must be emphasized to lower pesticide degradation costs, especially in the soil. Here, a decision-making system was used to determine the best microbial strain for the biodegradation of the pyrethroid-contaminated soil. In this system, the criteria chosen as: pH (C), Temp (C), RPM (C), Conc. (C), Degradation (%) (C) and Time required for degradation(hrs) (C); and five alternatives were Bacillus (A), Acinetobacter (A), Escherichia (A), Pseudomonas (A), and Fusarium (A). The best alternative was selected by applying the TOPSIS (technique for order performance by similarity to ideal solution) method, which evaluates based on their closeness to the ideal solution and how well they meet specific requirements. Among all the specified criteria, Acinetobacter (A) was the best and optimal based on the relative closeness value (( ) = 0.740 (A) > 0.544 (A) > 0.480 (A) > 0.403 (A) > 0.296 (A)). However, the ranking of the other alternatives is also obtained in the order Fusarium (A), Bacillus (A), Pseudomonas (A), Escherichia (A). Hence this study suggests Acinetobacter is the best microbial strain for biodegradation of pyrethroids; while least preference should be given to Escherichia. Acinetobacter, versatile metabolic nature with various xenobiotic compounds' degradation ability, is gram-negative, aerobic, coccobacilli, nonmotile, and nonspore forming bacteria. Due to less study about Acinetobacter it is not in that much frame as the other microorganisms. Hence, considering the Acinetobacter strain for the biodegradation study will give more optimal results than the other microbial strains. Novelty of this study, the TOPSIS method is applied first time in selecting the best microbial strain for the biodegradation of pyrethroid-contaminated soil, considering this selection process as multi-criteria decision-making (MCDM) problem.
Topics: Biodegradation, Environmental; Pyrethrins; Soil Pollutants; Soil Microbiology; Bacteria; Bacillus; Fusarium; Decision Making; Pseudomonas; Acinetobacter
PubMed: 38942772
DOI: 10.1038/s41598-024-59223-z -
Methods in Enzymology 2024Octocorals are the most prolific source of terpenoids in the marine environment, with more than 4000 different compounds known from the phylum to date. However, the...
Octocorals are the most prolific source of terpenoids in the marine environment, with more than 4000 different compounds known from the phylum to date. However, the biochemical and genetic origin of their production remained elusive until recent studies showed that octocorals encode genes responsible for the biosynthesis of terpenoids in their own chromosomal DNA rather than from microbial symbionts as originally proposed. The identified coral genes include those encoding a new group of class I terpene cyclases (TCs) clustered among other candidate classes of tailoring enzymes. Phylogenetic analyses established octocoral TCs as a monophyletic clade, distinct from TCs of plants, bacteria, and other organisms. The newly discovered group of TCs appears to be ubiquitous in octocorals and is evolutionarily ancient. Given the recent discovery of octocoral terpenoid biochemistry and only limited genomic data presently available, there is substantial potential for discovering new biosynthetic pathways from octocorals for terpene production. The following chapter outlines practical experimental procedures for octocoral DNA and RNA extraction, genome and transcriptome assembly and mining, TC cloning and gene expression, protein purification, and in vitro analyses.
Topics: Anthozoa; Terpenes; Animals; Phylogeny; Cloning, Molecular; Alkyl and Aryl Transferases
PubMed: 38942510
DOI: 10.1016/bs.mie.2024.02.011 -
Methods in Enzymology 2024Plants are prolific producers of terpenoids. Terpenoid biosynthesis is initiated by terpene synthases (TPS). In plants, two types of terpenes synthase genes are...
Plants are prolific producers of terpenoids. Terpenoid biosynthesis is initiated by terpene synthases (TPS). In plants, two types of terpenes synthase genes are recognized: typical plant TPS genes and microbial-terpene synthase like-genes (MTPSL). While TPS genes are ubiquitous in land plants, MTPSL genes appear to be restricted to non-seed land plants. Evolutionarily, TPS genes are specific to land plants, whereas MTPSL genes have related counterparts in other organisms, especially fungi and bacteria. The presence of microbial type TPS in plants, fungi and bacteria, with the latter two often being associated with plants, poses a challenge in accurately identifying bona fide MTPSL genes in plants. In this chapter, we present bioinformatic procedures designed to identify MTPSL genes in sequenced plant genomes and/or transcriptomes. Additionally, we outline validation methods for confirming the identified microbial-type TPS genes as genuine plant genes. The method described in this chapter can also be adopted to analyze microbial type TPS in organisms other than plants.
Topics: Alkyl and Aryl Transferases; Computational Biology; Plants; Terpenes; Phylogeny; Genes, Plant; Plant Proteins; Bacteria
PubMed: 38942508
DOI: 10.1016/bs.mie.2024.02.014 -
Poultry Science Jun 2024The black soldier fly (BSF, Hermetia illucens) is a resource insect that can utilize livestock and poultry feces. However, BSFs may also increase the risk of...
