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Raba G, Luis AS, Schneider H, Morell I, Jin C, Adamberg S, Hansson GC, Adamberg K, Arike L. Metaproteomics reveals parallel utilization of colonic mucin glycans and dietary fibers by the human gut microbiota. iScience 2024; 27:110093. [PMID: 38947523 PMCID: PMC11214529 DOI: 10.1016/j.isci.2024.110093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 02/29/2024] [Accepted: 05/21/2024] [Indexed: 07/02/2024] Open
Abstract
A diet lacking dietary fibers promotes the expansion of gut microbiota members that can degrade host glycans, such as those on mucins. The microbial foraging on mucin has been associated with disruptions of the gut-protective mucus layer and colonic inflammation. Yet, it remains unclear how the co-utilization of mucin and dietary fibers affects the microbiota composition and metabolic activity. Here, we used 14 dietary fibers and porcine colonic and gastric mucins to study the dynamics of mucin and dietary fiber utilization by the human fecal microbiota in vitro. Combining metaproteome and metabolites analyses revealed the central role of the Bacteroides genus in the utilization of complex fibers together with mucin while Akkermansia muciniphila was the main utilizer of sole porcine colonic mucin but not gastric mucin. This study gives a broad overview of the colonic environment in response to dietary and host glycan availability.
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Affiliation(s)
- Grete Raba
- Department of Chemistry and Biotechnology, Tallinn University of Technology, 12618 Tallinn, Estonia
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Ana S. Luis
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 41390 Gothenburg, Sweden
- SciLifeLab, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Hannah Schneider
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Indrek Morell
- Center of Food and Fermentation Technologies, 12618 Tallinn, Estonia
| | - Chunsheng Jin
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Signe Adamberg
- Department of Chemistry and Biotechnology, Tallinn University of Technology, 12618 Tallinn, Estonia
| | - Gunnar C. Hansson
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Kaarel Adamberg
- Department of Chemistry and Biotechnology, Tallinn University of Technology, 12618 Tallinn, Estonia
- Center of Food and Fermentation Technologies, 12618 Tallinn, Estonia
| | - Liisa Arike
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 41390 Gothenburg, Sweden
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Lin X, Hu T, Wu Z, Li L, Wang Y, Wen D, Liu X, Li W, Liang H, Jin X, Xu X, Wang J, Yang H, Kristiansen K, Xiao L, Zou Y. Isolation of potentially novel species expands the genomic and functional diversity of Lachnospiraceae. IMETA 2024; 3:e174. [PMID: 38882499 PMCID: PMC11170972 DOI: 10.1002/imt2.174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 12/06/2023] [Indexed: 06/18/2024]
Abstract
The Lachnospiraceae family holds promise as a source of next-generation probiotics, yet a comprehensive delineation of its diversity is lacking, hampering the identification of suitable strains for future applications. To address this knowledge gap, we conducted an in-depth genomic and functional analysis of 1868 high-quality genomes, combining data from public databases with our new isolates. This data set represented 387 colonization-selective species-level clusters, of which eight genera represented multilineage clusters. Pan-genome analysis, single-nucleotide polymorphism (SNP) identification, and probiotic functional predictions revealed that species taxonomy, habitats, and geography together shape the functional diversity of Lachnospiraceae. Moreover, analyses of associations with atherosclerotic cardiovascular disease (ACVD) and inflammatory bowel disease (IBD) indicated that several strains of potentially novel Lachnospiraceae species possess the capacity to reduce the abundance of opportunistic pathogens, thereby imparting potential health benefits. Our findings shed light on the untapped potential of novel species enabling knowledge-based selection of strains for the development of next-generation probiotics holding promise for improving human health and disease management.
