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Jimenez N, Norton T, Diadala G, Bell E, Valenti M, Farland LV, Mahnert N, Herbst-Kralovetz MM. Vaginal and rectal microbiome contribute to genital inflammation in chronic pelvic pain. BMC Med 2024; 22:283. [PMID: 38972981 PMCID: PMC11229265 DOI: 10.1186/s12916-024-03500-1] [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: 02/22/2024] [Accepted: 06/25/2024] [Indexed: 07/09/2024] Open
Abstract
BACKGROUND Chronic pelvic pain (CPP) is a multifactorial syndrome that can substantially affect a patient's quality of life. Endometriosis is one cause of CPP, and alterations of the immune and microbiome profiles have been observed in patients with endometriosis. The objective of this pilot study was to investigate differences in the vaginal and gastrointestinal microbiomes and cervicovaginal immune microenvironment in patients with CPP and endometriosis diagnosis compared to those with CPP without endometriosis and no CPP. METHODS Vaginal swabs, rectal swabs, and cervicovaginal lavages (CVL) were collected among individuals undergoing gynecologic laparoscopy. Participants were grouped based on patients seeking care for chronic pain and/or pathology results: CPP and endometriosis (CPP-Endo) (n = 35), CPP without endometriosis (n = 23), or patients without CPP or endometriosis (controls) (n = 15). Sensitivity analyses were performed on CPP with endometriosis location, stage, and co-occurring gynecologic conditions (abnormal uterine bleeding, fibroids). 16S rRNA sequencing was performed to profile the microbiome, and a panel of soluble immune mediators was quantified using a multiplex assay. Statistical analysis was conducted with SAS, R, MicrobiomeAnalyst, MetaboAnalyst, and QIIME 2. RESULTS Significant differences were observed between participants with CPP alone, CPP-Endo, and surgical controls for body mass index, ethnicity, diagnosis of ovarian cysts, and diagnosis of fibroids. In rectal microbiome analysis, both CPP alone and CPP-Endo exhibited lower alpha diversity than controls, and both CPP groups revealed enrichment of irritable bowel syndrome-associated bacteria. CPP-Endo exhibited an increased abundance of vaginal Streptococcus anginosus and rectal Ruminococcus. Patients with CPP and endometrioma (s) demonstrated increased vaginal Streptococcus, Lactobacillus, and Prevotella compared to other endometriosis sites. Further, abnormal uterine bleeding was associated with an increased abundance of bacterial vaginosis-associated bacteria. Immunoproteomic profiles were distinctly clustered by CPP alone and CPP-Endo compared to controls. CPP-Endo was enriched in TNF⍺, MDC, and IL-1⍺. CONCLUSIONS Vaginal and rectal microbiomes were observed to differ between patients with CPP alone and CPP with endometriosis, which may be useful in personalized treatment for individuals with CPP and endometriosis from those with other causes of CPP. Further investigation is warranted in patients with additional co-occurring conditions, such as AUB/fibroids, which add additional complexity to these conditions and reveal the enrichment of distinct pathogenic bacteria in both mucosal sites. This study provides foundational microbiome-immunoproteomic knowledge related to chronic pelvic pain, endometriosis, and co-occurring gynecologic conditions that can help improve the treatment of patients seeking care for pain.
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Affiliation(s)
- Nicole Jimenez
- Department of Obstetrics and Gynecology, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ, USA
| | - Taylor Norton
- Department of Obstetrics and Gynecology, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ, USA
- Department of Obstetrics and Gynecology, Banner University Medical Center Phoenix, Phoenix, AZ, USA
| | - Gurbeen Diadala
- Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Building ABC-1, Lab 331E, 425 N. 5 St, Phoenix, AZ, 85004, USA
| | - Emerald Bell
- Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Building ABC-1, Lab 331E, 425 N. 5 St, Phoenix, AZ, 85004, USA
- University of Arizona College of Nursing, Tucson, AZ, USA
| | - Michelle Valenti
- Department of Epidemiology and Biostatistics, Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ, USA
| | - Leslie V Farland
- UA Cancer Center, University of Arizona, Tucson, AZ, USA
- Department of Epidemiology and Biostatistics, Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ, USA
- Department of Obstetrics and Gynecology, College of Medicine Tucson, University of Arizona, Tucson, AZ, USA
| | - Nichole Mahnert
- Department of Obstetrics and Gynecology, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ, USA
- Department of Obstetrics and Gynecology, Banner University Medical Center Phoenix, Phoenix, AZ, USA
| | - Melissa M Herbst-Kralovetz
- Department of Obstetrics and Gynecology, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ, USA.
- Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Building ABC-1, Lab 331E, 425 N. 5 St, Phoenix, AZ, 85004, USA.
- UA Cancer Center, University of Arizona, Tucson, AZ, USA.
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202
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Hanke DM, Wang Y, Dagan T. Pseudogenes in plasmid genomes reveal past transitions in plasmid mobility. Nucleic Acids Res 2024; 52:7049-7062. [PMID: 38808675 PMCID: PMC11229322 DOI: 10.1093/nar/gkae430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 04/23/2024] [Accepted: 05/08/2024] [Indexed: 05/30/2024] Open
Abstract
Evidence for gene non-functionalization due to mutational processes is found in genomes in the form of pseudogenes. Pseudogenes are known to be rare in prokaryote chromosomes, with the exception of lineages that underwent an extreme genome reduction (e.g. obligatory symbionts). Much less is known about the frequency of pseudogenes in prokaryotic plasmids; those are genetic elements that can transfer between cells and may encode beneficial traits for their host. Non-functionalization of plasmid-encoded genes may alter the plasmid characteristics, e.g. mobility, or their effect on the host. Analyzing 10 832 prokaryotic genomes, we find that plasmid genomes are characterized by threefold-higher pseudogene density compared to chromosomes. The majority of plasmid pseudogenes correspond to deteriorated transposable elements. A detailed analysis of enterobacterial plasmids furthermore reveals frequent gene non-functionalization events associated with the loss of plasmid self-transmissibility. Reconstructing the evolution of closely related plasmids reveals that non-functionalization of the conjugation machinery led to the emergence of non-mobilizable plasmid types. Examples are virulence plasmids in Escherichia and Salmonella. Our study highlights non-functionalization of core plasmid mobility functions as one route for the evolution of domesticated plasmids. Pseudogenes in plasmids supply insights into past transitions in plasmid mobility that are akin to transitions in bacterial lifestyle.
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Affiliation(s)
- Dustin M Hanke
- Institute of General Microbiology, Kiel University, Kiel, Germany
| | - Yiqing Wang
- Institute of General Microbiology, Kiel University, Kiel, Germany
| | - Tal Dagan
- Institute of General Microbiology, Kiel University, Kiel, Germany
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203
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Senthakumaran T, Tannæs TM, Moen AEF, Brackmann SA, Jahanlu D, Rounge TB, Bemanian V, Tunsjø HS. Detection of colorectal-cancer-associated bacterial taxa in fecal samples using next-generation sequencing and 19 newly established qPCR assays. Mol Oncol 2024. [PMID: 38970464 DOI: 10.1002/1878-0261.13700] [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: 12/12/2023] [Revised: 05/15/2024] [Accepted: 06/28/2024] [Indexed: 07/08/2024] Open
Abstract
We have previously identified increased levels of distinct bacterial taxa within mucosal biopsies from colorectal cancer (CRC) patients. Following prior research, the aim of this study was to investigate the detection of the same CRC-associated bacteria in fecal samples and to evaluate the suitability of fecal samples as a non-invasive material for the detection of CRC-associated bacteria. Next-generation sequencing (NGS) of the 16S ribosomal RNA (rRNA) V4 region was performed to evaluate the detection of the CRC-associated bacteria in the fecal microbiota of cancer patients, patients with adenomatous polyp and healthy controls. Furthermore, 19 novel species-specific quantitative PCR (qPCR) assays were established to detect the CRC-associated bacteria. Approximately, 75% of the bacterial taxa identified in biopsies were reflected in fecal samples. NGS failed to detect low-abundance CRC-associated taxa in fecal samples, whereas qPCR exhibited high sensitivity and specificity in identifying all targeted taxa. Comparison of fecal microbial composition between the different patient groups showed enrichment of Fusobacterium nucleatum, Parvimonas micra, and Gemella morbillorum in cancer patients. Our findings suggest that low-abundance mucosa-associated bacteria can be detected in fecal samples using sensitive qPCR assays.
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Affiliation(s)
| | - Tone M Tannæs
- Section for Clinical Molecular Biology (EpiGen), Akershus University Hospital, Lørenskog, Norway
- Department of Clinical Molecular Biology, Institute of Clinical Medicine, University of Oslo, Norway
| | - Aina E F Moen
- Section for Clinical Molecular Biology (EpiGen), Akershus University Hospital, Lørenskog, Norway
- Department of Clinical Molecular Biology, Institute of Clinical Medicine, University of Oslo, Norway
- Department of Methods Development and Analytics, Norwegian Institute of Public Health, Oslo, Norway
| | - Stephan A Brackmann
- Department of Gastroenterology, Division of Medicine, Akershus University Hospital, Lørenskog, Norway
- Institute for Clinical Medicine, University of Oslo, Norway
| | - David Jahanlu
- Department of Life Sciences and Health, Oslo Metropolitan University, Norway
| | - Trine B Rounge
- Department of Pharmacy, Centre for Bioinformatics, University of Oslo, Norway
- Department of Research, Cancer Registry of Norway, Oslo, Norway
| | - Vahid Bemanian
- Department of Pathology, Akershus University Hospital, Lørenskog, Norway
| | - Hege S Tunsjø
- Department of Life Sciences and Health, Oslo Metropolitan University, Norway
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204
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Aihetanmu S, Liang Z, Zhang X, Luo B, Zhang H, Huang J, Tian F, Sun H, Ni Y. Genetic specialization of key bifidobacterial phylotypes in multiple mother-infant dyad cohorts from geographically isolated populations. Front Microbiol 2024; 15:1399743. [PMID: 39021621 PMCID: PMC11251887 DOI: 10.3389/fmicb.2024.1399743] [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: 03/12/2024] [Accepted: 05/10/2024] [Indexed: 07/20/2024] Open
Abstract
Little has been known about symbiotic relationships and host specificity for symbionts in the human gut microbiome so far. Bifidobacteria are a paragon of the symbiotic bacteria biota in the human gut. In this study, we characterized the population genetic structure of three bifidobacteria species from 58 healthy mother-infant pairs of three ethnic groups in China, geographically isolated, by Rep-PCR, multi-locus sequence analysis (MLSA), and in vitro carbohydrate utilization. One hundred strains tested were incorporated into 50 sequence types (STs), of which 29 STs, 17 STs, and 4 STs belong to B. longum subsp. longum, B. breve, and B. animalis subsp. lactis, respectively. The conspecific strains from the same mother-child pair were genetically very similar, supporting the vertical transmission of Bifidobacterium phylotypes from mother to offspring. In particular, results based on allele profiles and phylogeny showed that B. longum subsp. longum and B. breve exhibited considerable intraspecies genetic heterogeneity across three ethnic groups, and strains were clustered into ethnicity-specific lineages. Yet almost all strains of B. animalis subsp. lactis were incorporated into the same phylogenetic clade, regardless of ethnic origin. Our findings support the hypothesis of co-evolution between human gut symbionts and their respective populations, which is closely linked to the lifestyle of specific bacterial lineages. Hence, the natural and evolutionary history of Bifidobacterium species would be an additional consideration when selecting bifidobacterial strains for industrial and therapeutic applications.
