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Rodrigues JTD, Margalho LP, Pia AKR, Sierra H, Tavares L, Marquezini MG, Noronha MF, Cabral L, Junior WJFL, Sant'Ana AS. Comprehensive dynamics of bacterial and fungal diversity throughout concentrated chicken broth processing: Integrating culture-dependent and independent techniques. Int J Food Microbiol 2024; 424:110852. [PMID: 39141974 DOI: 10.1016/j.ijfoodmicro.2024.110852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 07/30/2024] [Accepted: 07/31/2024] [Indexed: 08/16/2024]
Abstract
This study presents comprehensive insights into the microbiological profile across all concentrated chicken broth processing stages, utilizing a combination of amplicon sequencing based on metataxonomic and culturing techniques. Samples were systematically collected throughout the production chain, with each batch yielding 10 samples per day across eight different dates. These samples underwent thorough analysis, including 16S rRNA and ITS sequencing (n = 30), culture-dependent microbiological tests (n = 40), and physical-chemical characterization (n = 10). Culturing analysis revealed the absence of Listeria monocytogenes and Salmonella spp. at any stage of processing, counts of various microorganisms such as molds, yeasts, Enterobacteria, and others remained below detection limits. Notably, spore counts of selected bacterial groups were observed post-processing, indicating the persistence of certain species, including Bacillus cereus and Clostridium perfringens, albeit in low counts. Furthermore, the study identified a diverse array of bacterial and fungal species throughout the processing chain, with notable occurrence of spore-forming bacteria. The presence of spore-forming bacteria in the final product, despite thermal processing, suggests the need for enhanced strategies to mitigate their introduction and persistence in the processing premises. Thus, this study offers valuable insights into microbial dynamics and diversity through processing concentrated chicken broth.
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Mafaldo ÍM, Araújo LM, Cabral L, Barão CE, Noronha MF, Fink JR, de Albuquerque TMR, Dos Santos Lima M, Vidal H, Pimentel TC, Magnani M. Cassava (Manihot esculenta) Brazilian cultivars have different chemical compositions, present prebiotic potential, and beneficial effects on the colonic microbiota of celiac individuals. Food Res Int 2024; 195:114909. [PMID: 39277216 DOI: 10.1016/j.foodres.2024.114909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 08/07/2024] [Accepted: 08/10/2024] [Indexed: 09/17/2024]
Abstract
The purpose of this study was to investigate the potential prebiotic properties of cassava cultivars from Northeast [Doce mel and Ourinho (OUR)] and South [Baiana, and IPR-Upira (UPI)] of Brazil in in vitro fermentation systems. The cultivars were evaluated for their chemical composition, and, then, two cultivars were selected (OUR and UPI) and subjected to in vitro gastrointestinal digestion to assess the effects on probiotics Lacticaseibacillus casei, Lactobacillus acidophilus, and Bifidobacterium animalis growth, metabolic activity, and prebiotic activity scores. Finally, the impact of cassava cultivars on the fecal microbiota of celiac individuals was evaluated using the 16S rRNA gene. Cassava cultivars have variable amounts of fiber, resistant starch, fructooligosaccharides (FOS), organic acids, phenolic compounds, and sugars, with OUR and UPI cultivars standing out. OUR and UPI cultivars contributed to the increase in the proliferation rates of L. casei (0.04-0.19), L. acidophilus (0.34-0.27), and B. animalis (0.10-0.03), resulting in more significant effects than FOS, an established prebiotic compound. Also, the positive scores of prebiotic activities with probiotic strains indicate OUR and UPI's ability to stimulate beneficial bacteria while limiting enteric competitors selectively. In addition, OUR and UPI promoted increased relative abundance of Bifidobacteriaceae, Enterococcaceae, and Lactobacillaceae in the fecal microbiota of celiac individuals while decreased Lachnospirales, Bacteroidales, and Oscillospirales. The results show that cassava cultivars caused beneficial changes in the composition and metabolic activity of the human intestinal microbiota of celiacs. OUR and UPI cultivars from the Northeast and South of Brazil could be considered potential prebiotic ingredients for use in the formulation of functional foods and dietary supplements.