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Affiliation(s)
- Xiaoqian Lin
- BGI Research Shenzhen China
- School of Bioscience and Biotechnology South China University of Technology Guangzhou China
| | | | - Zhinan Wu
- BGI Research Shenzhen China
- College of Life Sciences University of Chinese Academy of Sciences Beijing China
| | | | | | | | - Xudong Liu
- BGI Research Shenzhen China
- College of Life Sciences University of Chinese Academy of Sciences Beijing China
| | - Wenxi Li
- BGI Research Shenzhen China
- School of Bioscience and Biotechnology South China University of Technology Guangzhou China
| | | | | | - Xun Xu
- BGI Research Shenzhen China
| | - Jian Wang
- BGI Research Shenzhen China
- James D. Watson Institute of Genome Sciences Hangzhou China
| | - Huanming Yang
- BGI Research Shenzhen China
- James D. Watson Institute of Genome Sciences Hangzhou China
| | - Karsten Kristiansen
- BGI Research Shenzhen China
- Laboratory of Genomics and Molecular Biomedicine University of Copenhagen Copenhagen Denmark
| | - Liang Xiao
- BGI Research Shenzhen China
- College of Life Sciences University of Chinese Academy of Sciences Beijing China
- Shenzhen Engineering Laboratory of Detection and Intervention of human intestinal microbiome, BGI-Shenzhen Shenzhen China
| | - Yuanqiang Zou
- BGI Research Shenzhen China
- Laboratory of Genomics and Molecular Biomedicine University of Copenhagen Copenhagen Denmark
- Shenzhen Engineering Laboratory of Detection and Intervention of human intestinal microbiome, BGI-Shenzhen Shenzhen China
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Guta M, Abebe G, Bacha K, Cools P. Screening and characterization of thermostable enzyme-producing bacteria from selected hot springs of Ethiopia. Microbiol Spectr 2024; 12:e0371023. [PMID: 38294247 PMCID: PMC10913744 DOI: 10.1128/spectrum.03710-23] [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: 10/20/2023] [Accepted: 12/27/2023] [Indexed: 02/01/2024] Open
Abstract
Hot springs are potential sources of diverse arrays of microbes and their thermostable hydrolytic enzymes. Water and sediment samples were collected from three hot springs of Ethiopia and enriched on nutrient and thermus agar media to isolate pure cultures of potential microbes. A total of 252 bacterial isolates were screened and evaluated for the production of amylase, protease, cellulase, and lipase. About 95.23%, 84.12%, 76.58%, and 65.07% of the isolates displayed promising amylase, proteases, cellulase, and lipase activities, respectively. Based on the diameter of the clear zone formed, 45 isolates were further screened and identified to species level using matrix-assisted laser desorption/ionization time-of-flight-mass spectrometry analysis and 16S rRNA gene sequencing. Five of the 45 isolates showed significantly high (P < 0.05) clear zone ratios as compared to others. The identified isolates were categorized under five bacterial species, namely, Bacillus licheniformis, Bacillus cereus, Paenibacillus thiaminolyticus, Paenibacillus dendritiformis, and Brevibacillus borstelensis. The most dominant species (66.7%) was B. licheniformis. It could be concluded that hot springs of Ethiopia are potential sources of thermostable extracellular hydrolytic enzymes for various industrial applications. Further optimization of the growth conditions and evaluation for better productivity of the desired products is recommended before attempting for large-scale production of the hydrolytic enzymes. IMPORTANCE Thermostable microbial enzymes play an important role in industries due to their stability under harsh environmental conditions, including extreme temperatures. Despite their huge application in different industries, however, the thermostable enzymes of thermophilic microorganism origin have not yet been fully explored in Ethiopia. Here, we explored thermophilic bacteria and their enzymes from selected hot spring water and sediment samples. Accordingly, thermophilic bacteria were isolated and screened for the production of extracellular hydrolytic enzymes. Promising numbers of isolates were found as producers of the enzymes. The potent enzyme producers were further identified using matrix-assisted laser desorption/ionization time-of-flight-mass spectrometry analysis and 16S rRNA gene sequencing. The findings revealed the presence of potential hydrolytic enzyme-producing thermophilic bacteria in hot springs of Ethiopia and necessitate further comprehensive study involving other extreme environments. Our findings also revealed the potential of Ethiopian hot springs in the production of thermostable enzymes of significant application in different industries, including food industries.