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Affiliation(s)
| | - Zhixuan Liang
- School of Food Science and Technology, Shihezi University, Shihezi, China
| | - Xueling Zhang
- School of Food Science and Technology, Shihezi University, Shihezi, China
| | - Baolong Luo
- School of Food Science and Technology, Shihezi University, Shihezi, China
| | - Huimin Zhang
- School of Food Science and Technology, Shihezi University, Shihezi, China
| | - Jian Huang
- School of Food Science and Technology, Shihezi University, Shihezi, China
| | - Fengwei Tian
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Hailong Sun
- School of Food Science and Technology, Shihezi University, Shihezi, China
| | - Yongqing Ni
- School of Food Science and Technology, Shihezi University, Shihezi, China
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205
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Johnston IG. The Nitroplast and Its Relatives Support a Universal Model of Features Predicting Gene Retention in Endosymbiont and Organelle Genomes. Genome Biol Evol 2024; 16:evae132. [PMID: 38900924 PMCID: PMC11221429 DOI: 10.1093/gbe/evae132] [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: 04/22/2024] [Revised: 06/03/2024] [Accepted: 06/14/2024] [Indexed: 06/22/2024] Open
Abstract
Endosymbiotic relationships have shaped eukaryotic life. As endosymbionts coevolve with their host, toward full integration as organelles, their genomes tend to shrink, with genes being completely lost or transferred to the host nucleus. Modern endosymbionts and organelles show diverse patterns of gene retention, and why some genes and not others are retained in these genomes is not fully understood. Recent bioinformatic study has explored hypothesized influences on these evolutionary processes, finding that hydrophobicity and amino acid chemistry predict patterns of gene retention, both in organelles across eukaryotes and in less mature endosymbiotic relationships. The exciting ongoing elucidation of endosymbiotic relationships affords an independent set of instances to test this theory. Here, we compare the properties of retained genes in the nitroplast, recently reported to be an integrated organelle, two related cyanobacterial endosymbionts that form "spheroid bodies" in their host cells, and a range of other endosymbionts, with free-living relatives of each. We find that in each case, the symbiont's genome encodes proteins with higher hydrophobicity and lower amino pKa than their free-living relative, supporting the data-derived model predicting the retention propensity of genes across endosymbiont and organelle genomes.
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Affiliation(s)
- Iain G Johnston
- Department of Mathematics, University of Bergen, Bergen, Norway
- Computational Biology Unit, University of Bergen, Bergen, Norway
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206
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Li DD, Wang J, Jiang Y, Zhang P, Liu Y, Li YZ, Zhang Z. Quantifying functional redundancy in polysaccharide-degrading prokaryotic communities. MICROBIOME 2024; 12:120. [PMID: 38956705 PMCID: PMC11218364 DOI: 10.1186/s40168-024-01838-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 05/14/2024] [Indexed: 07/04/2024]
Abstract
BACKGROUND Functional redundancy (FR) is widely present, but there is no consensus on its formation process and influencing factors. Taxonomically distinct microorganisms possessing genes for the same function in a community lead to within-community FR, and distinct assemblies of microorganisms in different communities playing the same functional roles are termed between-community FR. We proposed two formulas to respectively quantify the degree of functional redundancy within and between communities and analyzed the FR degrees of carbohydrate degradation functions in global environment samples using the genetic information of glycoside hydrolases (GHs) encoded by prokaryotes. RESULTS Our results revealed that GHs are each encoded by multiple taxonomically distinct prokaryotes within a community, and the enzyme-encoding prokaryotes are further distinct between almost any community pairs. The within- and between-FR degrees are primarily affected by the alpha and beta community diversities, respectively, and are also affected by environmental factors (e.g., pH, temperature, and salinity). The FR degree of the prokaryotic community is determined by deterministic factors. CONCLUSIONS We conclude that the functional redundancy of GHs is a stabilized community characteristic. This study helps to determine the FR formation process and influencing factors and provides new insights into the relationships between prokaryotic community biodiversity and ecosystem functions. Video Abstract.
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Affiliation(s)
- Dan-Dan Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, China
| | - Jianing Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Yiru Jiang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Peng Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Ya Liu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China.
| | - Zheng Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China.
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207
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Sosa-Jiménez VM, Kvist S, Manzano-Marín A, Oceguera-Figueroa A. Discovery of a novel symbiotic lineage associated with a hematophagous leech from the genus Haementeria. Microbiol Spectr 2024; 12:e0428623. [PMID: 38842327 PMCID: PMC11218487 DOI: 10.1128/spectrum.04286-23] [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: 12/26/2023] [Accepted: 04/29/2024] [Indexed: 06/07/2024] Open
Abstract
Similarly to other strict blood feeders, leeches from the Haementeria genus (Hirudinida: Glossiphoniidae) have established a symbiotic association with bacteria harbored intracellularly in esophageal bacteriomes. Previous genome sequence analyses of these endosymbionts revealed co-divergence with their hosts, a strong genome reduction, and a simplified metabolism largely dedicated to the production of B vitamins, which are nutrients lacking from a blood diet. 'Candidatus Providencia siddallii' has been identified as the obligate nutritional endosymbiont of a monophyletic clade of Mexican and South American Haementeria spp. However, the Haementeria genus includes a sister clade of congeners from Central and South America, where the presence or absence of the aforementioned symbiont taxon remains unknown. In this work, we report on a novel bacterial endosymbiont found in a representative from this Haementeria clade. We found that this symbiont lineage has evolved from within the Pluralibacter genus, known mainly from clinical but also environmental strains. Similarly to Ca. Providencia siddallii, the Haementeria-associated Pluralibacter symbiont displays clear signs of genome reduction, accompanied by an A+T-biased sequence composition. Genomic analysis of its metabolic potential revealed a retention of pathways related to B vitamin biosynthesis, supporting its role as a nutritional endosymbiont. Finally, comparative genomics of both Haementeria symbiont lineages suggests that an ancient Providencia symbiont was likely replaced by the novel Pluralibacter one, thus constituting the first reported case of nutritional symbiont replacement in a leech without morphological changes in the bacteriome. IMPORTANCE Obligate symbiotic associations with a nutritional base have likely evolved more than once in strict blood-feeding leeches. Unlike those symbioses found in hematophagous arthropods, the nature, identity, and evolutionary history of these remains poorly studied. In this work, we further explored obligate nutritional associations between Haementeria leeches and their microbial symbionts, which led to the unexpected discovery of a novel symbiosis with a member of the Pluralibacter genus. When compared to Providencia siddallii, an obligate nutritional symbiont of other Haementeria leeches, this novel bacterial symbiont shows convergent retention of the metabolic pathways involved in B vitamin biosynthesis. Moreover, the genomic characteristics of this Pluralibacter symbiont suggest a more recent association than that of Pr. siddallii and Haementeria. We conclude that the once-thought stable associations between blood-feeding Glossiphoniidae and their symbionts (i.e., one bacteriome structure, one symbiont lineage) can break down, mirroring symbiont turnover observed in various arthropod lineages.
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Affiliation(s)
- Víctor Manuel Sosa-Jiménez
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Departamento de Zoología, Instituto de Biología, Universidad Nacional Autonoma de México, Ciudad de México, Mexico
| | - Sebastian Kvist
- Department of Natural History, Royal Ontario Museum, Toronto, Ontario, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Alejandro Manzano-Marín
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Alejandro Oceguera-Figueroa
- Departamento de Zoología, Instituto de Biología, Universidad Nacional Autonoma de México, Ciudad de México, Mexico
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208
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Vliex LMM, Penders J, Nauta A, Zoetendal EG, Blaak EE. The individual response to antibiotics and diet - insights into gut microbial resilience and host metabolism. Nat Rev Endocrinol 2024; 20:387-398. [PMID: 38486011 DOI: 10.1038/s41574-024-00966-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/20/2024] [Indexed: 06/16/2024]
Abstract
Antibiotic use disrupts microbial composition and activity in humans, but whether this disruption in turn affects host metabolic health is unclear. Cohort studies show associations between antibiotic use and an increased risk of developing obesity and type 2 diabetes mellitus. Here, we review available clinical trials and show the disruptive effect of antibiotic use on the gut microbiome in humans, as well as its impact on bile acid metabolism and microbial metabolites such as short-chain fatty acids. Placebo-controlled human studies do not show a consistent effect of antibiotic use on body weight and insulin sensitivity at a population level, but rather an individual-specific or subgroup-specific response. This response to antibiotic use is affected by the resistance and resilience of the gut microbiome, factors that determine the extent of disruption and the speed of recovery afterwards. Nutritional strategies to improve the composition and functionality of the gut microbiome, as well as its recovery after antibiotic use (for instance, with prebiotics), require a personalized approach to increase their efficacy. Improved insights into key factors that influence the individual-specific response to antibiotics and dietary intervention may lead to better efficacy in reversing or preventing antibiotic-induced microbial dysbiosis as well as strategies for preventing cardiometabolic diseases.
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Affiliation(s)
- Lars M M Vliex
- Department of Human Biology, NUTRIM, School for Nutrition and Translational Research in Metabolism, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - John Penders
- Department of Medical Microbiology, Infectious Diseases and Infection Prevention, NUTRIM, School for Nutrition and Translational Research in Metabolism, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Arjen Nauta
- FrieslandCampina, Amersfoort, The Netherlands
| | - Erwin G Zoetendal
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Ellen E Blaak
- Department of Human Biology, NUTRIM, School for Nutrition and Translational Research in Metabolism, Maastricht University Medical Center+, Maastricht, The Netherlands.
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209
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Munley JA, Kelly LS, Park G, Drury SK, Gillies GS, Coldwell PS, Kannan KB, Bible LE, Efron PA, Nagpal R, Mohr AM. Acute emergence of the intestinal pathobiome after postinjury pneumonia. J Trauma Acute Care Surg 2024; 97:65-72. [PMID: 38480488 PMCID: PMC11199099 DOI: 10.1097/ta.0000000000004300] [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] [Indexed: 06/26/2024]
Abstract
BACKGROUND Previous preclinical studies have demonstrated sex-specific alterations in the gut microbiome following traumatic injury or sepsis alone; however, the impact of host sex on dysbiosis in the setting of postinjury sepsis acutely is unknown. We hypothesized that multicompartmental injury with subsequent pneumonia would result in host sex-specific dysbiosis. METHODS Male and proestrus female Sprague-Dawley rats (n = 8/group) were subjected to either multicompartmental trauma (PT) (lung contusion, hemorrhagic shock, cecectomy, bifemoral pseudofracture), PT plus 2-hour daily restraint stress (PT/RS), PT with postinjury day 1 Pseudomonas aeruginosa pneumonia (PT-PNA), PT/RS with pneumonia (PT/RS-PNA), or naive controls. Fecal microbiome was measured on days 0 and 2 using high-throughput 16S rRNA sequencing and Quantitative Insights Into Microbial Ecology 2 bioinformatics analyses. Microbial α-diversity was assessed using Chao1 (number of different unique species) and Shannon (species richness and evenness) indices. β-diversity was assessed using principal coordinate analysis. Significance was defined as p < 0.05. RESULTS All groups had drastic declines in the Chao1 (α-diversity) index compared with naive controls ( p < 0.05). Groups PT-PNA and PT/RS-PNA resulted in different β-diversity arrays compared with uninfected counterparts (PT, PT/RS) ( p = 0.001). Postinjury sepsis cohorts showed a loss of commensal bacteria along with emergence of pathogenic bacteria, with blooms of Proteus in PT-PNA and Escherichia-Shigella group in PT/RS-PNA compared with other cohorts. At day 2, PT-PNA resulted in β-diversity, which was unique between males and females ( p = 0.004). Microbiome composition in PT-PNA males was dominated by Anaerostipes and Parasuterella , whereas females had increased Barnesiella and Oscillibacter . The PT/RS males had an abundance of Gastranaerophilales and Muribaculaceae . CONCLUSION Multicompartmental trauma complicated by sepsis significantly diminishes diversity and alters microbial composition toward a severely dysbiotic state early after injury, which varies between males and females. These findings highlight the role of sex in postinjury sepsis and the pathobiome, which may influence outcomes after severe trauma and sepsis.
