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International Microbiology : the... Nov 2022Raw milk samples were collected from 200 dairy cows belonging to Girolando 1/2, Gyr, Guzera, and Holstein breeds, and the bacterial diversity was explored using 16S rRNA...
Raw milk samples were collected from 200 dairy cows belonging to Girolando 1/2, Gyr, Guzera, and Holstein breeds, and the bacterial diversity was explored using 16S rRNA amplicon sequencing. SCC analysis showed that 69 animals were classified as affected with subclinical mastitis. The milk bacterial microbiome was dominated by Firmicutes, Proteobacteria, and Actinobacteria, with an increase of Firmicutes in animals with subclinical mastitis and Proteobacteria in healthy animals. At the family and genus level, the milk bacterial microbiome was dominated by Staphylococcus, Acinetobacter, Pseudomonas, members of the family Enterobacteriaceae, Lactococcus, Aerococcus, members of the family Rhizobiaceae, Anaerobacillus, Streptococcus, members of the family Intrasporangiaceae, members of the family Planococcaceae, Corynebacterium, Nocardioides, and Chryseobacterium. Significant differences in alpha and beta diversity analysis suggest an effect of udder health status and breed on the composition of raw bovine milk microbiota. LEfSe analysis showed 45 and 51 discriminative taxonomic biomarkers associated with udder health status and with one of the four breeds respectively, suggesting an effect of subclinical mastitis and breed on the microbiota of milk in cattle.
Topics: Animals; Bacteria; Cattle; Female; Health Status; Humans; Mastitis, Bovine; Microbiota; Milk; RNA, Ribosomal, 16S
PubMed: 35838927
DOI: 10.1007/s10123-022-00267-4 -
Archives of Microbiology Jul 20222,4,6-trinitrotoluene (TNT), a nitro-aromatic explosive commonly used for defense and several non-violent applications is contributing to serious environmental pollution...
2,4,6-trinitrotoluene (TNT), a nitro-aromatic explosive commonly used for defense and several non-violent applications is contributing to serious environmental pollution problems including human health. The current study investigated the remediation potential of a native soil isolate, i.e., Indiicoccus explosivorum (strain S5-TSA-19) isolated from collected samples of an explosive manufacturing site, against TNT. The survivability of I. explosivorum against explosives is indirectly justified through its isolation; thus, it is being chosen for further study. At a TNT concentration of 120 mg/L within an optimized environment (i.e., at 30 °C and 120 rpm), the isolate was continually incubated for 30 days in a minimal salt medium (MSM). The proliferation of the isolate and the concentration of TNT, nitrate, nitrite, and ammonium ion were evaluated at a particular time during the experiment. Within 168 h (i.e., 7 days) of incubation, I. explosivorum co-metabolically degraded 100% TNT. The biodegradation procedure succeeded the first-order kinetics mechanism. Formations of additional metabolites like 2,4-dinitrotoluene (DNT), 2,4-diamino-6-nitrotoluene (2-DANT), and 2-amino-4,6-dinitrotoluene (2-ADNT), were also witnessed. TNT seems to be non-toxic for the isolate, as it reproduced admirably in TNT presence. To date, it is the first report of Indiicoccus explosivorum, efficiently bio-remediating TNT, i.e., a nitro-aromatic compound via different degradation pathways, leading to the production of simpler as well as less harmful end products. Further, at the field-scale application, Indiicoccus explosivorum may be explored for the bioremediation of TNT (i.e., a nitro-aromatic compound)-contaminated effluents.
Topics: Humans; Biodegradation, Environmental; Kinetics; Planococcaceae; Trinitrotoluene
PubMed: 35778571
DOI: 10.1007/s00203-022-03057-8 -
Zoological Studies 2021Bacteria are known to have explicit roles within the microbiomes of host tissues, therefore examining these communities may prove useful in assessing host health and...