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Affiliation(s)
- Meseret Guta
- Department of Biology, Jimma University, Jimma, Ethiopia
| | - Genet Abebe
- Department of Biology, Jimma University, Jimma, Ethiopia
| | - Ketema Bacha
- Department of Biology, Jimma University, Jimma, Ethiopia
| | - Piet Cools
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
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Paripati N, Nesi L, Sterrett JD, Dawud LM, Kessler LR, Lowry CA, Perez LJ, DeSipio J, Phadtare S. Gut Microbiome and Lipidome Signatures in Irritable Bowel Syndrome Patients from a Low-Income, Food-Desert Area: A Pilot Study. Microorganisms 2023; 11:2503. [PMID: 37894161 PMCID: PMC10609137 DOI: 10.3390/microorganisms11102503] [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: 09/13/2023] [Revised: 09/29/2023] [Accepted: 10/02/2023] [Indexed: 10/29/2023] Open
Abstract
Irritable bowel syndrome (IBS) is a common gastroenterological disorder with triggers such as fructose. We showed that our IBS patients suffering from socioeconomic challenges have a significantly high consumption of high-fructose corn syrup (HFCS). Here, we characterize gut microbial dysbiosis and fatty acid changes, with respect to IBS, HFCS consumption, and socioeconomic factors. Fecal samples from IBS patients and healthy controls were subjected to microbiome and lipidome analyses. We assessed phylogenetic diversity and community composition of the microbiomes, and used linear discriminant analysis effect size (LEfSe), analysis of compositions of microbiomes (ANCOM) on highly co-occurring subcommunities (modules), least absolute shrinkage and selection operator (LASSO) on phylogenetic isometric log-ratio transformed (PhILR) taxon abundances to identify differentially abundant taxa. Based on a Procrustes randomization test, the microbiome and lipidome datasets correlated significantly (p = 0.002). Alpha diversity correlated with economic factors (p < 0.001). Multiple subsets of the phylogenetic tree were associated with HFCS consumption (p < 0.001). In IBS patients, relative abundances of potentially beneficial bacteria such as Monoglobaceae, Lachnospiraceae, and Ruminococcaceae were lower (p = 0.007), and Eisenbergiella, associated with inflammatory disorders, was higher. In IBS patients, certain saturated fatty acids were higher and unsaturated fatty acids were lower (p < 0.05). Our study aims first to underscore the influence of HFCS consumption and socioeconomic factors on IBS pathophysiology, and provides new insights that inform patient care.
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Affiliation(s)
- Nikita Paripati
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, NJ 08103, USA
- Department of Emergency Medicine, Penn Medicine, Pittsburgh, PA 15261, USA
| | - Lauren Nesi
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, NJ 08103, USA
- Department of Urology, Detroit Medical Center, Detroit, MI 4820, USA
| | - John D Sterrett
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Lamya'a M Dawud
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Lyanna R Kessler
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Christopher A Lowry
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Lark J Perez
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ 08028, USA
| | - Joshua DeSipio
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, NJ 08103, USA
- Department of Gastroenterology, Cooper University Hospital, Camden, NJ 08103, USA
| | - Sangita Phadtare
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, NJ 08103, USA
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Luo Z, Li M, Yang J, Li J, Zhang Y, Liu F, El-Omar E, Han L, Bian J, Gong L, Wang M. Ferulic acid attenuates high-fat diet-induced hypercholesterolemia by activating classic bile acid synthesis pathway. Front Nutr 2022; 9:976638. [PMID: 36211528 PMCID: PMC9536491 DOI: 10.3389/fnut.2022.976638] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 08/30/2022] [Indexed: 12/03/2022] Open
Abstract
Ferulic acid (FA), a natural phenolic phytochemical abundantly present in whole grains, displays promising therapeutic effects on hypercholesterolemia while its underlying mechanism not fully elucidated. This study aimed to investigate the cholesterol-lowering effect of FA in high-fat diet (HFD)-fed mice and its potential molecular mechanism. FA supplementation alleviated HFD-induced hypercholesterolemia (–13.2%, p < 0.05), along with increased excretion of bile acids (BAs) in feces (37.0%, p < 0.05). Mechanism studies showed that FA activated the expression of cholesterol 7α hydroxylase (CYP7A1), a rate-limiting enzyme in BA biosynthesis in the liver, which increased the BAs biosynthesis from cholesterol. Surprisingly, increased excretion of BAs in feces is a consequence, not a cause, of CYP7A1 activation. Furthermore, enterohepatic farnesoid X receptor (FXR) signaling is not involved in the activation of hepatic CYP7A1 by FA. In conclusion, FA activates CYP7A1 through non-FXR signaling, which on the one hand effectively prevents hypercholesterolemia, and on the other hand leads to secondary BAs elevation in plasma. The latter may be the key to the anti-obesity and hypoglycemic effects of FA.