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Affiliation(s)
- Jennifer A. Munley
- Department of Surgery and Sepsis and Critical Illness Research Center, University of Florida College of Medicine, Gainesville, Florida
| | - Lauren S. Kelly
- Department of Surgery and Sepsis and Critical Illness Research Center, University of Florida College of Medicine, Gainesville, Florida
| | - Gwoncheol Park
- Department of Nutrition and Integrative Physiology, Florida State University, Tallahassee, Florida
| | - Stacey K. Drury
- Department of Surgery and Sepsis and Critical Illness Research Center, University of Florida College of Medicine, Gainesville, Florida
| | - Gwendolyn S. Gillies
- Department of Surgery and Sepsis and Critical Illness Research Center, University of Florida College of Medicine, Gainesville, Florida
| | - Preston S. Coldwell
- Department of Surgery and Sepsis and Critical Illness Research Center, University of Florida College of Medicine, Gainesville, Florida
| | - Kolenkode B. Kannan
- Department of Surgery and Sepsis and Critical Illness Research Center, University of Florida College of Medicine, Gainesville, Florida
| | - Letitia E. Bible
- Department of Surgery and Sepsis and Critical Illness Research Center, University of Florida College of Medicine, Gainesville, Florida
| | - Philip A. Efron
- Department of Surgery and Sepsis and Critical Illness Research Center, University of Florida College of Medicine, Gainesville, Florida
| | - Ravinder Nagpal
- Department of Nutrition and Integrative Physiology, Florida State University, Tallahassee, Florida
| | - Alicia M. Mohr
- Department of Surgery and Sepsis and Critical Illness Research Center, University of Florida College of Medicine, Gainesville, Florida
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Huang Y, Li Y, Guan D, Pan Y, Yang C, Liu H, Chen C, Chen W, Liu J, Wan T, Zhuang L, Wang Q, Zhang Y. Acorus tatarinowii oils exert protective effects on microglia-mediated inflammatory injury via restoring gut microbiota composition in experimental stroke rats. Brain Res Bull 2024; 213:110990. [PMID: 38821245 DOI: 10.1016/j.brainresbull.2024.110990] [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: 02/06/2024] [Revised: 05/20/2024] [Accepted: 05/27/2024] [Indexed: 06/02/2024]
Abstract
Growing evidence has demonstrated that gut microbiota could be developed as a therapeutic target due to its contribution to microglia activation in the pathological process of ischemic stroke. Acorus tatarinowii oils (AT oils), which is considered as the active fraction of a traditional Chinese herbal medicine Acorus tatarinowii, exerts various bioactivities and prebiotic effects. However, it remains unclear that the effect of AT oils on inflammatory response after ischemic stroke and whether its underlying mechanism is associated to gut microbiota and the intestinal barrier. In the current study, we aim to investigate the anti-microglial neuroinflammation mechanism of AT oils in a middle cerebral artery occlusion model of ischemic stroke. The compositions of AT oils were identified by GC-MS. Our results demonstrated that AT oils could effectively relieve cerebral infarction, inhibit neuronal apoptosis, degrade the release of pro-inflammatory factors (TNF-α, IL-17, IL-6 and IFN-γ), and mediate the polarization of microglia. Moreover, AT oils restored the composition and the balance of gut microbiota in stroke rats, and reduced abundance of opportunistic genera including Verrucomicrobia, Akkermansia and Tenericutes, as well as increased beneficial bacteria abundance such as Tenericutes and Prevotella_copri. To investigate the role of gut microbiota on AT oils against ischemic stroke, we conducted the fecal microbiota transplantation (FMT) experiments with gut microbiota consumption, which suggested that the depletion of gut microbiota took away the protective effect of AT oils, confirming the importance of gut microbiota in the protective effect of AT oils on ischemic stroke. FMT experiments have demonstrated that AT oils preserved the gut permeability and blood-brain barrier, as well as mediated the microglial phenotype under the intervention of gut microbiota. In summary, AT oils could efficaciously moderate neuronal damage and intervene microglial phenotype by reversing gut microbiota disorder in ischemic stroke rats.
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Affiliation(s)
- Yueyue Huang
- Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510405, China; Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510405, China; The First Affiliated Hospital of Guangxi University of Chinese Medicine, Nanning, Guangxi 530022, China
| | - Yongyi Li
- Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510405, China; Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510405, China
| | - Danni Guan
- Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510405, China; Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510405, China
| | - Yaru Pan
- Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510405, China; Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510405, China
| | - Chao Yang
- Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510405, China; Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510405, China
| | - Huina Liu
- Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510405, China; The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510405, China; Guangdong Clinical Research Academy of Chinese Medicine, Guangzhou, Guangdong 510405, China
| | - Chaoyan Chen
- Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510405, China; Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510405, China
| | - Weitao Chen
- Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510405, China; Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510405, China
| | - Jinman Liu
- Affiliated Jiangmen TCM Hospital, Ji'nan University, Jiangmen, Guangdong 529000, China
| | - Ting Wan
- Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510405, China; The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510405, China; Guangdong Clinical Research Academy of Chinese Medicine, Guangzhou, Guangdong 510405, China
| | - Lixing Zhuang
- Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510405, China; The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510405, China; Guangdong Clinical Research Academy of Chinese Medicine, Guangzhou, Guangdong 510405, China
| | - Qi Wang
- Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510405, China; Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510405, China.
| | - Yifan Zhang
- Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510405, China; The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510405, China; Guangdong Clinical Research Academy of Chinese Medicine, Guangzhou, Guangdong 510405, China.
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211
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Singh A, Pratap SG, Raj A. Occurrence and dissemination of antibiotics and antibiotic resistance in aquatic environment and its ecological implications: a review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:47505-47529. [PMID: 39028459 DOI: 10.1007/s11356-024-34355-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 07/07/2024] [Indexed: 07/20/2024]
Abstract
The occurrence of antibiotics and antibiotic-resistant bacteria (ARBs), genes (ARGs), and mobile genetic elements (MGEs) in aquatic systems is growing global public health concern. These emerging micropollutants, stemming from improper wastewater treatment and disposal, highlight the complex and evolving nature of environmental pollution. Current literature reveals potential biases, such as a geographical focus on specific regions, leading to an insufficient understanding of the global distribution and dynamics of antibiotic resistance in aquatic systems. There is methodological inconsistency across studies, making it challenging to compare findings. Potential biases include sample collection inconsistencies, detection sensitivity variances, and data interpretation variability. Gaps in understanding include the need for comprehensive, standardized long-term monitoring programs, elucidating the environmental fate and transformation of antibiotics and resistance genes. This review summarizes current knowledge on the occurrence and dissemination of emerging micropollutants, their ecological impacts, and the global health implications of antimicrobial resistance. It highlights the need for interdisciplinary collaborations among researchers, policymakers, and stakeholders to address the challenges posed by antibiotic resistance in aquatic resistance in aquatic systems effectively. This review highlights widespread antibiotic and antibiotic resistance in aquatic environment, driven by human and agricultural activities. It underscores the ecological consequences, including disrupted microbial communities and altered ecosystem functions. The findings call for urgent measures to mitigate antibiotics pollution and manage antibiotic resistance spread in water bodies.
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Affiliation(s)
- Anjali Singh
- Environmental Microbiology Laboratory, Environmental Toxicology Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan 31, Mahatma Gandhi Marg, Lucknow, 226 001, Uttar Pradesh, India
- School of Environmental Science, Babu Banarsi Das University, Lucknow, 227015, Uttar Pradesh, India
| | - Shalini G Pratap
- School of Environmental Science, Babu Banarsi Das University, Lucknow, 227015, Uttar Pradesh, India
| | - Abhay Raj
- Environmental Microbiology Laboratory, Environmental Toxicology Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan 31, Mahatma Gandhi Marg, Lucknow, 226 001, Uttar Pradesh, India.
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212
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Yang Y, Xu Z, Guo J, Xiong Z, Hu B. Exploring the gut microbiome-Postoperative Cognitive Dysfunction connection: Mechanisms, clinical implications, and future directions. Brain Behav Immun Health 2024; 38:100763. [PMID: 38682010 PMCID: PMC11052898 DOI: 10.1016/j.bbih.2024.100763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Revised: 03/22/2024] [Accepted: 03/28/2024] [Indexed: 05/01/2024] Open
Abstract
Postoperative Cognitive Dysfunction (POCD) is a common yet poorly understood complication of surgery that can lead to long-term cognitive decline. The gut-brain axis, a bidirectional communication system between the central nervous system and the gut microbiota, plays a significant role in maintaining cognitive health. The potential for anesthetic agents and perioperative medications to modulate the gut microbiota and influence the trajectory of POCD suggests the need for a more integrated approach in perioperative care. Perioperative medications, including opioids and antibiotics, further compound these disruptions, leading to dysbiosis and consequent systemic and neuroinflammation implicated in cognitive impairment. Understanding how surgical interventions and associated treatments affect this relationship is crucial for developing strategies to reduce the incidence of POCD. Strategies to preserve and promote a healthy gut microbiome may mitigate the risk and severity of POCD. Future research should aim to clarify the mechanisms linking gut flora alterations to cognitive outcomes and explore targeted interventions, such as probiotic supplementation and microbiota-friendly prescription practices, to safeguard cognitive function postoperatively.
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Affiliation(s)
- Yan Yang
- Department of Anesthesiology, Xuzhou Renci Hospital, Xuzhou, 221000, Jiangsu Province, China
| | - Zhipeng Xu
- Department of Anesthesiology, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, 2800 Gongwei Road, Pudong, Shanghai, 201399, China
| | - Jianrong Guo
- School of Gongli Hospital Medical Technology, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Zhiqiang Xiong
- Shanghai Engineering Research Center of Food Microbiology, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Baoji Hu
- Department of Anesthesiology, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, 2800 Gongwei Road, Pudong, Shanghai, 201399, China
- School of Gongli Hospital Medical Technology, University of Shanghai for Science and Technology, Shanghai, 200093, China
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213
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Colizzi FS, Martínez-Torres D, Helfrich-Förster C. The circadian and photoperiodic clock of the pea aphid. J Comp Physiol A Neuroethol Sens Neural Behav Physiol 2024; 210:627-639. [PMID: 37482577 PMCID: PMC11226554 DOI: 10.1007/s00359-023-01660-8] [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: 04/28/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 07/25/2023]
Abstract
The pea aphid, Acyrthosiphon pisum, is a paradigmatic photoperiodic species that exhibits a remarkable annual life cycle, which is tightly coupled to the seasonal changes in day length. During spring and summer, characterised by longer days, aphid populations consist exclusively of viviparous females that reproduce parthenogenetically. When autumn comes and the days shorten, aphids switch their reproductive mode and generate males and oviparous sexual females, which mate and produce cold-resistant eggs that overwinter and survive the unfavourable season. While the photoperiodic responses have been well described, the nature of the timing mechanisms which underlie day length discrimination are still not completely understood. Experiments from the 1960's suggested that aphids rely on an 'hourglass' clock measuring the elapsed time during the dark night by accumulating a biochemical factor, which reaches a critical threshold at a certain night length and triggers the switch in reproduction mode. However, the photoperiodic responses of aphids can also be attributed to a strongly dampened circadian clock. Recent studies have uncovered the molecular components and the location of the circadian clock in the brain of the pea aphid and revealed that it is well connected to the neurohormonal system controlling aphid reproduction. We provide an overview of the putative mechanisms of photoperiodic control in aphids, from the photoreceptors involved in this process to the circadian clock and the neuroendocrine system.