Bacteria are known to have explicit roles within the microbiomes of host tissues, therefore examining these communities may prove useful in assessing host health and responses to environmental change. The present study contributes to the emerging, yet understudied, field of microbiome research in elasmobranchs. We provide a screening of the culturable bacteria communities found on multiple tissue sites on the body surface of blacktip (), bull (), and tiger () sharks near Miami, Florida. Tissue sites include mouth, gills, skin, and any visible wounds. The study adds to our understanding of the diversity of bacteria present on sharks in comparison to their natural environment. We also compare bacterial groups found within wounds in shark skin to healthy tissue sites on the same individual. Results indicate that wounds on an individual may allow for opportunistic bacteria to invade or overgrow where they would not normally be found, which may have potential health consequences for sharks that become wounded due to fishing practices. Identified bacteria belonged to the , , and phyla, known to be prominent bacterial groups associated with marine organisms. Results indicate shark species-specific differences in bacterial communities, including the presence of bacteria belonging to exclusively on the skin of tiger sharks. To our knowledge, this is the first report of this family in any elasmobranch. While most tissue sites displayed commensal bacteria identified in similar studies, known pathogens belonging to and were identified in the wounds of blacktip and bull sharks. Some bacteria may be normal residents, but the loss of protective dermal denticles due to a wound may allow colonization by pathogens. Continued research is needed to explore microbial communities associated with sharks and their influence on host health.
PubMed: 35774257
DOI: 10.6620/ZS.2021.60-69 -
Frontiers in Medicine 2022To determine whether gut microbiota, fatty metabolism and cytokines were associated with immune thrombocytopenia (ITP).
OBJECTIVE
To determine whether gut microbiota, fatty metabolism and cytokines were associated with immune thrombocytopenia (ITP).
METHODS
In total, 29 preliminarily diagnosed ITP patients and 33 healthy volunteers were enrolled. Fecal bacterial were analyzed based on 16S rRNA sequencing. Plasma cytokines and motabolites were analyzed using flow cytometry and liquid chromatography-mass spectrometry (LC-MS), respectively.
RESULTS
, , and were enriched at the genus level in ITP patients, while , , were depleted. At the phylum level, the relative abundance of and increased in ITP patients, while , , and the ratio decreased. Plasma levels of 5-hydroxyeicosatetraenoic acid (5-HETE), 6-trans-12-epi-leukotriene B4 (6t,12e-LTB), and resolvin D2 (RvD) were upregulated, and stachydrine, dowicide A, dodecanoylcarnitine were downregulated in ITP patients. Furthermore, RvD is positively correlated with order , 5-HETE is positively correlated with genus , and 6t,12e-LTB is positively correlated with genus . In addition, stachydrine is positively correlated with family , dowicide A is positively correlated with class , and dodecanoylcarnitine is positively correlated with order . Plasma levels of interleukin-6 (IL-6) and tumor necrosis factor-α (TNF-α) were upregulated in ITP patients.
CONCLUSION
Our study revealed a relationship between microbiota and fatty metabolism in ITP. Gut microbiota may participate in the pathogenesis of ITP through affecting cytokine secretion, interfering with fatty metabolism.
PubMed: 35665326
DOI: 10.3389/fmed.2022.810612 -
Frontiers in Microbiology 2022Malic acid is a component of the rhizosphere exudate and is vital for crop growth. However, little information is available about the effects of external applications of...
Malic acid is a component of the rhizosphere exudate and is vital for crop growth. However, little information is available about the effects of external applications of malic acid on the nutrient absorption and quality of grape fruit, and few studies have been performed on the relationship between the changes in the rhizosphere microbial community and nutrient absorption and fruit quality of grapes after adding malic acid. Here, the LM (low concentration of malic acid) and HM (high concentration of malic acid) treatments comprised 5% and 10% malic acid (the ratio of acid to the total weight of the fertilizer) combined with NPK fertilizer, respectively. Applying malic acid changed the grape rhizosphere microbial community structure and community-level physiological profile (CLPP) significantly, and HM had a positive effect on the utilization of substrates. The microbial community structure in the rhizosphere of the grapes with added malic acid was closely related to the CLPP. The N and P content in the leaves and fruits increased after applying malic acid compared to the control, while K content in the fruits increased significantly. In addition, malic acid significantly reduced the weight per fruit, significantly increased soluble sugar content (SSC) and vitamin C content of the fruit, and significantly improved the fruit sugar-acid ratio and grape tasting score. Moreover, the principal component analysis and grape nutrient and fruit quality scores showed that grape nutrients and fruit quality were significantly affected by malic acid and ranked as 5% malic acid > 10% malic acid > control. Pearson's correlation heatmap of microbial composition, nutrient absorption and fruit quality of the grapes showed that the grape microbial community was closely related to grape nutrients and fruit quality. Adding malic acid was positively correlated to , , and . Furthermore, , , and were closely related to grape nutrient absorption and fruit quality. and were positively correlated with total soluble sugar, while and were positively correlated with titratable acid. Hence, and were the key bacteria that played a major role in grape fruit quality and nutrient absorption after applying malic acid water-soluble fertilizer.