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Affiliation(s)
- Zhixin Luo
- College of Food Science and Engineering, Northwest A&F University, Yangling, China
| | - Mengqian Li
- College of Food Science and Engineering, Northwest A&F University, Yangling, China
| | - Jiachuan Yang
- College of Food Science and Engineering, Northwest A&F University, Yangling, China
| | - Jia Li
- College of Food Science and Engineering, Northwest A&F University, Yangling, China
| | - Yao Zhang
- College of Food Science and Engineering, Northwest A&F University, Yangling, China
| | - Fang Liu
- College of Food Science and Engineering, Northwest A&F University, Yangling, China
| | - Emad El-Omar
- Microbiome Research Centre, St George and Sutherland Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Lin Han
- College of Food Science and Engineering, Northwest A&F University, Yangling, China
- *Correspondence: Lin Han,
| | - Ji Bian
- Kolling Institute, Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Royal North Shore Hospital, St Leonards, NSW, Australia
- Ji Bian,
| | - Lan Gong
- Microbiome Research Centre, St George and Sutherland Clinical School, University of New South Wales, Sydney, NSW, Australia
- Lan Gong,
| | - Min Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling, China
- Min Wang,
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Zhou T, Wu J, Zeng Y, Li J, Yan J, Meng W, Han H, Feng F, He J, Zhao S, Zhou P, Wu Y, Yang Y, Han R, Jin W, Li X, Yang Y, Li X. SARS-CoV-2 triggered oxidative stress and abnormal energy metabolism in gut microbiota. MedComm (Beijing) 2022; 3:e112. [PMID: 35281785 PMCID: PMC8906553 DOI: 10.1002/mco2.112] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 12/02/2021] [Accepted: 12/03/2021] [Indexed: 12/19/2022] Open
Abstract
Specific roles of gut microbes in COVID-19 progression are critical. However, the circumstantial mechanism remains elusive. In this study, shotgun metagenomic or metatranscriptomic sequencing was performed on fecal samples collected from 13 COVID-19 patients and controls. We analyzed the structure of gut microbiota, identified the characteristic bacteria, and selected biomarkers. Further, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations were employed to correlate the taxon alterations and corresponding functions. The gut microbiota of COVID-19 patients was characterized by the enrichment of opportunistic pathogens and depletion of commensals. The abundance of Bacteroides spp. displayed an inverse relationship with COVID-19 severity, whereas Actinomyces oris, Escherichia coli, and Streptococcus parasanguini were positively correlated with disease severity. The genes encoding oxidoreductase were significantly enriched in gut microbiome of COVID-19 group. KEGG annotation indicated that the expression of ABC transporter was upregulated, while the synthesis pathway of butyrate was aberrantly reduced. Furthermore, increased metabolism of lipopolysaccharide, polyketide sugar, sphingolipids, and neutral amino acids were found. These results suggested the gut microbiome of COVID-19 patients was in a state of oxidative stress. Healthy gut microbiota may enhance antiviral defenses via butyrate metabolism, whereas the accumulation of opportunistic and inflammatory bacteria may exacerbate COVID-19 progression.