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Affiliation(s)
- Francesca Sara Colizzi
- University of Würzburg, Neurobiology and Genetics, Biocenter, Am Hubland, 97074, Würzburg, Germany
| | - David Martínez-Torres
- Institut de Biologia Integrativa de Sistemes, Parc Cientific Universitat de València, C/ Catedrático José Beltrán nº 2, 46980, Paterna,, València, Spain
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214
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Ribeiro FM, Anderson M, Aguiar S, Gabriela E, Petriz B, Franco OL. Systematic review and meta-analysis of gut peptides expression during fasting and postprandial states in individuals with obesity. Nutr Res 2024; 127:27-39. [PMID: 38843565 DOI: 10.1016/j.nutres.2024.04.007] [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: 02/01/2024] [Revised: 04/28/2024] [Accepted: 04/28/2024] [Indexed: 07/28/2024]
Abstract
Gut peptides play a role in signaling appetite control in the hypothalamus. Limited knowledge exists regarding the release of these peptides in individuals with obesity before and during external stimuli. We hypothesize that the expression of gut peptides is different in the fasting and postprandial states in the scenario of obesity. PubMed/MEDLINE, Scopus, and Science Direct electronic databases were searched. The meta-analysis was performed using Review Manager Software. Randomized controlled trials that measured gut peptides in both obese and lean subjects were included in the analysis. A total of 552 subjects with obesity were enrolled in 25 trials. The gut peptide profile did not show any significant difference between obese and lean subjects for glucagon-like peptide 1 (95% confidence interval [CI], -1.21 to 0.38; P = .30), peptide YY (95% CI, -1.47 to 0.18; P = .13), and cholecystokinin (95% CI, -1.25 to 1.28; P = .98). Gut peptides are decreased by an increased high-fat, high-carbohydrate diet and by decreased chewing. There is no statistically significant difference in gut peptides between individuals with obesity and leanness in a fasting state. However, the release of gut peptides is affected in individuals with obesity following external stimuli, such as dietary interventions and chewing. Further studies are necessary to investigate the relationship between various stimuli and the release of gut peptides, as well as their impact on appetite regulation in subjects with obesity.
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Affiliation(s)
- Filipe M Ribeiro
- Postgraduate Program in Physical Education, Catholic University of Brasilia, Brasilia, DF, Brazil; Center for Proteomic and Biochemical Analysis, Post-Graduation in Genomic and Biotechnology Sciences, Catholic University of Brasilia, Brasília, DF, Brazil; Laboratory of Molecular Exercise Physiology - University Center - UDF, Brasilia, DF, Brazil
| | - Maycon Anderson
- Center for Proteomic and Biochemical Analysis, Post-Graduation in Genomic and Biotechnology Sciences, Catholic University of Brasilia, Brasília, DF, Brazil; Laboratory of Molecular Exercise Physiology - University Center - UDF, Brasilia, DF, Brazil
| | - Samuel Aguiar
- Center for Proteomic and Biochemical Analysis, Post-Graduation in Genomic and Biotechnology Sciences, Catholic University of Brasilia, Brasília, DF, Brazil; Laboratory of Molecular Exercise Physiology - University Center - UDF, Brasilia, DF, Brazil
| | - Elza Gabriela
- Laboratory of Molecular Exercise Physiology - University Center - UDF, Brasilia, DF, Brazil
| | - Bernardo Petriz
- Center for Proteomic and Biochemical Analysis, Post-Graduation in Genomic and Biotechnology Sciences, Catholic University of Brasilia, Brasília, DF, Brazil; Laboratory of Molecular Exercise Physiology - University Center - UDF, Brasilia, DF, Brazil
| | - Octavio L Franco
- Postgraduate Program in Physical Education, Catholic University of Brasilia, Brasilia, DF, Brazil; Center for Proteomic and Biochemical Analysis, Post-Graduation in Genomic and Biotechnology Sciences, Catholic University of Brasilia, Brasília, DF, Brazil; S-Inova Biotech, Catholic University Dom Bosco, Biotechnology Program, Campo Grande, MS, Brazil.
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215
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Valdés‐Bango M, Gracia M, Rubio E, Vergara A, Casals‐Pascual C, Ros C, Rius M, Martínez‐Zamora MÁ, Mension E, Quintas L, Carmona F. Comparative analysis of endometrial, vaginal, and gut microbiota in patients with and without adenomyosis. Acta Obstet Gynecol Scand 2024; 103:1271-1282. [PMID: 38661227 PMCID: PMC11168268 DOI: 10.1111/aogs.14847] [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: 01/10/2024] [Revised: 03/30/2024] [Accepted: 04/02/2024] [Indexed: 04/26/2024]
Abstract
INTRODUCTION Alterations in microbiota composition have been implicated in a variety of human diseases. Patients with adenomyosis present immune dysregulation leading to a persistent chronic inflammatory response. In this context, the hypothesis that alterations in the microbiota may be involved in the pathogenesis of adenomyosis, by affecting the epigenetic, immunologic, and biochemical functions of the host, has recently been postulated. The aim of the present study was to compare the microbiota composition in the vagina, endometrium, and gut of individuals with and without adenomyosis. MATERIAL AND METHODS Cross-sectional study including 38 adenomyosis patients and 46 controls, performed between September 2021 and October 2022 in a university hospital-based research center. The diagnosis of adenomyosis was based on sonographic criteria. Fecal, vaginal, and endometrial samples were collected. Study of the microbiota using 16S rRNA gene sequencing. RESULTS Patients with adenomyosis exhibited a significant reduction in the gut microbial alpha diversity compared with healthy controls (Chao1 p = 0.012, Fisher p = 0.005, Observed species p = 0.005). Beta-diversity analysis showed significant differences in the compositions of both gut and vaginal microbiota between adenomyosis patients and the control group (Adonis p-value = 0.001; R2 = 0.03 and Adonis p-value = 0.034; R2 = 0.04 respectively). Specific bacterial taxa were found to be either overrepresented (Rhodospirillales, Ruminococcus gauvreauii group, Ruminococcaceae, and Actinomyces) or underrepresented in the gut and endometrial microbiota of adenomyosis patients compared with controls. Distinct microbiota profiles were identified among patients with internal and external adenomyosis phenotypes. CONCLUSIONS The study revealed reduced gut microbiota diversity in adenomyosis patients, accompanied by distinct compositions in gut and vaginal microbiota compared with controls. Overrepresented or underrepresented bacterial taxa were noted in the gut and endometrial microbiota of adenomyosis patients, with variations in microbiota profiles among those with internal and external adenomyosis phenotypes. These findings suggest a potential association between microbiota and adenomyosis, indicating the need for further research to comprehensively understand the implications of these differences.
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Affiliation(s)
- Marta Valdés‐Bango
- Endometriosis Unit, Gynecology Department, Institute Clinic of Gynecology, Obstetrics and Neonatology (ICGON), Hospital Clinic of BarcelonaUniversitat de BarcelonaBarcelonaSpain
| | - Meritxell Gracia
- Endometriosis Unit, Gynecology Department, Institute Clinic of Gynecology, Obstetrics and Neonatology (ICGON), Hospital Clinic of BarcelonaUniversitat de BarcelonaBarcelonaSpain
| | - Elisa Rubio
- Department of Clinical Microbiology, Hospital Clinic of BarcelonaUniversitat de BarcelonaBarcelonaSpain
| | - Andrea Vergara
- Department of Clinical Microbiology, Hospital Clinic of BarcelonaUniversitat de BarcelonaBarcelonaSpain
- Barcelona Institute for Global Health (ISGlobal)BarcelonaSpain
- CIBER Enfermedades Infecciosas (CIBERINFEC)Instituto Salud Carlos IIIMadridSpain
| | - Climent Casals‐Pascual
- Department of Clinical Microbiology, Hospital Clinic of BarcelonaUniversitat de BarcelonaBarcelonaSpain
- Barcelona Institute for Global Health (ISGlobal)BarcelonaSpain
- CIBER Enfermedades Infecciosas (CIBERINFEC)Instituto Salud Carlos IIIMadridSpain
| | - Cristina Ros
- Endometriosis Unit, Gynecology Department, Institute Clinic of Gynecology, Obstetrics and Neonatology (ICGON), Hospital Clinic of BarcelonaUniversitat de BarcelonaBarcelonaSpain
| | - Mariona Rius
- Endometriosis Unit, Gynecology Department, Institute Clinic of Gynecology, Obstetrics and Neonatology (ICGON), Hospital Clinic of BarcelonaUniversitat de BarcelonaBarcelonaSpain
| | - Maria Ángeles Martínez‐Zamora
- Endometriosis Unit, Gynecology Department, Institute Clinic of Gynecology, Obstetrics and Neonatology (ICGON), Hospital Clinic of BarcelonaUniversitat de BarcelonaBarcelonaSpain
| | - Eduard Mension
- Endometriosis Unit, Gynecology Department, Institute Clinic of Gynecology, Obstetrics and Neonatology (ICGON), Hospital Clinic of BarcelonaUniversitat de BarcelonaBarcelonaSpain
| | - Lara Quintas
- Endometriosis Unit, Gynecology Department, Institute Clinic of Gynecology, Obstetrics and Neonatology (ICGON), Hospital Clinic of BarcelonaUniversitat de BarcelonaBarcelonaSpain
| | - Francisco Carmona
- Endometriosis Unit, Gynecology Department, Institute Clinic of Gynecology, Obstetrics and Neonatology (ICGON), Hospital Clinic of BarcelonaUniversitat de BarcelonaBarcelonaSpain
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216
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Gilkes JM, Frampton RA, Board AJ, Hudson AO, Price TG, Morris VK, Crittenden DL, Muscroft‐Taylor AC, Sheen CR, Smith GR, Dobson RCJ. A new lysine biosynthetic enzyme from a bacterial endosymbiont shaped by genetic drift and genome reduction. Protein Sci 2024; 33:e5083. [PMID: 38924211 PMCID: PMC11201819 DOI: 10.1002/pro.5083] [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: 01/23/2024] [Revised: 05/16/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024]
Abstract
The effect of population bottlenecks and genome reduction on enzyme function is poorly understood. Candidatus Liberibacter solanacearum is a bacterium with a reduced genome that is transmitted vertically to the egg of an infected psyllid-a population bottleneck that imposes genetic drift and is predicted to affect protein structure and function. Here, we define the function of Ca. L. solanacearum dihydrodipicolinate synthase (CLsoDHDPS), which catalyzes the committed branchpoint reaction in diaminopimelate and lysine biosynthesis. We demonstrate that CLsoDHDPS is expressed in Ca. L. solanacearum and expression is increased ~2-fold in the insect host compared to in planta. CLsoDHDPS has decreased thermal stability and increased aggregation propensity, implying mutations have destabilized the enzyme but are compensated for through elevated chaperone expression and a stabilized oligomeric state. CLsoDHDPS uses a ternary-complex kinetic mechanism, which is to date unique among DHDPS enzymes, has unusually low catalytic ability, but an unusually high substrate affinity. Structural studies demonstrate that the active site is more open, and the structure of CLsoDHDPS with both pyruvate and the substrate analogue succinic-semialdehyde reveals that the product is both structurally and energetically different and therefore evolution has in this case fashioned a new enzyme. Our study suggests the effects of genome reduction and genetic drift on the function of essential enzymes and provides insights on bacteria-host co-evolutionary associations. We propose that bacteria with endosymbiotic lifestyles present a rich vein of interesting enzymes useful for understanding enzyme function and/or informing protein engineering efforts.