PubMed: 35663858
DOI: 10.3389/fmicb.2022.850807 -
Journal of Bacteriology Jun 2022The current classification of the phylum (new name, ) features eight distinct classes, six of which include known spore-forming bacteria. In Bacillus subtilis,...
The current classification of the phylum (new name, ) features eight distinct classes, six of which include known spore-forming bacteria. In Bacillus subtilis, sporulation involves up to 500 genes, many of which do not have orthologs in other bacilli and/or clostridia. Previous studies identified about 60 sporulation genes of B. subtilis that were shared by all spore-forming members of the . These genes are referred to as the sporulation core or signature, although many of these are also found in genomes of nonsporeformers. Using an expanded set of 180 firmicute genomes from 160 genera, including 76 spore-forming species, we investigated the conservation of the sporulation genes, in particular seeking to identify lineages that lack some of the genes from the conserved sporulation core. The results of this analysis confirmed that many small acid-soluble spore proteins (SASPs), spore coat proteins, and germination proteins, which were previously characterized in bacilli, are missing in spore-forming members of and other classes of . A particularly dramatic loss of sporulation genes was observed in the spore-forming members of the families and . Fifteen species from diverse lineages were found to carry (-interrupting) elements of different sizes that all encoded SpoIVCA-like recombinases but did not share any other genes. Phylogenetic trees built from concatenated alignments of sporulation proteins and ribosomal proteins showed similar topology, indicating an early origin and subsequent vertical inheritance of the sporulation genes. Many members of the phylum () are capable of producing endospores, which enhance the survival of important Gram-positive pathogens that cause such diseases as anthrax, botulism, colitis, gas gangrene, and tetanus. We show that the core set of sporulation genes, defined previously through genome comparisons of several bacilli and clostridia, is conserved in a wide variety of sporeformers from several distinct lineages of . We also detected widespread loss of sporulation genes in many organisms, particularly within the families and Members of these families, such as Lysinibacillus sphaericus and Clostridium innocuum, could be excellent model organisms for studying sporulation mechanisms, such as engulfment, formation of the spore coat, and spore germination.
Topics: Bacillus; Bacillus subtilis; Bacterial Proteins; Clostridium; Firmicutes; Humans; Phylogeny; Spores, Bacterial
PubMed: 35638784
DOI: 10.1128/jb.00079-22 -
Current Microbiology May 2022Gut microbiota is a complex ecosystem composed by trillions of microorganisms that are crucial for human health or disease status. Currently, there are two...
Gut microbiota is a complex ecosystem composed by trillions of microorganisms that are crucial for human health or disease status. Currently, there are two methodological options to explore its complexity: metagenomics and culturomics. Culturomics is an approach that uses multiple culture conditions (days of incubation, enrichment factors and growth temperature) and MALDI-TOF mass spectrometry for the identification of bacterial species and sequencing when this method fails. In this paper, we describe how Colturomic's protocol has allowed the first isolation in human sample of Rummeliibacillus suwonensis, a Gram positive, facultative anaerobe bacterium. The bacterium was isolated from feces of a 69 years old male with amyotrophic lateral sclerosis (ALS) recruited for a clinical trial assessing safety and efficacy of fecal microbiota transplantation in ALS. The first isolation of the microorganism dates back to 2013 from the soil of a South Korean mountain area. In this report, morphological description, biochemical characterization and antibiotic susceptibility tests were performed to outline the bacterial properties.
Topics: Aged; Amyotrophic Lateral Sclerosis; Feces; Humans; Male; Planococcaceae; RNA, Ribosomal, 16S
PubMed: 35595837
DOI: 10.1007/s00284-022-02806-8 -
Applied Microbiology and Biotechnology May 2022Microbially induced calcium carbonate precipitation (MICP) is ubiquitous in the earth's lithosphere and brings the inspiration of bionic cementation technology. Over...