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Affiliation(s)
- Tuoyu Zhou
- Ministry of Education Key Laboratory of Cell Activities and Stress AdaptationsSchool of Life SciencesLanzhou UniversityLanzhouP. R. China
| | - Jingyuan Wu
- Gansu Province Key Laboratory Biotherapy and Regenerative MedicineThe First Hospital of Lanzhou UniversityLanzhouP. R. China
| | - Yufei Zeng
- State Key Joint Laboratory of Environment Simulation and Pollution ControlSchool of EnvironmentTsinghua UniversityBeijingP. R. China
| | - Junfeng Li
- Gansu Province Key Laboratory Biotherapy and Regenerative MedicineThe First Hospital of Lanzhou UniversityLanzhouP. R. China
| | - Jun Yan
- Gansu Province Key Laboratory Biotherapy and Regenerative MedicineThe First Hospital of Lanzhou UniversityLanzhouP. R. China
| | - Wenbo Meng
- Gansu Province Key Laboratory Biotherapy and Regenerative MedicineThe First Hospital of Lanzhou UniversityLanzhouP. R. China
| | - Huawen Han
- Ministry of Education Key Laboratory of Cell Activities and Stress AdaptationsSchool of Life SciencesLanzhou UniversityLanzhouP. R. China
| | - Fengya Feng
- Ministry of Education Key Laboratory of Cell Activities and Stress AdaptationsSchool of Life SciencesLanzhou UniversityLanzhouP. R. China
| | - Jufang He
- Gansu Province Key Laboratory Biotherapy and Regenerative MedicineThe First Hospital of Lanzhou UniversityLanzhouP. R. China
| | - Shuai Zhao
- Ministry of Education Key Laboratory of Cell Activities and Stress AdaptationsSchool of Life SciencesLanzhou UniversityLanzhouP. R. China
| | - Ping Zhou
- Gansu Province Key Laboratory Biotherapy and Regenerative MedicineThe First Hospital of Lanzhou UniversityLanzhouP. R. China
| | - Ying Wu
- Ministry of Education Key Laboratory of Cell Activities and Stress AdaptationsSchool of Life SciencesLanzhou UniversityLanzhouP. R. China
| | - Yanlin Yang
- Gansu Province Key Laboratory Biotherapy and Regenerative MedicineThe First Hospital of Lanzhou UniversityLanzhouP. R. China
| | - Rong Han
- Ministry of Education Key Laboratory of Cell Activities and Stress AdaptationsSchool of Life SciencesLanzhou UniversityLanzhouP. R. China
| | - Weilin Jin
- Medical Frontier Innovation Research CenterThe First Hospital of Lanzhou UniversityLanzhouP. R. China
| | - Xun Li
- Gansu Province Key Laboratory Biotherapy and Regenerative MedicineThe First Hospital of Lanzhou UniversityLanzhouP. R. China
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution ControlSchool of EnvironmentTsinghua UniversityBeijingP. R. China
| | - Xiangkai Li
- Ministry of Education Key Laboratory of Cell Activities and Stress AdaptationsSchool of Life SciencesLanzhou UniversityLanzhouP. R. China
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Identification, characterization and hydrolase producing performance of thermophilic bacteria: geothermal hot springs in the Eastern and Southeastern Anatolia Regions of Turkey. Antonie van Leeuwenhoek 2022; 115:253-270. [PMID: 35031914 PMCID: PMC8760091 DOI: 10.1007/s10482-021-01678-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 10/18/2021] [Indexed: 10/28/2022]
Abstract
In the last two decades, researchers have increasingly focused on the rich microorganism-based diversity of natural hot spring sources to explore the benefits of thermophiles in industrial and biotechnological fields. Within the scope of this study, a total of 83 thermophilic Bacilli strains were isolated from 7 different geothermal hot springs (at temperatures ranging between 40 and 85 °C) located in the Eastern and Southeastern Anatolia Regions of Turkey. The physiological, morphological, biochemical and molecular properties of the isolates were determined. As a result of the 16S rRNA gene sequence analysis, 5 different species (Bacillus licheniformis, Bacillus sp., Bacillus subtilis, Geobacillus kaustophilus, and Weizmannia coagulans,) were identified. B. licheniformis and B. subtilis were the most frequently encountered species among those obtained from the researched hot spring sources. Phylogenetic analysis was conducted to evaluate the phylogenetic relationships of the isolated species. The results showed that there was no significant difference between the groups and the bacteria in terms of the locations or optimum temperatures of the isolates. The bacterial isolates were screened for amylase, cellulase, lipase and protease hydrolytic enzyme activities. The hydrolytic enzyme production potentials among the isolates were identified in 68 (82%) isolates for amylase, 34 (41%) for cellulase, 69 (83%) for lipase and 73 (88%) for protease. All isolates were found to have at least one or more extracellular enzyme activities. Additionally, it was determined that 27 of the existing isolates (32.8%) were able to produce all of the aforementioned hydrolytic enzymes.