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Casarin RCV, Silva RVCD, Paz HEDS, Stolf CS, Carvalho LM, Noronha MF, Sallum AW, Monteiro MDF. Metatranscriptomic analysis shows functional alterations in subgingival biofilm in young smokers with periodontitis: a pilot study. J Appl Oral Sci 2024; 32:e20240031. [PMID: 39166556 PMCID: PMC11364450 DOI: 10.1590/1678-7757-2024-0031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 06/24/2024] [Indexed: 08/23/2024] Open
Abstract
OBJECTIVE This study aimed to assess the influence of smoking on the subgingival metatranscriptomic profile of young patients affected by stage III/IV and generalized periodontal disease. METHODOLOGY In total, six young patients, both smokers and non-smokers (n=3/group), who were affected by periodontitis were chosen. The STROBE (Strengthening the Reporting of Observational Studies in Epidemiology) guidelines for case-control reporting were followed. Periodontal clinical measurements and subgingival biofilm samples were collected. RNA was extracted from the biofilm and sequenced via Illumina HiSeq. Differential expression analysis used Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, and differentially expressed genes were identified using the Sleuth package in R, with a statistical cutoff of ≤0.05. RESULTS This study found 3351 KEGGs in the subgingival biofilm of both groups. Smoking habits altered the functional behavior of subgingival biofilm, resulting in 304 differentially expressed KEGGs between groups. Moreover, seven pathways were modulated: glycan degradation, galactose metabolism, glycosaminoglycan degradation, oxidative phosphorylation, peptidoglycan biosynthesis, butanoate metabolism, and glycosphingolipid biosynthesis. Smoking also altered antibiotic resistance gene levels in subgingival biofilm by significantly overexpressing genes related to beta-lactamase, permeability, antibiotic efflux pumps, and antibiotic-resistant synthetases. CONCLUSION Due to the limitations of a small sample size, our data suggest that smoking may influence the functional behavior of subgingival biofilm, modifying pathways that negatively impact the behavior of subgingival biofilm, which may lead to a more virulent community.
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Choi BI, Fontes Noronha M, Kaindl J, Wolfe AJ. Complete genome sequences of Aerococcus loyolae ATCC TSD-300 T, Aerococcus mictus ATCC TSD-301 T, and Aerococcus tenax ATCC TSD-302 T. Microbiol Resour Announc 2024; 13:e0015624. [PMID: 38651909 PMCID: PMC11237779 DOI: 10.1128/mra.00156-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 04/05/2024] [Indexed: 04/25/2024] Open
Abstract
Previously identified under the single designation of Aerococcus urinae, three distinct taxonomic species have been distinguished as Aerococcus loyolae, Aerococcus mictus, and Aerococcus tenax. Here, we present the complete genome sequences of the type strains of these species assembled via a combination of short-read and long-read sequencing techniques.Registered at ClinicalTrials.gov (NCT01166438).
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Valiauga R, Talley S, Khemmani M, Fontes Noronha M, Gogliotti R, Wolfe AJ, Campbell E. Sex-dependent effects of carbohydrate source and quantity on caspase-1 activity in the mouse central nervous system. J Neuroinflammation 2024; 21:151. [PMID: 38840215 PMCID: PMC11155082 DOI: 10.1186/s12974-024-03140-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 05/23/2024] [Indexed: 06/07/2024] Open
Abstract
BACKGROUND Mounting evidence links glucose intolerance and diabetes as aspects of metabolic dysregulation that are associated with an increased risk of developing dementia. Inflammation and inflammasome activation have emerged as a potential link between these disparate pathologies. As diet is a key factor in both the development of metabolic disorders and inflammation, we hypothesize that long term changes in dietary factors can influence nervous system function by regulating inflammasome activity and that this phenotype would be sex-dependent, as sex hormones are known to regulate metabolism and immune processes. METHODS 5-week-old male and female transgenic mice expressing a caspase-1 bioluminescent reporter underwent cranial window surgeries and were fed control (65% complex carbohydrates, 15% fat), high glycemic index (65% carbohydrates from sucrose, 15% fat), or ketogenic (1% complex carbohydrates, 79% fat) diet from 6 to 26 weeks of age. Glucose regulation was assessed with a glucose tolerance test following a 4-h morning fast. Bioluminescence in the brain was quantified using IVIS in vivo imaging. Blood cytokine levels were measured using cytokine bead array. 16S ribosomal RNA gene amplicon sequencing of mouse feces was performed to assess alterations in the gut microbiome. Behavior associated with these dietary changes was also evaluated. RESULTS The ketogenic diet caused weight gain and glucose intolerance in both male and female mice. In male mice, the high glycemic diet led to increased caspase-1 biosensor activation over the course of the study, while in females the ketogenic diet drove an increase in biosensor activation compared to their respective controls. These changes correlated with an increase in inflammatory cytokines present in the serum of test mice and the emergence of anxiety-like behavior. The microbiome composition differed significantly between diets; however no significant link between diet, glucose tolerance, or caspase-1 signal was established. CONCLUSIONS Our findings suggest that diet composition, specifically the source and quantity of carbohydrates, has sex-specific effects on inflammasome activation in the central nervous system and behavior. This phenotype manifested as increased anxiety in male mice, and future studies are needed to determine if this phenotype is linked to alterations in microbiome composition.