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Affiliation(s)
- Jenna M. Gilkes
- Biomolecular Interaction CentreSchool of Biological Sciences, University of CanterburyChristchurchNew Zealand
- The New Zealand Institute for Plant and Food Research LimitedLincolnNew Zealand
- Callaghan Innovation, University of CanterburyChristchurchNew Zealand
| | - Rebekah A. Frampton
- The New Zealand Institute for Plant and Food Research LimitedLincolnNew Zealand
| | - Amanda J. Board
- Biomolecular Interaction CentreSchool of Biological Sciences, University of CanterburyChristchurchNew Zealand
| | - André O. Hudson
- Rochester Institute of Technology, Thomas H. Gosnell School of Life SciencesRochesterNew YorkUSA
| | - Thomas G. Price
- Biomolecular Interaction CentreSchool of Chemical and Physical Sciences, University of CanterburyChristchurchNew Zealand
| | - Vanessa K. Morris
- Biomolecular Interaction CentreSchool of Biological Sciences, University of CanterburyChristchurchNew Zealand
| | - Deborah L. Crittenden
- Biomolecular Interaction CentreSchool of Chemical and Physical Sciences, University of CanterburyChristchurchNew Zealand
| | | | - Campbell R. Sheen
- Callaghan Innovation, University of CanterburyChristchurchNew Zealand
| | - Grant R. Smith
- The New Zealand Institute for Plant and Food Research LimitedLincolnNew Zealand
| | - Renwick C. J. Dobson
- Biomolecular Interaction CentreSchool of Biological Sciences, University of CanterburyChristchurchNew Zealand
- Bio21 Molecular Science and Biotechnology Institute, Department of Biochemistry and Molecular BiologyUniversity of MelbourneParkvilleVictoriaAustralia
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217
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Baquero F, Pérez-Cobas AE, Aracil-Gisbert S, Coque TM, Zamora J. Selection versus transmission: Quantitative and organismic biology in antibiotic resistance. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 121:105606. [PMID: 38768878 DOI: 10.1016/j.meegid.2024.105606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 05/12/2024] [Accepted: 05/17/2024] [Indexed: 05/22/2024]
Abstract
We aimed to determine the importance of selection (mostly dependent on the anthropogenic use of antimicrobials) and transmission (mostly dependent on hygiene and sanitation) as drivers of the spread of antibiotic-resistant bacterial populations. The first obstacle to estimating the relative weight of both independent variables is the lack of detailed quantitative data concerning the number of bacterial cells, potentially either pathogenic or harmless, and bacterial species exposed to antimicrobial action in the microbiotas of specific environments. The second obstacle is the difficulty of considering the relative importance of the transmission and selection exerting their combined effects on antibiotic resistance across eco-biological levels. As a consequence, advances are urgently required in quantitative biology and organismic biology of antimicrobial resistance. The absolute number of humans exposed to antibiotics and the absolute number of potentially pathogenic and commensal bacteria in their microbiomes should influence both the selection and transmission of resistant bacterial populations. The "whole Earth" microbiome, with astonishingly high numbers of bacterial cells and species, which are also exposed to anthropogenic antimicrobials in various biogeographical spaces, shapes the antibiotic resistance landscape. These biogeographical spaces influence various intensities of selection and transmission of potentially pathogenic bacteria. While waiting for more precise data, biostatistics analysis and mathematical or computational modeling can provide proxies to compare the influence of selection and transmission in resistant bacteria. In European countries with lower sanitation levels, antibiotic consumption plays a major role in increasing antibiotic resistance; however, this is not the case in countries with high sanitation levels. Although both independent variables are linked, their relative influence on the level of antibiotic resistance varies according to the particular location. Therefore, interventions directed to decrease antibiotic resistance should be designed "a la carte" for specific locations with particular ecological conditions, including sanitation facilities.
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Affiliation(s)
- F Baquero
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain; Center for Biomedical Research in Epidemiology and Public Health Network (CIBERESP-Group 33), Madrid, Spain.
| | - A E Pérez-Cobas
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain; Center for Biomedical Research in Infectious Diseases Network (CIBERINFEC), Madrid, Spain
| | - S Aracil-Gisbert
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain; Center for Biomedical Research in Infectious Diseases Network (CIBERINFEC), Madrid, Spain
| | - T M Coque
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain; Center for Biomedical Research in Infectious Diseases Network (CIBERINFEC), Madrid, Spain
| | - J Zamora
- Clinical Biostatistics Unit, Ramón y Cajal University Hospital, and Ramón y Cajal Institute for Health Research (IRYCIS) Madrid, Spain; Center for Biomedical Research in Epidemiology and Public Health Network (CIBERESP-Group 42), Madrid, Spain; Institute of Metabolism and Systems Research, Biostatistics in Maternal and Perinatal Health, University of Birmingham, UK
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218
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Garber AI, Ramírez GA, D'Hondt S. Genomic stasis over millions of years in subseafloor sediment. Environ Microbiol 2024; 26:e16674. [PMID: 39146976 DOI: 10.1111/1462-2920.16674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 06/29/2024] [Indexed: 08/17/2024]
Abstract
One of the significant challenges in microbiology is to understand the extent and mechanisms of evolution within life beneath the surface of the Earth. The population bottleneck that microbes in deep marine sediment experience implies that mutational and population genetic forces could lead to higher levels of relaxed selection and an increase in pseudogenes. To investigate this hypothesis, a group of Thalassospira strains were isolated from subseafloor sediment that is 3 to 6 million years old, as reported by Orsi and colleagues in 2021. These isolates, representing lineages that have been buried for millions of years, offer an excellent opportunity to study the evolution of life beneath the seafloor over a long period. The existence of closely related strains from environments on the surface of the Earth enabled us to examine the impact of selection within each group. We discovered that isolates from beneath the seafloor show lineage-specific similarities to Thalassospira from the surface world, both in the overall intensity of selection on the genome and in the specific genes affected by mutation. We found no signs of increased relaxed selection or other notable genomic changes in the genomes of the Thalassospira isolates from beneath the seafloor, suggesting that these subseafloor isolates were awakened from a million-year near-stasis. The unique genomic characteristics of each Thalassospira lineage from beneath the seafloor must then reflect genetic changes that surface-inhabiting decendants acquired in the past 3-6 million years. Remarkably, Thalassospira lineages beneath the surface appear to have stably maintained their genomes in the midst of metabolic dormancy and extremely long generation times.
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Affiliation(s)
- Arkadiy I Garber
- Biodesign Institute, School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Gustavo A Ramírez
- Department of Biological Sciences, California State University Los Angeles, Los Angeles, California, USA
| | - Steven D'Hondt
- Graduate School of Oceanography, University of Rhode Island, Narragansett, Rhode Island, USA
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Ding M, Yan J, Chen Y, Liu J, Chao G, Zhang S. Changes in M6A methylation: A key factor in the vicious cycle of flora -gut aging. Ageing Res Rev 2024; 98:102351. [PMID: 38820855 DOI: 10.1016/j.arr.2024.102351] [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: 12/09/2023] [Revised: 05/16/2024] [Accepted: 05/27/2024] [Indexed: 06/02/2024]
Abstract
The aging process significantly impacts the gastrointestinal tract and various bodily systems, exacerbating age-related diseases. Research suggests a correlation between an imbalance in intestinal flora and gut aging, yet the precise mechanism remains incompletely elucidated. Epigenetic modifications, particularly m6A methylation, play a pivotal role in driving aging and are closely associated with gut aging. Maintaining a healthy balance of intestinal microbes is contingent upon m6A methylation, which is believed to be crucial in the vicious cycle of gut aging and intestinal flora. This article highlights the importance of m6A methylation in the nexus between gut aging and flora. It proposes the potential for targeted m6A methylation to break the vicious cycle of gut aging and flora imbalance, offering novel perspectives on attenuating or reversing gut aging.
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Affiliation(s)
- Menglu Ding
- The Second Affiliated Hospital of Zhejiang Chinese Medical University (The Xin Hua Hospital of Zhejiang Province), Hangzhou, PR China; Department of General Practice, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou 310000, PR China
| | - Junbin Yan
- The Second Affiliated Hospital of Zhejiang Chinese Medical University (The Xin Hua Hospital of Zhejiang Province), Hangzhou, PR China; Department of General Practice, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou 310000, PR China
| | - Yuxuan Chen
- The Second Affiliated Hospital of Zhejiang Chinese Medical University (The Xin Hua Hospital of Zhejiang Province), Hangzhou, PR China; Department of General Practice, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou 310000, PR China
| | - Jinguo Liu
- The Second Affiliated Hospital of Zhejiang Chinese Medical University (The Xin Hua Hospital of Zhejiang Province), Hangzhou, PR China; Department of General Practice, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou 310000, PR China
| | - Guanqun Chao
- The Second Affiliated Hospital of Zhejiang Chinese Medical University (The Xin Hua Hospital of Zhejiang Province), Hangzhou, PR China; Department of General Practice, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou 310000, PR China.
| | - Shuo Zhang
- The Second Affiliated Hospital of Zhejiang Chinese Medical University (The Xin Hua Hospital of Zhejiang Province), Hangzhou, PR China; Department of General Practice, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou 310000, PR China.
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Singh J, Vanlallawmzuali, Singh A, Biswal S, Zomuansangi R, Lalbiaktluangi C, Singh BP, Singh PK, Vellingiri B, Iyer M, Ram H, Udey B, Yadav MK. Microbiota-brain axis: Exploring the role of gut microbiota in psychiatric disorders - A comprehensive review. Asian J Psychiatr 2024; 97:104068. [PMID: 38776563 DOI: 10.1016/j.ajp.2024.104068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/28/2024] [Accepted: 05/01/2024] [Indexed: 05/25/2024]
Abstract
Mental illness is a hidden epidemic in modern science that has gradually spread worldwide. According to estimates from the World Health Organization (WHO), approximately 10% of the world's population suffers from various mental diseases each year. Worldwide, financial and health burdens on society are increasing annually. Therefore, understanding the different factors that can influence mental illness is required to formulate novel and effective treatments and interventions to combat mental illness. Gut microbiota, consisting of diverse microbial communities residing in the gastrointestinal tract, exert profound effects on the central nervous system through the gut-brain axis. The gut-brain axis serves as a conduit for bidirectional communication between the two systems, enabling the gut microbiota to affect emotional and cognitive functions. Dysbiosis, or an imbalance in the gut microbiota, is associated with an increased susceptibility to mental health disorders and psychiatric illnesses. Gut microbiota is one of the most diverse and abundant groups of microbes that have been found to interact with the central nervous system and play important physiological functions in the human gut, thus greatly affecting the development of mental illnesses. The interaction between gut microbiota and mental health-related illnesses is a multifaceted and promising field of study. This review explores the mechanisms by which gut microbiota influences mental health, encompassing the modulation of neurotransmitter production, neuroinflammation, and integrity of the gut barrier. In addition, it emphasizes a thorough understanding of how the gut microbiome affects various psychiatric conditions.
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Affiliation(s)
- Jawahar Singh
- Department of Psychiatry, All India Institute of Medical Sciences (AIIMS), Bathinda, Punjab, India
| | - Vanlallawmzuali
- Department of Biotechnology, Mizoram Central University, Pachhunga University College Campus, Aizawl, Mizoram, India
| | - Amit Singh
- Department of Microbiology Central University of Punjab, Bathinda 151401, India
| | - Suryanarayan Biswal
- Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda 151401, India
| | - Ruth Zomuansangi
- Department of Microbiology Central University of Punjab, Bathinda 151401, India
| | - C Lalbiaktluangi
- Department of Microbiology Central University of Punjab, Bathinda 151401, India
| | - Bhim Pratap Singh
- Department of Agriculture and Environmental Sciences (AES), National Institute of Food Technology Entrepreneurship and Management (NIFTEM), Sonepat, Haryana, India
| | - Prashant Kumar Singh
- Department of Biotechnology, Pachhunga University College Campus, Mizoram University (A Central University), Aizawl 796001, Mizoram, India
| | - Balachandar Vellingiri
- Stem cell and Regenerative Medicine/Translational Research, Department of Zoology, School of Basic Sciences, Central University of Punjab (CUPB), Bathinda, Punjab 151401, India
| | - Mahalaxmi Iyer
- Department of Microbiology Central University of Punjab, Bathinda 151401, India
| | - Heera Ram
- Department of Zoology, Jai Narain Vyas University, Jodhpur, Rajasthan 342001, India
| | - Bharat Udey
- Department of Psychiatry, All India Institute of Medical Sciences (AIIMS), Bathinda, Punjab, India
| | - Mukesh Kumar Yadav
- Department of Microbiology Central University of Punjab, Bathinda 151401, India.