Microbially induced calcium carbonate precipitation (MICP) is ubiquitous in the earth's lithosphere and brings the inspiration of bionic cementation technology. Over recent years, MICP has been proposed as a potential solution to address many environmental and engineering issues. However, the stability of cemented precipitations generated via MICP technology, especially the characteristics and change mechanism of crystal forms, is still unclear, which substantially hindered the understanding of biomineralization and prohibited the application and upscaling of MICP technology. Here, Sporosarcina pasteurii was selected as a model microbe to induce calcium carbonate mineralization in a series of standard nutrient solutions. The authors studied the process of precipitation from amorphous calcium carbonate to calcite crystal form and revealed the assembly behavior and mechanism of precipitations by FTIR, SEM, TEM and EDS. In the two crystal forms of induced calcium carbonate, the relative position and content of C, O, N, P and Ca elements were only slightly different. The molecular attachment and structural match of organic matrix made the crystals form change. Finally, a self-assembly theory was proposed to MICP, and it provided a solid theoretical basis for the technical specification of MICP technology in engineering application. KEY POINTS: • Organic matrix is intensively involved in MICP by forming functional groups. • Molecular attachment and structural match cause calcite crystal evolution. • A self-assembly theory is proposed for MICP.
Topics: Biomineralization; Calcium Carbonate; Chemical Precipitation; Sporosarcina
PubMed: 35501489
DOI: 10.1007/s00253-022-11938-7 -
Environmental Pollution (Barking, Essex... Jul 2022The widely detected pyrene (PYR) is prone to accumulate and pose risks to the soil ecosystem. In this study, an aerobic closed microcosm was constructed to assess the...
The widely detected pyrene (PYR) is prone to accumulate and pose risks to the soil ecosystem. In this study, an aerobic closed microcosm was constructed to assess the effects of PYR at the environmental concentration (12.09 mg kg) on the structure, interactions, and metabolism of carbon sources of soil microbial communities. The results found that half-life of PYR was 37 d and its aerobic biodegradation was mainly implemented by both Gram-negative and Gram-positive bacteria as revealed by the quantitative results. High-throughput sequencing based on 16 S rRNA and ITS genes showed that PYR exposure interfered more significantly with the diversity and abundance of the bacterial community than that of the fungal community. For bacteria, rare species were sensitive to PYR, while Gemmatimonadota, Gaiellales, and Planococcaceae involved in organic pollutants detoxification and degradation were tolerant of PYR stress. Co-occurrence network analysis demonstrated that PYR enhanced the intraspecific cooperation within the bacterial community and altered the patterns of trophic interaction in the fungal community. Furthermore, the keystone taxa and their topological roles were altered, potentially inducing functionality changes. Function annotation suggested PYR inhibited the nitrogen fixation and ammonia oxidation processes but stimulated methylotrophy and methanol oxidation, especially on day 7. For the metabolism, microbial communities accelerated the metabolism of nitrogenous carbon sources (e.g. amine) to meet the physiological needs under PYR stress. This study clarifies the impacts of PYR on the structure, metabolism, and potential N and C cycling functions of soil microbial communities, deepening the knowledge of the environmental risks of PYR.
Topics: Bacteria; Carbon; Microbiota; Pyrenes; Soil; Soil Microbiology
PubMed: 35429592
DOI: 10.1016/j.envpol.2022.119301 -
Journal of Biotechnology May 2022The microbiologically induced calcite precipitation (MICP) can be an emerging approach that could tap onto soil bacterial diversity and use as a bioremediation...
The microbiologically induced calcite precipitation (MICP) can be an emerging approach that could tap onto soil bacterial diversity and use as a bioremediation technique. Based on the concept that bacteria with biomineralization capacity could be effective CaCO inductance agents, this study aimed to evaluate the simultaneous influence of 11 operational and environmental factors on the MICP process, for the first time. Therefore, Bacillus muralis, B. lentus, B. simplex, B. firmus, and B. licheniformis, isolated from alkaline soils, were used in the selection of the best performing bacterium compared with a well-known MICP bioagent Sporosarcina pasteurii DSM 33. Plackett-Burman's experimental design was labouring to screen all independent variables for their significances on five outputs (pH value, number of viable cells and spores, amount of urea and CaCO precipitate). According to experimentally obtained data, an artificial neural network model based on the Broyden-Fletcher-Goldfarb-Shanno algorithm showed good prediction capabilities, while differences in the relative influences were observed at the bacterial strain level. B. licheniformis turn out to be the most potent bioagent, with a maximum amount of CaCO precipitate of 3.14 g/100 mL in the optimal conditions.
Topics: Bacillus; Bacteria; Biomineralization; Calcium Carbonate; Chemical Precipitation; Soil; Sporosarcina
PubMed: 35427694
DOI: 10.1016/j.jbiotec.2022.04.002