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de Assis BBT, Pimentel TC, Vidal H, Dos Santos Lima M, de Sousa Galvão M, Madruga MS, Noronha MF, Cabral L, Magnani M. Mangaba pulp fermented with Lacticaseibacillus casei 01 has improved chemical, technological, and sensory properties and positively impacts the colonic microbiota of vegan adults. Food Res Int 2024; 186:114403. [PMID: 38729705 DOI: 10.1016/j.foodres.2024.114403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 04/17/2024] [Accepted: 04/20/2024] [Indexed: 05/12/2024]
Abstract
This study aimed to evaluate the functional, technological, and sensory aspects of mangaba (Hancornia speciosa Gomes) fruit pulp fermented with the probiotic Lacticaseibacillus casei 01 (LC1) during refrigerated storage (7 °C, 28 days). The effects of the fermented mangaba pulp on the modulation of the intestinal microbiota of healthy vegan adults were also assessed. Mangaba pulp allowed high viability of LC1 during storage and after simulated gastrointestinal conditions (≥7 log CFU/g). The fermented mangaba pulp showed lower pH and total soluble solids, and higher titratable acidity, and concentrations of lactic, acetic, citric, and propionic acids during storage compared to non-fermented pulp. Also, it presented a higher concentration of bioaccessible phenolics and volatiles, and improved sensory properties (yellow color, brightness, fresh appearance, and typical aroma and flavor). Fermented mangaba pulp added to in vitro cultured colonic microbiota of vegan adults decreased the pH values and concentrations of maltose, glucose, and citric acid while increasing rhamnose and phenolic contents. Fermented mangaba pulp promoted increases in the abundance of Dorea, Romboutsia, Faecalibacterium, Lachnospira, and Lachnospiraceae ND3007 genera and positively impacted the microbial diversity. Findings indicate that mangaba pulp fermented with LC1 has improved chemical composition and functionality, inducing changes in the colonic microbiota of vegan adults associated with potential benefits for human health.
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Lamichhane J, Choi BI, Stegman N, Fontes Noronha M, Wolfe AJ. Macrolide Resistance in the Aerococcus urinae Complex: Implications for Integrative and Conjugative Elements. Antibiotics (Basel) 2024; 13:433. [PMID: 38786161 PMCID: PMC11117264 DOI: 10.3390/antibiotics13050433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Revised: 05/06/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
The recognition of the Aerococcus urinae complex (AUC) as an emerging uropathogen has led to growing concerns due to a limited understanding of its disease spectrum and antibiotic resistance profiles. Here, we investigated the prevalence of macrolide resistance within urinary AUC isolates, shedding light on potential genetic mechanisms. Phenotypic testing revealed a high rate of macrolide resistance: 45%, among a total of 189 urinary AUC isolates. Genomic analysis identified integrative and conjugative elements (ICEs) as carriers of the macrolide resistance gene ermA, suggesting horizontal gene transfer as a mechanism of resistance. Furthermore, comparison with publicly available genomes of related pathogens revealed high ICE sequence homogeneity, highlighting the potential for cross-species dissemination of resistance determinants. Understanding mechanisms of resistance is crucial for developing effective surveillance strategies and improving antibiotic use. Furthermore, the findings underscore the importance of considering the broader ecological context of resistance dissemination, emphasizing the need for community-level surveillance to combat the spread of antibiotic resistance within the urinary microbiome.