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Kan L, Guo F, Liu Y, Pham VH, Guo Y, Wang Z. Probiotics Bacillus licheniformis Improves Intestinal Health of Subclinical Necrotic Enteritis-Challenged Broilers. Front Microbiol 2021; 12:623739. [PMID: 34084155 PMCID: PMC8168541 DOI: 10.3389/fmicb.2021.623739] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 03/25/2021] [Indexed: 12/18/2022] Open
Abstract
Necrotic enteritis infection poses a serious threat to poultry production, and there is an urgent need for searching effective antibiotic alternatives to control it with the global ban on in-feed antibiotics. This study was conducted to investigate the effects of dietary Bacillus licheniformis replacing enramycin on the growth performance and intestinal health of subclinical necrotic enteritis (SNE)-challenged broilers. In total, 504 1-day-old Arbor Acres male chickens were selected and subsequently assigned into three treatments, including PC (basal diet + SNE challenge), PA (basal diet extra 10 mg/kg enramycin + SNE challenge), and PG (basal diet extra 3.20 × 109 and 1.60 × 109 CFU B. licheniformis per kg diet during 1-21 days and 22-42 days, respectively + SNE challenge). Results showed that B. licheniformis significantly decreased the intestinal lesion scores and down-regulated the Claudin-3 mRNA levels in jejunum of SNE-infected broilers on day 25, but increased the mucin-2 gene expression in broilers on day 42. In addition, B. licheniformis significantly up-regulated the mRNA levels of TRIF and NF-κB of SNE-challenged broilers compared with the control group on day 25 and TLR-4, TRIF compared with the control and the antibiotic group on day 42. The mRNA expression of growth factors (GLP-2 and TGF-β2) and HSPs (HSP60, HSP70, and HSP90) were up-regulated in B. licheniformis supplementary group on days 25 and 42 compared with group PC. LEfSe analysis showed that the relative abundance of Lachnospiraceae_UCG_010 was enriched in the PG group; nevertheless, Clostridiales_vadinBB60 and Rnminococcaceae_NK4A214 were in PA. PICRUSt analysis found that the metabolism of cofactors and vitamins, amino acid metabolism, and carbohydrate metabolism pathways were enriched, whereas energy metabolism, membrane transport, cell motility, and lipid metabolism were suppressed in B. licheniformis-supplemented groups as compared with the PC control. In conclusion, dietary supplementation of B. licheniformis alleviated the intestinal damage caused by SNE challenge that coincided with modulating intestinal microflora structure and barrier function as well as regulating intestinal mucosal immune responses.
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Affiliation(s)
| | | | | | | | | | - Zhong Wang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
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Khan I, Li XA, Law B, U KI, Pan BQ, Lei C, Hsiao WLW. Correlation of gut microbial compositions to the development of Kawasaki disease vasculitis in children. Future Microbiol 2020; 15:591-600. [PMID: 32490694 DOI: 10.2217/fmb-2019-0301] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Aim: Here, we hypothesize that dysbiotic gut microbiota might contribute to the development of Kawasaki disease (KD), a pediatric disease with unknown etiology. This is the second report on gut microbiota composition in KD patients. Materials & results: 16S amplicon sequencing was performed on fecal DNA samples and revealed predominance of bacterial pathogens, such as Fusobacterium, Neisseria, Shigella and Streptococcus, in the gut of KD patients, but absent or suppressed after immunoglobulin/antibiotics therapy. In addition, beneficial bacteria propagated after the therapy. Conclusion: We conclude that prevalence of Fusobacteria, Shigella and Streptococcus might contribute to KD pathogenesis.