The black soldier fly (BSF, Hermetia illucens) is a resource insect that can utilize livestock and poultry feces. However, BSFs may also increase the risk of transmission of antibiotic resistance genes (AGRs) that are widespread in livestock and poultry farm environments. Therefore, we aimed to evaluate the biosecurity risks of different BSF treatments in the laying chicken food chain using the "chicken manure-BSF-laying hens" model. Our results indicated that different BSF treatments significantly affected antibiotic residue, ARGs, MGEs, bacterial antibiotic resistance, and bacterial microbial community composition in the food chain of laying hens fed BSFs. These risks can be effectively reduced through starvation treatment and high-temperature grinding treatment. Comprehensive risk assessment analysis revealed that starvation combined with high-temperature milling (Group H) had the greatest effect.
PubMed: 38941787
DOI: 10.1016/j.psj.2024.103965 -
PloS One 2024A growing increase in the number of serious infections caused by multidrug resistant bacteria (MDR) is challenging our society. Despite efforts to discover novel...
A growing increase in the number of serious infections caused by multidrug resistant bacteria (MDR) is challenging our society. Despite efforts to discover novel therapeutic options, few antibiotics targeting MDR have been approved by the Food and Drug Administration (FDA). Lactic acid bacteria have emerged as a promising therapeutic alternative due to their demonstrated ability to combat MDR pathogens in vitro. Our previous co-culture studies showed Lacticaseibacillus rhamnosus CRL 2244 as having a potent killing effect against carbapenem-resistant Acinetobacter baumannii (CRAB) strains. Here we report that cell-free conditioned media (CFCM) samples obtained from Lcb. rhamnosus CRL 2244 cultures incubated at different times display antimicrobial activity against 43 different pathogens, including CRAB, methicillin-resistant Staphylococcus aureus (MRSA) and carbapenemase Klebsiella pneumoniae (KPC)-positive strains. Furthermore, transwell and ultrafiltration analyses together with physical and chemical/biochemical tests showed that Lcb. rhamnosus CRL 2244 secretes a <3 kDa metabolite(s) whose antimicrobial activity is not significantly impaired by mild changes in pH, temperature and various enzymatic treatments. Furthermore, sensitivity and time-kill assays showed that the bactericidal activity of the Lcb. rhamnosus CRL 2244 metabolite(s) enhances the activity of some current FDA approved antibiotics. We hypothesize that this observation could be due to the effects of Lcb. rhamnosus CRL 2244 metabolite(s) on cell morphology and the enhanced transcriptional expression of genes coding for the phenylacetate (PAA) and histidine catabolic Hut pathways, metal acquisition and biofilm formation, all of which are associated with bacterial virulence. Interestingly, the extracellular presence of Lcb. rhamnosus CRL 2244 induced the transcription of the gene coding for the CidA/LgrA protein, which is involved in programmed cell death in some bacteria. Overall, the findings presented in this report underscore the promising potential of the compound(s) released by Lcb. rhamnosus CRL2244 as an alternative and/or complementary option to treat infections caused by A. baumannii as well as other MDR bacterial pathogens.
Topics: Lacticaseibacillus rhamnosus; Anti-Bacterial Agents; Drug Resistance, Multiple, Bacterial; Microbial Sensitivity Tests; Acinetobacter baumannii; Drug Synergism; Methicillin-Resistant Staphylococcus aureus; Culture Media, Conditioned; Bacterial Proteins
PubMed: 38941324
DOI: 10.1371/journal.pone.0306273 -
Methods in Molecular Biology (Clifton,... 2024The strong influence of microbiomes on areas such as ecology and human health has become widely recognized in the past years. Accordingly, various techniques for the...
The strong influence of microbiomes on areas such as ecology and human health has become widely recognized in the past years. Accordingly, various techniques for the investigation of the composition and function of microbial community samples have been developed. Metaproteomics, the comprehensive analysis of the proteins from microbial communities, allows for the investigation of not only the taxonomy but also the functional and quantitative composition of microbiome samples. Due to the complexity of the investigated communities, methods developed for single organism proteomics cannot be readily applied to metaproteomic samples. For this purpose, methods specifically tailored to metaproteomics are required. In this work, a detailed overview of current bioinformatic solutions and protocols in metaproteomics is given. After an introduction to the proteomic database search, the metaproteomic post-processing steps are explained in detail. Ten specific bioinformatic software solutions are focused on, covering various steps including database-driven identification and quantification as well as taxonomic and functional assignment.
Topics: Proteomics; Computational Biology; Workflow; Software; Microbiota; Humans; Databases, Protein; Metagenomics
PubMed: 38941024
DOI: 10.1007/978-1-0716-3910-8_16 -
Methods in Molecular Biology (Clifton,... 2024Root metaproteome analysis can reveal the functions that govern plant-microbe and microbe-microbe interactions under specific environmental conditions. Efficient protein...
Root metaproteome analysis can reveal the functions that govern plant-microbe and microbe-microbe interactions under specific environmental conditions. Efficient protein extraction method from microbes associated with plant roots is crucial for the comprehensive analysis of the metaproteome. In this chapter, a straightforward protein extraction method for roots of Arabidopsis inoculated with a microbial community that uses only milligrams of tissue is outlined. In addition, the plant inoculation using a synthetic community (SynCom) and the methods for a nanoflow liquid chromatography coupled to a high-resolution/high-accuracy mass spectrometer (LC-MS/MS) are described.
Topics: Arabidopsis; Plant Roots; Proteomics; Tandem Mass Spectrometry; Chromatography, Liquid; Workflow; Bacteria; Proteome
PubMed: 38941015
DOI: 10.1007/978-1-0716-3910-8_7