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Du J, Khemmani M, Halverson T, Ene A, Limeira R, Tinawi L, Hochstedler-Kramer BR, Noronha MF, Putonti C, Wolfe AJ. Cataloging the phylogenetic diversity of human bladder bacterial isolates. Genome Biol 2024; 25:75. [PMID: 38515176 PMCID: PMC10958879 DOI: 10.1186/s13059-024-03216-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 03/14/2024] [Indexed: 03/23/2024] Open
Abstract
BACKGROUND Although the human bladder is reported to harbor unique microbiota, our understanding of how these microbial communities interact with their human hosts is limited, mostly owing to the lack of isolates to test mechanistic hypotheses. Niche-specific bacterial collections and associated reference genome databases have been instrumental in expanding knowledge of the microbiota of other anatomical sites, such as the gut and oral cavity. RESULTS To facilitate genomic, functional, and experimental analyses of the human bladder microbiota, we present a bladder-specific bacterial isolate reference collection comprising 1134 genomes, primarily from adult females. These genomes were culled from bacterial isolates obtained by a metaculturomic method from bladder urine collected by transurethral catheterization. This bladder-specific bacterial isolate reference collection includes 196 different species, including representatives of major aerobes and facultative anaerobes, as well as some anaerobes. It captures 72.2% of the genera found when re-examining previously published 16S rRNA gene sequencing of 392 adult female bladder urine samples. Comparative genomic analysis finds that the taxonomies and functions of the bladder microbiota share more similarities with the vaginal microbiota than the gut microbiota. Whole-genome phylogenetic and functional analyses of 186 bladder Escherichia coli isolates and 387 gut Escherichia coli isolates support the hypothesis that phylogroup distribution and functions of Escherichia coli strains differ dramatically between these two very different niches. CONCLUSIONS This bladder-specific bacterial isolate reference collection is a unique resource that will enable bladder microbiota research and comparison to isolates from other anatomical sites.
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Iara Gomes de Oliveira L, Karoline Almeida da Costa W, de Candido de Oliveira F, França Bezerril F, Priscila Alves Maciel Eireli L, Dos Santos Lima M, Fontes Noronha M, Cabral L, Wagner R, Colombo Pimentel T, Magnani M. Ginger beer derived from back-slopping: Volatile compounds, microbial communities on activation and fermentation, metabolites and sensory characteristics. Food Chem 2024; 435:137640. [PMID: 37804728 DOI: 10.1016/j.foodchem.2023.137640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 09/25/2023] [Accepted: 09/29/2023] [Indexed: 10/09/2023]
Abstract
Physicochemical parameters, microbial diversity using sequencing and amplicon, and metabolite concentrations from Ginger Bug and Ginger Beer were characterized. Furthermore, the sensory aspects of the beverage were determined. The longer ginger bug activation time (96 h) resulted in higher production of organic acids and alcohols, increased phenolic and volatile compounds concentration, greater microbial diversity, and increased lactic acid bacteria and yeasts. In the same way, the longer fermentation time (14 days) of ginger beer resulted in higher ethanol content, volatile compounds, and phenolic compounds, in addition to better sensory characteristics. Our results showed that ginger beer produced with ginger bug and fermented for 14 days showed better volatile and phenolic compound profiles, physicochemical parameters, microbial diversity, and sensory characteristics.