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Affiliation(s)
- Imran Khan
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science & Technology, Macau SAR, China
| | - Xiao-ang Li
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science & Technology, Macau SAR, China
| | - Betty Law
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science & Technology, Macau SAR, China
| | - Ka In U
- Department of Pediatrics, Kiang Wu Hospital, Macau SAR, China
| | - Bao Quan Pan
- Department of Pediatrics, Kiang Wu Hospital, Macau SAR, China
| | - Cheng Lei
- Department of Pediatrics, Kiang Wu Hospital, Macau SAR, China
| | - WL Wendy Hsiao
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science & Technology, Macau SAR, China
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Kostrzewa M, Nagy E, Schröttner P, Pranada AB. How MALDI-TOF mass spectrometry can aid the diagnosis of hard-to-identify pathogenic bacteria - the rare and the unknown. Expert Rev Mol Diagn 2019; 19:667-682. [PMID: 31303071 DOI: 10.1080/14737159.2019.1643238] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Introduction: Ten years after its introduction into clinical microbiology, MALDI-TOF mass spectrometry has become the standard routine identification tool for bacteria in most laboratories. The technology has accelerated analyses and improved the quality of results. The greatest significance has been observed for bacteria that were challenging to be identified by traditional methods. Areas covered: We searched in existing literature (Pubmed) for reports how MALDI-TOF MS has contributed to identification of rare and unknown bacteria from different groups. We describe how this has improved the diagnostics in different groups of bacteria. Reference patterns for strains which yet cannot be assigned to a known species even enable the search for related bacteria in studies as well as in routine diagnostics. MALDI-TOF MS can help to discover and investigate new species and their clinical relevance. It is a powerful tool in the elucidation of the bacterial composition of complex microbiota in culturomics studies. Expert opinion: MALDI-TOF MS has improved the diagnosis of bacterial infections. It also enables knowledge generation for prospective diagnostics. The term 'hard-to-identify' might only be rarely attributed to bacteria in the future. Novel applications are being developed, e.g. subspecies differentiation, typing, and antibiotic resistance testing which may further contribute to improved microbial diagnostics.
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Affiliation(s)
- Markus Kostrzewa
- Bioanalytical Development, Bruker Daltonik GmbH , Bremen , Germany
| | - Elisabeth Nagy
- Institute of Clinical Microbiology, University of Szeged , Szeged , Hungary
| | - Percy Schröttner
- Institut für Medizinische Mikrobiologie und Hygiene, Technische Universität Dresden , Dresden , Germany
| | - Arthur B Pranada
- Department of Medical Microbiology, MVZ Dr. Eberhard & Partner Dortmund (ÜBAG) , Dortmund , Germany
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Munson E, Carroll KC. An Update on the Novel Genera and Species and Revised Taxonomic Status of Bacterial Organisms Described in 2016 and 2017. J Clin Microbiol 2019; 57:e01181-18. [PMID: 30257907 PMCID: PMC6355528 DOI: 10.1128/jcm.01181-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Recognition and acknowledgment of novel bacterial taxonomy and nomenclature revisions can impact clinical practice, disease epidemiology, and routine clinical microbiology laboratory operations. The Journal of Clinical Microbiology (JCM) herein presents its biannual report summarizing such changes published in the years 2016 and 2017, as published and added by the International Journal of Systematic and Evolutionary Microbiology Noteworthy discussion centers around descriptions of novel Corynebacteriaceae and an anaerobic mycolic acid-producing bacterium in the suborder Corynebacterineae; revisions within the Propionibacterium, Clostridium, Borrelia, and Enterobacter genera; and a major reorganization of the family Enterobacteriaceae. JCM intends to sustain this series of reports as advancements in molecular genetics, whole-genome sequencing, and studies of the human microbiome continue to produce novel taxa and clearer understandings of bacterial relatedness.