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Chen X, Zou T, Zeng Q, Chen Y, Zhang C, Jiang S, Ding G. Metagenomic analysis reveals ecological and functional signatures of oral phageome associated with severe early childhood caries. J Dent 2024; 146:105059. [PMID: 38801939 DOI: 10.1016/j.jdent.2024.105059] [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: 12/15/2023] [Revised: 05/05/2024] [Accepted: 05/07/2024] [Indexed: 05/29/2024] Open
Abstract
OBJECTIVES Severe early childhood caries (S-ECC) is highly prevalent, affecting children's oral health. S-ECC development is closely associated with the complex oral microbial microbiome and its microorganism interactions, such as the imbalance of bacteriophages and bacteria. Till now, little is known about oral phageome on S-ECC. Therefore, this study aimed to investigate the potential role of the oral phageome in the pathogenesis of S-ECC. METHODS Unstimulated saliva (2 mL) was collected from 20 children with and without S-ECC for metagenomics analysis. Metagenomics sequencing and bioinformatic analysis were performed to determine the two groups' phageome diversity, taxonomic and functional annotations. Statistical analysis and visualization were performed with R and SPSS Statistics software. RESULTS 85.7 % of the extracted viral sequences were predicted from phages, in which most phages were classified into Myoviridae, Siphoviridae, and Podoviridae. Alpha diversity decreased, and Beta diversity increased in the S-ECC phageome compared to the healthy group. The abundance of Podoviridae phages increased, and the abundance of Inoviridae, Herelleviridae, and Streptococcus phages decreased in the S-ECC group. Functional annotation revealed increased annotation on glycoside hydrolases and nucleotide metabolism, decreased glycosyl transferases, carbohydrate-binding modules, and biogenic metabolism in the S-ECC phageome. CONCLUSIONS Metagenomic analysis revealed reduced Streptococcus phages and significant changes in functional annotations within the S-ECC phageome. These findings suggest a potential weakening of the regulatory influence of oral bacteria, which may indicate the development of innovative prevention and treatment strategies for S-ECC. These implications deserve further investigation and hold promise for advancing our understanding and management of S-ECC. CLINICAL SIGNIFICANCE The findings of this study indicate that oral phageomes are associated with bacterial genomes and metabolic processes, affecting the development of S-ECC. The reduced modulatory effect of the oral phageome in counteracting S-ECC's cariogenic activity suggests a new avenue for the prevention and treatment of S-ECC.
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Affiliation(s)
- Xin Chen
- Shenzhen Children's Hospital of China Medical University (CMU), Shenzhen, PR China; Department of Stomatology, Shenzhen Children's Hospital, Shenzhen, PR China
| | - Ting Zou
- Shenzhen Stomatology Hospital (Pingshan), Southern Medical University, Shenzhen, Guangdong, PR China
| | - Qinglu Zeng
- The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, PR China
| | - Yubing Chen
- The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, PR China
| | - Chengfei Zhang
- Endodontology, Restorative Dental Sciences, Faculty of Dentistry, The University of Hong Kong, Hong Kong, PR China
| | - Shan Jiang
- Shenzhen Stomatology Hospital (Pingshan), Southern Medical University, Shenzhen, Guangdong, PR China.
| | - Guicong Ding
- Shenzhen Children's Hospital of China Medical University (CMU), Shenzhen, PR China; Department of Stomatology, Shenzhen Children's Hospital, Shenzhen, PR China.
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Nannini G, Di Gloria L, Russo E, Sterrantino G, Kiros ST, Coppi M, Niccolai E, Baldi S, Ramazzotti M, Di Pilato V, Lagi F, Bartolucci G, Rossolini GM, Bartoloni A, Amedei A. Oral microbiota signatures associated with viremia and CD4 recovery in treatment-naïve HIV-1-infected patients. Microbes Infect 2024; 26:105339. [PMID: 38636822 DOI: 10.1016/j.micinf.2024.105339] [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: 01/07/2024] [Revised: 04/11/2024] [Accepted: 04/11/2024] [Indexed: 04/20/2024]
Abstract
PURPOSE Few reports focused on the role of oral microbiome diversity in HIV infection. We characterized the microbiota-immunity axis in a cohort of treatment-naïve HIV-1-infected patients undergoing antiretroviral therapy (ART) focusing on the oral microbiome (OM) and immunological responsivity. METHODS The sequencing of 16S rRNA V3-V4 hypervariable region was performed on salivary samples of 15 healthy control (HC) and 12 HIV + patients before starting ART and after reaching virological suppression. Then, we correlated the OM composition with serum cytokines and the Short Chain Fatty acids (SCFAs). RESULTS The comparison between HIV patients and HC oral microbiota showed differences in the bacterial α-diversity and richness. We documented a negative correlation between oral Prevotella and intestinal valeric acid at before starting ART and a positive correlation between oral Veillonella and gut acetic acid after reaching virological suppression. Finally, an increase in the phylum Proteobacteria was observed comparing saliva samples of immunological responders (IRs) patients against immunological non-responders (INRs). CONCLUSIONS For the first time, we described an increase in the oral pro-inflammatory Proteobacteria phylum in INRs compared to IRs. We provided more evidence that saliva could be a non-invasive and less expensive approach for research involving the oral cavity microbiome in HIV patients.
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Affiliation(s)
- Giulia Nannini
- Department of Experimental and Clinical Medicine, University of Florence, Florence 50134, Italy
| | - Leandro Di Gloria
- Department of Biomedical, Experimental and Clinical "Mario Serio", University of Florence, Florence 50134, Italy
| | - Edda Russo
- Department of Experimental and Clinical Medicine, University of Florence, Florence 50134, Italy
| | - Gaetana Sterrantino
- Department of Experimental and Clinical Medicine, University of Florence, Florence 50134, Italy
| | - Seble Tekle Kiros
- Department of Experimental and Clinical Medicine, University of Florence, Florence 50134, Italy; Clinical Microbiology and Virology Unit, Careggi University Hospital, Florence, Italy
| | - Marco Coppi
- Department of Experimental and Clinical Medicine, University of Florence, Florence 50134, Italy
| | - Elena Niccolai
- Department of Experimental and Clinical Medicine, University of Florence, Florence 50134, Italy
| | - Simone Baldi
- Department of Experimental and Clinical Medicine, University of Florence, Florence 50134, Italy
| | - Matteo Ramazzotti
- Department of Biomedical, Experimental and Clinical "Mario Serio", University of Florence, Florence 50134, Italy
| | - Vincenzo Di Pilato
- Department of Surgical Sciences and Integrated Diagnostics, University of Genoa, Genoa, Italy
| | - Filippo Lagi
- Department of Experimental and Clinical Medicine, University of Florence, Florence 50134, Italy
| | - Gianluca Bartolucci
- Department of Neurosciences, Psychology, Drug Research and Child Health, University of Florence, Florence 50019, Italy
| | - Gian Maria Rossolini
- Department of Experimental and Clinical Medicine, University of Florence, Florence 50134, Italy; Clinical Microbiology and Virology Unit, Careggi University Hospital, Florence, Italy
| | - Alessandro Bartoloni
- Department of Experimental and Clinical Medicine, University of Florence, Florence 50134, Italy; Infectious and Tropical Diseases Unit, Careggi University Hospital, Florence, Italy
| | - Amedeo Amedei
- Department of Experimental and Clinical Medicine, University of Florence, Florence 50134, Italy.
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Liu Z, Dai J, Liu R, Shen Z, Huang A, Huang Y, Wang L, Chen P, Zhou Z, Xiao H, Chen X, Yang X. Complex insoluble dietary fiber alleviates obesity and liver steatosis, and modulates the gut microbiota in C57BL/6J mice fed a high-fat diet. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024; 104:5462-5473. [PMID: 38348948 DOI: 10.1002/jsfa.13380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 02/06/2024] [Accepted: 02/07/2024] [Indexed: 02/28/2024]
Abstract
BACKGROUND Obesity has been demonstrated as a risk factor that seriously affects health. Insoluble dietary fiber (IDF), as a major component of dietary fiber, has positive effects on obesity, inflammation and diabetes. RESULTS In this study, complex IDF was prepared using 50% enoki mushroom IDF, 40% carrot IDF, and 10% oat IDF. The effects and potential mechanism of complex IDF on obesity were investigated in C57BL/6 mice fed a high-fat diet. The results showed that feeding diets containing 5% complex IDF for 8 weeks significantly reduced mouse body weight, epididymal lipid index, and ectopic fat deposition, and improved mouse liver lipotoxicity (reduced serum levels of alanine aminotransferase, aspartate aminotransferase, and alkaline phosphatase), fatty liver, and short-chain fatty acid composition. High-throughput sequencing of 16S rRNA and analysis of fecal metabolomics showed that the intervention with complex IDF reversed the high-fat-diet-induced dysbiosis of gut microbiota, which is associated with obesity and intestinal inflammation, and affected metabolic pathways, such as primary bile acid biosynthesis, related to fat digestion and absorption. CONCLUSION Composite IDF intervention can effectively inhibit high-fat-diet-induced obesity and related symptoms and affect the gut microbiota and related metabolic pathways in obesity. Complex IDF has potential value in the prevention of obesity and metabolic syndrome. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Zurui Liu
- School of Food and Bioengineering, Xihua University, Chengdu, People's Republic of China
| | - Juan Dai
- School of Laboratory Medicine, Chengdu Medical College, Chengdu, People's Republic of China
| | - Ruijia Liu
- School of Food and Bioengineering, Xihua University, Chengdu, People's Republic of China
| | - Ziyi Shen
- School of Food and Bioengineering, Xihua University, Chengdu, People's Republic of China
| | - Ai Huang
- School of Food and Bioengineering, Xihua University, Chengdu, People's Republic of China
| | - YuKun Huang
- School of Food and Bioengineering, Xihua University, Chengdu, People's Republic of China
| | - Lijun Wang
- School of Food and Bioengineering, Xihua University, Chengdu, People's Republic of China
| | - Pengfei Chen
- School of Food and Bioengineering, Xihua University, Chengdu, People's Republic of China
| | - Zheng Zhou
- School of Food and Bioengineering, Xihua University, Chengdu, People's Republic of China
| | - Hang Xiao
- Department of Food Science, University of Massachusetts, Amherst, Massachusetts, USA
| | - Xianggui Chen
- School of Food and Bioengineering, Xihua University, Chengdu, People's Republic of China
- Chongqing Key Laboratory of Specialty Food Co-Built by Sichuan and Chongqing, Chengdu, People's Republic of China
| | - Xiao Yang
- School of Food and Bioengineering, Xihua University, Chengdu, People's Republic of China
- Chongqing Key Laboratory of Specialty Food Co-Built by Sichuan and Chongqing, Chengdu, People's Republic of China
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Dunham SJB, Avelar‐Barragan J, Rothman JA, Adams ED, Faraci G, Forner S, Kawauchi S, Tenner AJ, Green KN, LaFerla FM, MacGregor GR, Mapstone M, Whiteson KL. Sex-specific associations between AD genotype and the microbiome of human amyloid beta knock-in (hAβ-KI) mice. Alzheimers Dement 2024; 20:4935-4950. [PMID: 38572865 PMCID: PMC11247698 DOI: 10.1002/alz.13794] [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: 10/24/2023] [Revised: 02/20/2024] [Accepted: 02/23/2024] [Indexed: 04/05/2024]
Abstract
INTRODUCTION Emerging evidence links changes in the gut microbiome to late-onset Alzheimer's disease (LOAD), necessitating examination of AD mouse models with consideration of the microbiome. METHODS We used shotgun metagenomics and untargeted metabolomics to study the human amyloid beta knock-in (hAβ-KI) murine model for LOAD compared to both wild-type (WT) mice and a model for early-onset AD (3xTg-AD). RESULTS Eighteen-month female (but not male) hAβ-KI microbiomes were distinct from WT microbiomes, with AD genotype accounting for 18% of the variance by permutational multivariate analysis of variance (PERMANOVA). Metabolomic diversity differences were observed in females, however no individual metabolites were differentially abundant. hAβ-KI mice microbiomes were distinguishable from 3xTg-AD animals (81% accuracy by random forest modeling), with separation primarily driven by Romboutsia ilealis and Turicibacter species. Microbiomes were highly cage specific, with cage assignment accounting for more than 40% of the PERMANOVA variance between the groups. DISCUSSION These findings highlight a sex-dependent variation in the microbiomes of hAβ-KI mice and underscore the importance of considering the microbiome when designing studies that use murine models for AD. HIGHLIGHTS Microbial diversity and the abundance of several species differed in human amyloid beta knock-in (hAβ-KI) females but not males. Correlations to Alzheimer's disease (AD) genotype were stronger for the microbiome than the metabolome. Microbiomes from hAβ-KI mice were distinct from 3xTg-AD mice. Cage effects accounted for most of the variance in the microbiome and metabolome.