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Cole EB, Khemmani M, Liu H, Halverson TM, Noronha MF, Forster CS, Wolfe AJ, Shaikh N. Urogenital urobiome of healthy children does not differ from that of children with bladder and bowel dysfunction. J Pediatr Urol 2023; 19:368.e1-368.e8. [PMID: 37117081 PMCID: PMC10524508 DOI: 10.1016/j.jpurol.2023.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 03/30/2023] [Accepted: 04/10/2023] [Indexed: 04/30/2023]
Abstract
INTRODUCTION The pediatric urinary microbiome (urobiome) has been studied in the context of healthy children and children with genitourinary pathologies including neuropathic bladder, urinary tract infection (UTI) and nephrolithiasis. Little is known about the urobiome of children with bladder and bowel dysfunction (BBD), a condition that is an established risk factor of UTI. We hypothesized that the symptoms of a child with BBD may be related to urobiome composition. OBJECTIVE To evaluate the urogenital urobiome's role in BBD, we compared the urogenital urobiomes of children with and without BBD. STUDY DESIGN We performed a prospective case-control pilot study at a single large, academic children's hospital. Cases included toilet trained prepubertal females over 2 years of age with BBD established through a validated scoring system and controls included asymptomatic, presumably healthy, children. Children were excluded if they had symptoms or lab work consistent with a concurrent UTI or antibiotic course for any reason within the prior 14 days. We performed 16 S ribosomal RNA gene sequencing and expanded quantitative urine culture on clean catch urine samples. To compare within sample (alpha) diversity, we used the Kruskal-Wallis test. To compare between sample (beta) diversity, we calculated the Bray-Curtis distance and performed the PERMANOVA test. RESULTS Data from 25 children with BBD and 8 asymptomatic controls were analyzed. The demographic and clinical characteristics of the two comparison groups were similar, though a higher proportion of Black children were included in the asymptomatic control group. Neither alpha diversity nor beta diversity was significantly different between the two groups. The core microbiome of the BBD group included all the genera in the core urogenital urobiome of the controls, plus additional genera associated with opportunistic infection and/or UTI, including Escherichia, Campylobacter and Streptococcus. DISCUSSION The results of both the 16 S sequencing and expanded quantitative urine culture in this small study suggest that the urogenital urobiomes of children with BBD do not differ significantly from those of asymptomatic children. However, the core urogenital urobiome of children with BBD included genera associated with opportunistic infection and/or UTI. This study was limited by the sample collection method ("clean catch" midstream voided urine samples, which introduce the possibility of vulvovaginal contamination), small sample size, and unequal balance of patient characteristics between the two study groups. CONCLUSION The urogenital urobiomes of children with and without BBD do not appear to significantly differ. Larger studies are needed to confirm these findings.
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Du J, Khemmani M, Halverson T, Ene A, Limeira R, Tinawi L, Hochstedler-Kramer BR, Noronha MF, Putonti C, Wolfe AJ. Cataloging the Phylogenetic Diversity of Human Bladder Bacterial Isolates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.23.541916. [PMID: 37292924 PMCID: PMC10245883 DOI: 10.1101/2023.05.23.541916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Although the human bladder is reported to harbor unique microbiota, our understanding of how these microbial communities interact with their human hosts is limited, mostly owing to the lack of isolates to test mechanistic hypotheses. Niche-specific bacterial collections and associated reference genome databases have been instrumental in expanding knowledge of the microbiota of other anatomical sites, e.g., the gut and oral cavity. To facilitate genomic, functional, and experimental analyses of the human bladder microbiota, here we present a bladder-specific bacterial reference collection comprised of 1134 genomes. These genomes were culled from bacterial isolates obtained by a metaculturomic method from bladder urine collected by transurethral catheterization. This bladder-specific bacterial reference collection includes 196 different species, including representatives of major aerobes and facultative anaerobes, as well as some anaerobes. It captures 72.2 % of the genera found when we reexamined previously published 16S rRNA gene sequencing of 392 adult female bladder urine samples. Comparative genomic analysis found that the taxonomies and functions of the bladder microbiota shared more similarities with the vaginal microbiota than the gut microbiota. Whole-genome phylogenetic and functional analyses of 186 bladder E. coli isolates and 387 gut E. coli isolates supports the hypothesis that phylogroup distribution and functions of E. coli strains differ dramatically between these two very different niches. This bladder-specific bacterial reference collection is a unique resource that will enable hypothesis-driven bladder microbiota research and comparison to isolates from other anatomical sites.