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Affiliation(s)
- Erik Munson
- College of Health Sciences, Marquette University, Milwaukee, Wisconsin, USA
| | - Karen C Carroll
- Division of Medical Microbiology, Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Validation of MALDI-TOF MS Biotyper database optimized for anaerobic bacteria: The ENRIA project. Anaerobe 2018; 54:224-230. [DOI: 10.1016/j.anaerobe.2018.03.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 03/06/2018] [Accepted: 03/09/2018] [Indexed: 12/25/2022]
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Adamberg K, Adamberg S. Selection of fast and slow growing bacteria from fecal microbiota using continuous culture with changing dilution rate. MICROBIAL ECOLOGY IN HEALTH AND DISEASE 2018; 29:1549922. [PMID: 30532686 PMCID: PMC6282430 DOI: 10.1080/16512235.2018.1549922] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Revised: 11/11/2018] [Accepted: 11/12/2018] [Indexed: 02/08/2023]
Abstract
Background: Nutrient and energy metabolism in human colon depends on bacterial growth rate that is determined by the colonic transit rate. Objective: A novel approach, De-stat culture was used to distinguish the fast and slow growing sub-populations from fecal microbiota. Design: The enrichment and metabolism of bacteria from pooled fecal cultures of children was studied at dilution rates D = 0.2-0.0 1/h in mucin-supplemented media containing either arabinogalactan or apple pectin. Results: The study revealed clear differentiation of the fecal microbiota at higher (above 0.1 1/h) and lower (below 0.1 1/h) dilution rates, along with metabolic changes. Similarity of the fast and slow growing bacteria was observed in two different fecal pools and on both substrates, suggesting the dilution rate as the main triggering parameter for selection of bacteria. At high dilution rates, the species Collinsella aerofaciens, Dorea longicatena, Escherichia coli, Lachnoclostridium torques, and different Bacteroides (B. caccae, B. fragilis, B. ovatus, B. thetaiotaomicron, B. vulgatus) were dominant in both media variants. At low dilution rates, Akkermansia muciniphila, Eisenbergiella tayi, Negativicoccus succinivorans, and a group of Ruminococcaceae became dominant in both media and in both fecal pools. This change in bacterial population accompanied by the increased production of propionic and butyric acids as well as higher consumption of alanine and branched chain amino acids at low dilution rates. Conclusions: The study suggests that specific growth rate has important effect on the dynamics of colon microbiota. Manipulation of the proportions of fast and slow growing gut bacteria through modulation of the transit rate could be a target in human nutrition studies. The De-stat study would enable to predict changes in microbiota composition associated with the decrease or increase of the colonic transit rate.
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Affiliation(s)
- K Adamberg
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia.,Center of Food and Fermentation Technologies, Tallinn, Estonia
| | - S Adamberg
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
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Togo AH, Diop A, Million M, Maraninchi M, Lagier JC, Robert C, Di Pinto F, Raoult D, Fournier PE, Bittar F. Draft Genome and Description of Eisenbergiella massiliensis Strain AT11 T: A New Species Isolated from Human Feces After Bariatric Surgery. Curr Microbiol 2018; 75:1274-1281. [PMID: 29858619 DOI: 10.1007/s00284-018-1520-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 05/29/2018] [Indexed: 12/19/2022]
Abstract
A novel strain of a Gram-stain negative, non-motile, non-spore forming rod-shaped, obligate anaerobic bacterium, designated AT11T, was isolated from a stool sample of a morbidly obese woman living in Marseille, France. This bacterium was characterized using biochemical, chemotaxonomic, and phylogenetic methods. The 16S rRNA gene sequence analysis showed that strain AT11T had a 97.8% nucleotide sequence similarity with Eisenbergiella tayi strain B086562T, the closest species with standing in nomenclature. The major cellular fatty acids of the novel isolate were C16:0 followed by saturated or unsaturated C18 fatty acids (C18:1n9, C18:1n5 and C18:0). The draft genome of strain AT11T is 7,114,554 bp long with 48% G+C content. 6176 genes were predicted, including 6114 protein-coding genes and 62 were RNAs (with 2 5S rRNA genes, two 16S rRNA genes, two 23S rRNA genes, and 56 tRNA genes). The digital DNA-DNA hybridization (dDDH) relatedness between the new isolate and E. tayi strain B086562T was 23.1% ± 2.2. Based on the phenotypic, chemotaxonomic, genomic, and phylogenetic characteristics, Eisenbergiella massiliensis sp. nov., is proposed. The type strain is AT11T (= DSM 100838T = CSUR P2478T).
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Affiliation(s)
- Amadou H Togo
- Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - Awa Diop
- Aix Marseille Univ, IRD, APHM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France
| | - Matthieu Million
- Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - Marie Maraninchi
- Aix Marseille Univ, NORT "Nutrition, Obesity and Risk of Thrombosis", INSERM1062, INRA1260, 13385, Marseille, France
| | | | - Catherine Robert
- Aix Marseille Univ, IRD, APHM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France
| | - Fabrizio Di Pinto
- Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - Didier Raoult
- Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | | | - Fadi Bittar
- Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France.
- IHU-Méditerranée Infection, 19-21 Bd Jean Moulin, 13005, Marseille, France.
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