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Affiliation(s)
- Sage J. B. Dunham
- Department of Molecular Biology & BiochemistryUniversity of California IrvineIrvineCaliforniaUSA
| | - Julio Avelar‐Barragan
- Department of Molecular Biology & BiochemistryUniversity of California IrvineIrvineCaliforniaUSA
| | - Jason A. Rothman
- Department of Molecular Biology & BiochemistryUniversity of California IrvineIrvineCaliforniaUSA
| | - Eric D. Adams
- Department of Molecular Biology & BiochemistryUniversity of California IrvineIrvineCaliforniaUSA
| | - Gina Faraci
- Department of Molecular Biology & BiochemistryUniversity of California IrvineIrvineCaliforniaUSA
| | - Stefania Forner
- Institute for Memory Impairments and Neurological Disorders (UCI MIND)University of California IrvineIrvineCaliforniaUSA
| | - Shimako Kawauchi
- Department of Anatomy and NeurobiologyDevelopmental Biology CenterUniversity of California IrvineCollege of MedicineIrvineCaliforniaUSA
| | - Andrea J. Tenner
- Department of Molecular Biology & BiochemistryDepartment of Neurobiology and BehaviorDepartment of Pathology and Laboratory MedicineSchool of MedicineInstitute for Memory Impairments and Neurological Disorders (UCI MIND)University of California IrvineIrvineCaliforniaUSA
| | - Kim N. Green
- Institute for Memory Impairments and Neurological Disorders (UCI MIND), Department of Neurobiology and BehaviorSchool of Biological SciencesCenter for Neural Circuit MappingUniversity of California IrvineIrvineCaliforniaUSA
| | - Frank M. LaFerla
- Institute for Memory Impairments and Neurological Disorders (UCI MIND)Department of Neurobiology and BehaviorUniversity of California IrvineIrvineCaliforniaUSA
| | - Grant R. MacGregor
- Department of Developmental and Cell BiologyUniversity of California IrvineIrvineCaliforniaUSA
| | - Mark Mapstone
- Department of NeurologyUniversity of California IrvineIrvineCaliforniaUSA
| | - Katrine L. Whiteson
- Department of Molecular Biology & BiochemistryUniversity of California IrvineIrvineCaliforniaUSA
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Song Y, Zhang J, Li Y, Wang Y, Wan Y. Potential Protective Effect of Selenium-Enriched Lactobacillus plantarum on Cadmium-Induced Liver Injury in Mice. J Microbiol Biotechnol 2024; 34:1328-1339. [PMID: 38754999 PMCID: PMC11239402 DOI: 10.4014/jmb.2312.12051] [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: 01/02/2024] [Revised: 03/25/2024] [Accepted: 04/05/2024] [Indexed: 05/18/2024]
Abstract
Cadmium (Cd) is a prevalent environmental contaminant that poses a potential hazard to the health of both humans and animals. In this study, biosynthesized selenium-enriched Lactobacillus plantarum and selenium nanoparticles (SeNPs) were developed and evaluated for their protective effects against Cd-induced hepatic injury in mice through oral administration for 4 weeks. Cadmium exposure resulted in severe impairment of liver function, as evidenced by increased levels of serum markers of liver injury and, oxidative stress and significant damage to liver tissue, and a notable decrease in the diversity of the intestinal microbiota. Oral administration of Se-enriched L. plantarum (LS) reduced cadmium accumulation in the liver by 49.5% and, restored other cadmium-induced damage markers to normal levels. A comparison of the effects with those of L. plantarum (L) and SeNPs isolated from LS revealed that LS could more effectively alleviate hepatic oxidative stress and reduce the intrahepatic inflammatory responses of the liver, further protecting against cadmium-induced liver injury. These findings suggest that the development of LS may be effective at protecting the liver and intestinal tract from cadmium-induced damage.
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Affiliation(s)
- Yanyan Song
- College of Biochemical Engineering, Beijing Union University, Beijing 100023, P.R. China
| | - Jing Zhang
- College of Biochemical Engineering, Beijing Union University, Beijing 100023, P.R. China
| | - Yidan Li
- College of Biochemical Engineering, Beijing Union University, Beijing 100023, P.R. China
| | - Yuxuan Wang
- College of Biochemical Engineering, Beijing Union University, Beijing 100023, P.R. China
| | - Yingxin Wan
- College of Biochemical Engineering, Beijing Union University, Beijing 100023, P.R. China
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226
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Lee YE, Im DS. Euiin-Tang Attenuates Obesity-Induced Asthma by Resolving Metaflammation. Pharmaceuticals (Basel) 2024; 17:853. [PMID: 39065704 PMCID: PMC11279728 DOI: 10.3390/ph17070853] [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: 06/14/2024] [Revised: 06/24/2024] [Accepted: 06/27/2024] [Indexed: 07/28/2024] Open
Abstract
Euiin-tang reduces obesity and hypertension. Patients with obesity may develop obesity-induced asthma (OIA) owing to phlegm dampness. This study aimed to determine whether euiin-tang alleviates high-fat diet (HFD)-induced OIA in C57BL/6 mice. OIA was developed by HFD feeding for 15 weeks in C57BL/6 mice, and euiin-tang (5 mg/10 g/day) was orally administered for the last five weeks. Oral administration of euiin-tang suppressed HFD-induced changes in body weight, liver weight, airway hypersensitivity (AHR), and immune cell infiltration in bronchoalveolar lavage fluid. Histological analysis revealed that euiin-tang treatment suppressed HFD-induced mucosal inflammation, hypersecretion, and fibrosis. The lungs and gonadal white adipose tissue showed increased expression of inflammatory cytokines (IL-1β, IL-17A, TNF-α, IL-6, IL-13, IFN-γ, MPO, and CCL2) following HFD, whereas euiin-tang inhibited this increase. HFD also increased the number of pro-inflammatory CD86+ M1 macrophages and decreased the number of anti-inflammatory CD206+ M2 macrophages in the lungs, whereas euiin-tang treatment reversed these effects. HFD induced a decrease in adiponectin and an increase in leptin, which was reversed by euiin-tang. Therefore, euiin-tang may be a potential therapeutic agent for OIA because it suppresses metaflammation as demonstrated in the present study.
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Affiliation(s)
| | - Dong-Soon Im
- Department of Basic Pharmaceutical Sciences, Graduate School, Kyung Hee University, Seoul 02447, Republic of Korea;
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227
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Kooij KL, Andreani NA, van der Gun LL, Keller L, Trinh S, van der Vijgh B, Luijendijk M, Dempfle A, Herpertz-Dahlmann B, Seitz J, van Elburg A, Danner UN, Baines J, Adan RAH. Fecal microbiota transplantation of patients with anorexia nervosa did not alter flexible behavior in rats. Int J Eat Disord 2024. [PMID: 38934721 DOI: 10.1002/eat.24231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 04/11/2024] [Accepted: 04/30/2024] [Indexed: 06/28/2024]
Abstract
OBJECTIVE Patients with anorexia nervosa (AN) are often anxious, display inflexible behavior and disrupted reward processing. Emerging evidence suggests that gut dysbiosis in patients contributes to the disease phenotype and progression. METHODS In a preclinical study, we explored whether AN-derived microbiota impacts cognitive flexibility, anxiety, and dopamine signaling using fecal microbiota transplantation (FMT) in tyrosine hydroxylase-cre rats. We performed probabilistic reversal learning task (PRLT) at the baseline, after antibiotic treatment, and following FMT from patients with AN and controls. We assessed flexible behavior, task engagement, and ventral tegmental area (VTA) dopamine signaling during and in the absence of reward. Furthermore, anxiety-like behavior was evaluated with open field (OF) and elevated plus maze (EPM) tests. RESULTS Neither antibiotic-induced dysbiosis nor AN FMT led to significant alterations in the number of reversals or lever press strategies after reinforced or nonreinforced lever presses (win and lose-stay) in the PRLT. However, the number of initiated trials decreased after antibiotic treatment while remaining unchanged after FMT. No significant differences were observed in VTA dopamine activity, anxiety measures in the OF and EPM tests. Microbiome analysis revealed limited overlap between the microbiota of the donors and recipients. DISCUSSION No evidence was found that the microbiota of patients compared to controls, nor a depleted microbiome impacts cognitive flexibility. Nonetheless, antibiotic-induced dysbiosis resulted in reduced task engagement during the PRLT. The relatively low efficiency of the FMT is a limitation of our study and highlights the need for improved protocols to draw robust conclusions in future studies. PUBLIC SIGNIFICANCE While our study did not reveal direct impacts of AN-associated gut microbiota on cognitive flexibility or anxiety behaviors in our preclinical model, we observed a decrease in task engagement after antibiotic-induced dysbiosis, underscoring that the presence of a gut microbiome matters. Our findings underscore the need for further refinement in FMT protocols to better elucidate the complex interplay between gut microbiota and behaviors characteristic of anorexia nervosa.
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Affiliation(s)
- Karlijn L Kooij
- UMC Brain Center, Department of Translational Neuroscience, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Altrecht Eating Disorders Rintveld, Zeist, The Netherlands
| | - Nadia Andrea Andreani
- Section Evolutionary Medicine, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Section Evolutionary Medicine, Institute for Experimental Medicine, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Luna L van der Gun
- UMC Brain Center, Department of Translational Neuroscience, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Lara Keller
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital RWTH Aachen, Aachen, Germany
| | - Stefanie Trinh
- Institute of Neuroanatomy, RWTH Aachen University, Aachen, Germany
| | | | - Mieneke Luijendijk
- UMC Brain Center, Department of Translational Neuroscience, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Astrid Dempfle
- Institute of Medical Informatics and Statistics, Kiel University, Kiel, Germany
| | | | - Jochen Seitz
- Institute of Neuroanatomy, RWTH Aachen University, Aachen, Germany
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, LVR University Hospital Essen, Essen, Germany
| | - Annemarie van Elburg
- Altrecht Eating Disorders Rintveld, Zeist, The Netherlands
- Faculty of Social Sciences, Utrecht University, Utrecht, The Netherlands
| | - Unna N Danner
- Altrecht Eating Disorders Rintveld, Zeist, The Netherlands
| | - John Baines
- Section Evolutionary Medicine, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Section Evolutionary Medicine, Institute for Experimental Medicine, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Roger A H Adan
- UMC Brain Center, Department of Translational Neuroscience, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Altrecht Eating Disorders Rintveld, Zeist, The Netherlands
- Department of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
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228
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Kallapura G, Prakash AS, Sankaran K, Manjappa P, Chaudhary P, Ambhore S, Dhar D. Microbiota based personalized nutrition improves hyperglycaemia and hypertension parameters and reduces inflammation: a prospective, open label, controlled, randomized, comparative, proof of concept study. PeerJ 2024; 12:e17583. [PMID: 38948211 PMCID: PMC11214429 DOI: 10.7717/peerj.17583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 05/27/2024] [Indexed: 07/02/2024] Open
Abstract
Background Recent studies suggest that gut microbiota composition, abundance and diversity can influence many chronic diseases such as type 2 diabetes. Modulating gut microbiota through targeted nutrition can provide beneficial effects leading to the concept of personalized nutrition for health improvement. In this prospective clinical trial, we evaluated the impact of a microbiome-based targeted personalized diet on hyperglycaemic and hyperlipidaemic individuals. Specifically, BugSpeaks®-a microbiome profile test that profiles microbiota using next generation sequencing and provides personalized nutritional recommendation based on the individual microbiota profile was evaluated. Methods A total of 30 participants with type 2 diabetes and hyperlipidaemia were recruited for this study. The microbiome profile of the 15 participants (test arm) was evaluated using whole genome shotgun metagenomics and personalized nutritional recommendations based on their microbiota profile were provided. The remaining 15 participants (control arm) were provided with diabetic nutritional guidance for 3 months. Clinical and anthropometric parameters such as HbA1c, systolic/diastolic pressure, c-reactive protein levels and microbiota composition were measured and compared during the study. Results The test arm (microbiome-based nutrition) showed a statistically significant decrease in HbA1c level from 8.30 (95% confidence interval (CI), [7.74-8.85]) to 6.67 (95% CI [6.2-7.05]), p < 0.001 after 90 days. The test arm also showed a 5% decline in the systolic pressure whereas the control arm showed a 7% increase. Incidentally, a sub-cohort of the test arm of patients with >130 mm Hg systolic pressure showed a statistically significant decrease of systolic pressure by 14%. Interestingly, CRP level was also found to drop by 19.5%. Alpha diversity measures showed a significant increase in Shannon diversity measure (p < 0.05), after the microbiome-based personalized dietary intervention. The intervention led to a minimum two-fold (Log2 fold change increase in species like Phascolarctobacterium succinatutens, Bifidobacterium angulatum, and Levilactobacillus brevis which might have a beneficial role in the current context and a similar decrease in species like Alistipes finegoldii, and Sutterella faecalis which have been earlier shown to have some negative effects in the host. Overall, the study indicated a net positive impact of the microbiota based personalized dietary regime on the gut microbiome and correlated clinical parameters.