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Brandão LR, de Brito Alves JL, da Costa WKA, Ferreira GDAH, de Oliveira MP, Gomes da Cruz A, Braga VDA, Aquino JDS, Vidal H, Noronha MF, Cabral L, Pimentel TC, Magnani M. Live and ultrasound-inactivated Lacticaseibacillus casei modulate the intestinal microbiota and improve biochemical and cardiovascular parameters in male rats fed a high-fat diet. Food Funct 2021; 12:5287-5300. [PMID: 34009228 DOI: 10.1039/d1fo01064f] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
This study aimed to evaluate the effects of ingestion of live (9 log CFU mL-1) and ultrasound-inactivated (paraprobiotic, 20 kHz, 40 min) Lacticaseibacillus casei 01 cells for 28 days on healthy parameters (biochemical and cardiovascular) and intestinal microbiota (amplicon sequencing of 16S ribosomal RNA) of rats fed a high-fat diet. Twenty-four male Wistar rats were divided into four groups of six animals: CTL (standard diet), HFD (high-fat diet), HFD-LC (high-fat diet and live L. casei), and HFD-ILC (high-fat diet and inactivated L. casei). The administration of live and ultrasound-inactivated L. casei prevented the increase (p < 0.05) in cholesterol levels (total and LDL) and controlled the insulin resistance in rats fed a high-fat diet. Furthermore, it promoted a modulation of the intestinal microbial composition by increasing (p < 0.05) beneficial bacteria (Lachnospiraceae and Ruminoccocaceae) and decreasing (p < 0.05) harmful bacteria (Clostridiaceae, Enterobacteriaceae, and Helicobacteriacea), attenuating the effects promoted by the HFD ingestion. Only live cells could increase (p < 0.05) the HDL-cholesterol, while only inactivated cells caused attenuation (p < 0.05) of the blood pressure. Results show beneficial effects of live and inactivated L. casei 01 and indicate that ultrasound inactivation produces a paraprobiotic with similar or improved health properties compared to live cells.
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Rodrigues VCDC, Duque ALRF, Fino LDC, Simabuco FM, Sartoratto A, Cabral L, Noronha MF, Sivieri K, Antunes AEC. Modulation of the intestinal microbiota and the metabolites produced by the administration of ice cream and a dietary supplement containing the same probiotics. Br J Nutr 2020; 124:1-12. [PMID: 32138793 DOI: 10.1017/s0007114520000896] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The aim of the present work was to compare the capacity to modulate the intestinal microbiota and the production of metabolites after 14 d administration of a commercial dietary supplement and a manufactured ice cream, both containing the same quantity of inulin and the same viable counts of Lactobacillus acidophilus LA-5 and Bifidobacterium animalis BB-12, using the Simulator of the Human Intestinal Microbial Ecosystem (SHIME®) model. Samples of the colonic contents were evaluated microbiologically by real-time quantitative PCR (qRT-PCR) and next-generation sequencing and chemically by the production of SCFA (acetate, propionate and butyrate) and ammonium ions ($\text{NH}_4^ + $). Statistical analyses were carried out for all the variables using the two-way ANOVA followed by the Tukey multiple comparisons test (P < 0·05) for metabolite production, qRT-PCR and the bioinformatics analysis for microbiota diversity. Dietary supplement and ice cream were able to deliver the probiotic L. acidophilus and B. animalis to the simulated colon and modulate the microbiota, increasing beneficial micro-organisms such as Bifidobacterium spp., Bacteroides spp. and Faecalibacterium spp. for dietary supplement administration, and Lactobacillus spp. for ice cream supplementation. However, the ice cream matrix was probably more favourable for the maintenance of the metabolic activity of the probiotics in the SHIME® model, due to the larger amounts of acetate, propionate, butyrate and ammonium ions obtained after 14 d of supplementation. In conclusion, both ways of probiotic supplementation could be efficient, each with its own particularities.
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Sousa STPD, Cabral L, Lacerda-Júnior GV, Noronha MF, Ottoni JR, Sartoratto A, Oliveira VMD. Exploring the genetic potential of a fosmid metagenomic library from an oil-impacted mangrove sediment for metabolism of aromatic compounds. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 189:109974. [PMID: 31761556 DOI: 10.1016/j.ecoenv.2019.109974] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 10/10/2019] [Accepted: 11/13/2019] [Indexed: 06/10/2023]
Abstract
Aromatic hydrocarbons (AH) are widely distributed in nature, and many of them have been reported as relevant environmental pollutants and valuable carbon sources for different microorganisms. In this work, high-throughput sequencing of a metagenomic fosmid library was carried out to evaluate the functional and taxonomic diversity of genes involved in aromatic compounds degradation in oil-impacted mangrove sediments. In addition, activity-based approach and gas chromatography were used to assess the degradation potential of fosmid clones. Results indicated that AH degradation genes, such as monooxygenases and dioxygenases, were grouped into the following categories: anaerobic degradation of aromatic compounds (20.34%), metabolism of central aromatic intermediates (35.40%) and peripheral pathways for catabolism of aromatic compounds (22.56%). Taxonomic affiliation of genes related to aromatic compounds metabolism revealed the prevalence of the classes Alphaproteobacteria, Actinobacteria, Betaproteobacteria, Gammaproteobacteria and Deltaproteobacteria. Aromatic hydrocarbons (phenol, naphthalene, phenanthrene, pyrene and benzopyrene) were used as the only carbon source to screen clones with degradation potential. Of the 2500 clones tested, 48 showed some respiratory activity in at least one of the five carbon sources used. The hydrocarbon degradation ability of the top ten fosmid clones was confirmed by GC-MS. Further, annotation of assembled metagenomic fragments revealed ORFs corresponding to proteins and functional domains directly or indirectly involved in the aromatic compound metabolism, such as catechol 2,3-dioxygenase and ferredoxin oxidoreductase. Finally, these data suggest that the indigenous mangrove sediment microbiota developed essential mechanisms towards ecosystem remediation of petroleum hydrocarbon impact.
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Cabral L, Noronha MF, de Sousa STP, Lacerda-Júnior GV, Richter L, Fostier AH, Andreote FD, Hess M, Oliveira VMD. The metagenomic landscape of xenobiotics biodegradation in mangrove sediments. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 179:232-240. [PMID: 31051396 DOI: 10.1016/j.ecoenv.2019.04.044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 04/08/2019] [Accepted: 04/15/2019] [Indexed: 06/09/2023]
Abstract
Metagenomics is a powerful approach to study microorganisms present in any given environment and their potential to maintain and improve ecosystem health without the need of cultivating these microorganisms in the laboratory. In this study, we combined a cultivation-independent metagenomics approach with functional assays to identify the detoxification potential of microbial genes evaluating their potential to contribute to xenobiotics resistance in oil-impacted mangrove sediments. A metagenomic fosmid library containing 12,960 clones from highly contaminated mangrove sediment was used in this study. For assessment of metal resistance, clones were grown in culture medium with increasing concentrations of mercury. The analyses metagenomic library sequences revealed the presence of genes related to heavy metals and antibiotics resistance in the oil-impacted mangrove microbiome. The taxonomic profiling of these sequences suggests that at the genus level, Geobacter was the most abundant genus in our dataset. A functional screening assessment of the metagenomic library successfully detected 24 potential heavy metal tolerant clones, six of which were capable of growing with increased concentrations of mercury. The genetic characterization of selected clones allowed the detection of genes related to detoxification processes, such as chromate transport protein ChrA, haloacid dehalogenase-like hydrolase, lipopolysaccharide transport system, and 3-oxoacyl-[acyl-carrier-protein] reductase. Clones were capable of growing in medium containing increased concentrations of metals and antibiotics, but none manifested strong mercury removal from culture medium characteristic of mercuric reductase activity. These results suggest that resistance to xenobiotic stress varies greatly and that additional studies to elucidate the potential of metal biotransformation need to be carried out with the goal of improving bioremediation application.
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Noronha MF, Lacerda Júnior GV, Gilbert JA, de Oliveira VM. Taxonomic and functional patterns across soil microbial communities of global biomes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 609:1064-1074. [PMID: 28787780 DOI: 10.1016/j.scitotenv.2017.07.159] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 07/17/2017] [Accepted: 07/18/2017] [Indexed: 05/24/2023]
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Noronha MF, Veras CT, Leite IC, Martins MS, Braga Neto F, Silver L. [The development of diagnosis-related groups--DRG's. Methodology for classifying hospital patients]. Rev Saude Publica 1991; 25:198-208. [PMID: 1820605 DOI: 10.1590/s0034-89101991000300007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The history of Diagnosis Related Groups (DRG's), a system for classifying patients in acute care hospitals, developed by researchers at Yale University, USA, is reviewed. DRGs are an instrument for measuring the hospital product, primarily from a management viewpoint. Starting with a review of the definitions of hospital product, the article follows the course from the first DRGs through the most recent revision, providing a summary of potential and current applications of the system in several countries, which range from payment mechanism to uses in quality control.
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