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Samulėnaitė S, García-Blanco A, Mayneris-Perxachs J, Domingo-Rodríguez L, Cabana-Domínguez J, Fernàndez-Castillo N, Gago-García E, Pineda-Cirera L, Burokas A, Espinosa-Carrasco J, Arboleya S, Latorre J, Stanton C, Hosomi K, Kunisawa J, Cormand B, Fernández-Real JM, Maldonado R, Martín-García E. Gut microbiota signatures of vulnerability to food addiction in mice and humans. Gut 2024:gutjnl-2023-331445. [PMID: 38926079 DOI: 10.1136/gutjnl-2023-331445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 04/01/2024] [Indexed: 06/28/2024]
Abstract
OBJECTIVE Food addiction is a multifactorial disorder characterised by a loss of control over food intake that may promote obesity and alter gut microbiota composition. We have investigated the potential involvement of the gut microbiota in the mechanisms underlying food addiction. DESIGN We used the Yale Food Addiction Scale (YFAS) 2.0 criteria to classify extreme food addiction in mouse and human subpopulations to identify gut microbiota signatures associated with vulnerability to this disorder. RESULTS Both animal and human cohorts showed important similarities in the gut microbiota signatures linked to food addiction. The signatures suggested possible non-beneficial effects of bacteria belonging to the Proteobacteria phylum and potential protective effects of Actinobacteria against the development of food addiction in both cohorts of humans and mice. A decreased relative abundance of the species Blautia wexlerae was observed in addicted humans and of Blautia genus in addicted mice. Administration of the non-digestible carbohydrates, lactulose and rhamnose, known to favour Blautia growth, led to increased relative abundance of Blautia in mice faeces in parallel with dramatic improvements in food addiction. A similar improvement was revealed after oral administration of Blautia wexlerae as a beneficial microbe. CONCLUSION By understanding the crosstalk between this behavioural alteration and gut microbiota, these findings constitute a step forward to future treatments for food addiction and related eating disorders.
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Affiliation(s)
- Solveiga Samulėnaitė
- Laboratory of Neuropharmacology-Neurophar, Department of Medicine and Life Sciences, Pompeu Fabra University, Barcelona, Spain
- Department of Biological Models, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Alejandra García-Blanco
- Laboratory of Neuropharmacology-Neurophar, Department of Medicine and Life Sciences, Pompeu Fabra University, Barcelona, Spain
| | - Jordi Mayneris-Perxachs
- Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IdibGi), Girona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
- Department of Diabetes, Endocrinology and Nutrition, Dr Josep Trueta University Hospital, Girona, Spain
| | - Laura Domingo-Rodríguez
- Laboratory of Neuropharmacology-Neurophar, Department of Medicine and Life Sciences, Pompeu Fabra University, Barcelona, Spain
| | - Judit Cabana-Domínguez
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras, (CIBERER), Madrid, Spain
- Institut de Biomedicina de la Universitat de Barcelona, (IBUB), Barcelona, Spain
- Institut de Recerca Sant Joan de Déu (IR-SJD), Esplugues de Llobregat, Barcelona, Spain
| | - Noèlia Fernàndez-Castillo
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras, (CIBERER), Madrid, Spain
- Institut de Biomedicina de la Universitat de Barcelona, (IBUB), Barcelona, Spain
- Institut de Recerca Sant Joan de Déu (IR-SJD), Esplugues de Llobregat, Barcelona, Spain
| | - Edurne Gago-García
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras, (CIBERER), Madrid, Spain
- Institut de Biomedicina de la Universitat de Barcelona, (IBUB), Barcelona, Spain
- Institut de Recerca Sant Joan de Déu (IR-SJD), Esplugues de Llobregat, Barcelona, Spain
| | - Laura Pineda-Cirera
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras, (CIBERER), Madrid, Spain
- Institut de Biomedicina de la Universitat de Barcelona, (IBUB), Barcelona, Spain
- Institut de Recerca Sant Joan de Déu (IR-SJD), Esplugues de Llobregat, Barcelona, Spain
| | - Aurelijus Burokas
- Department of Biological Models, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | | | - Silvia Arboleya
- APC Microbiome Institute, University College Cork, Cork, Ireland
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Villaviciosa, Asturias, Spain
| | - Jessica Latorre
- Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IdibGi), Girona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
- Department of Diabetes, Endocrinology and Nutrition, Dr Josep Trueta University Hospital, Girona, Spain
| | - Catherine Stanton
- APC Microbiome Institute, University College Cork, Cork, Ireland
- Teagasc Food Research Centre, Moorepark, Fermoy, Co, Cork, Ireland
| | - Koji Hosomi
- Laboratory of Vaccine Materials and Laboratory of Gut Environmental System, Microbial Research Center for Health and Medicine, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Ibaraki, Osaka, Japan. (NIBIOHN), Ibaraki, Osaka, Japan
| | - Jun Kunisawa
- Laboratory of Vaccine Materials and Laboratory of Gut Environmental System, Microbial Research Center for Health and Medicine, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Ibaraki, Osaka, Japan. (NIBIOHN), Ibaraki, Osaka, Japan
| | - Bru Cormand
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras, (CIBERER), Madrid, Spain
- Institut de Biomedicina de la Universitat de Barcelona, (IBUB), Barcelona, Spain
- Institut de Recerca Sant Joan de Déu (IR-SJD), Esplugues de Llobregat, Barcelona, Spain
| | - Jose Manuel Fernández-Real
- Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IdibGi), Girona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
- Department of Diabetes, Endocrinology and Nutrition, Dr Josep Trueta University Hospital, Girona, Spain
- Department of Medical Sciences, Faculty of Medicine, University of Girona, Girona, Spain
| | - Rafael Maldonado
- Laboratory of Neuropharmacology-Neurophar, Department of Medicine and Life Sciences, Pompeu Fabra University, Barcelona, Spain
- Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Elena Martín-García
- Laboratory of Neuropharmacology-Neurophar, Department of Medicine and Life Sciences, Pompeu Fabra University, Barcelona, Spain
- Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
- Departament de Psicobiologia i Metodologia de les Ciències de la Salut, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Spain
- Institut de Neurociències, Universitat Autònoma de Barcelona, Barcelona, Spain
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230
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Sipos D, Varga A, Kappéter Á, Halda-Kiss B, Kása P, Pál S, Kocsis B, Péterfi Z. Encapsulation protocol for fecal microbiota transplantation. Front Cell Infect Microbiol 2024; 14:1424376. [PMID: 38988813 PMCID: PMC11233434 DOI: 10.3389/fcimb.2024.1424376] [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: 04/27/2024] [Accepted: 06/10/2024] [Indexed: 07/12/2024] Open
Abstract
Introduction Clostridioides difficile infections (CDI) continue to pose a challenge for clinicians. Fecal microbiota transplantation (FMT) is an effective treatment option in CDI. Furthermore, recent and ongoing studies suggest potential benefits of FMT in other diseases as well. Methods We would like to present a novel protocol for encapsulation of lyophilized fecal material. Our method provides with better compliance as well as improved flexibility, storage and safety. Results FMT was conducted in 28 patients with an overall success rate of 82,14% using apsules containing lyophilized stool. 16 of patients were given capsules with lessened bacteria counts. The success rate in this group was 93,75%. Discussion The results highlight the still unanswered questions about the mechanism of action and contribute to a wider use of FMT in the clinical praxis and in research.
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Affiliation(s)
- Dávid Sipos
- 1st Department of Internal Medicine - Department of Infectology, University of Pécs Clinical Centre, Pécs, Hungary
| | - Adorján Varga
- Department of Medical Microbiology and Immunology, University of Pécs Medical School, Clinical Centre, Pécs, Hungary
| | - Ágnes Kappéter
- 1st Department of Internal Medicine - Department of Infectology, University of Pécs Clinical Centre, Pécs, Hungary
| | - Bernadett Halda-Kiss
- 1st Department of Internal Medicine - Department of Infectology, University of Pécs Clinical Centre, Pécs, Hungary
| | - Péter Kása
- Institute of Pharmaceutical Technology and Biopharmacy, University of Pécs Faculty of Pharmacy, Pécs, Hungary
| | - Szilárd Pál
- Institute of Pharmaceutical Technology and Biopharmacy, University of Pécs Faculty of Pharmacy, Pécs, Hungary
| | - Béla Kocsis
- Department of Medical Microbiology and Immunology, University of Pécs Medical School, Clinical Centre, Pécs, Hungary
| | - Zoltán Péterfi
- 1st Department of Internal Medicine - Department of Infectology, University of Pécs Clinical Centre, Pécs, Hungary
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231
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Bepler T, Barrera MD, Rooney MT, Xiong Y, Kuang H, Goodell E, Goodwin MJ, Harbron E, Fu R, Mihailescu M, Narayanan A, Cotten ML. Antiviral activity of the host defense peptide piscidin 1: investigating a membrane-mediated mode of action. Front Chem 2024; 12:1379192. [PMID: 38988727 PMCID: PMC11233706 DOI: 10.3389/fchem.2024.1379192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 05/08/2024] [Indexed: 07/12/2024] Open
Abstract
Outbreaks of viral diseases are on the rise, fueling the search for antiviral therapeutics that act on a broad range of viruses while remaining safe to human host cells. In this research, we leverage the finding that the plasma membranes of host cells and the lipid bilayers surrounding enveloped viruses differ in lipid composition. We feature Piscidin 1 (P1), a cationic host defense peptide (HDP) that has antimicrobial effects and membrane activity associated with its N-terminal region where a cluster of aromatic residues and copper-binding motif reside. While few HDPs have demonstrated antiviral activity, P1 acts in the micromolar range against several enveloped viruses that vary in envelope lipid composition. Notably, it inhibits HIV-1, a virus that has an envelope enriched in cholesterol, a lipid associated with higher membrane order and stability. Here, we first document through plaque assays that P1 boasts strong activity against SARS-CoV-2, which has an envelope low in cholesterol. Second, we extend previous studies done with homogeneous bilayers and devise cholesterol-containing zwitterionic membranes that contain the liquid disordered (Ld; low in cholesterol) and ordered (Lo, rich in cholesterol) phases. Using dye leakage assays and cryo-electron microscopy on vesicles, we show that P1 has dramatic permeabilizing capability on the Lo/Ld, an effect matched by a strong ability to aggregate, fuse, and thin the membranes. Differential scanning calorimetry and NMR experiments demonstrate that P1 mixes the lipid content of vesicles and alters the stability of the Lo. Structural studies by NMR indicate that P1 interacts with the Lo/Ld by folding into an α-helix that lies parallel to the membrane surface. Altogether, these results show that P1 is more disruptive to phase-separated than homogenous cholesterol-containing bilayers, suggesting an ability to target domain boundaries. Overall, this multi-faceted research highlights how a peptide that interacts strongly with membranes through an aromatic-rich N-terminal motif disrupt viral envelope mimics. This represents an important step towards the development of novel peptides with broad-spectrum antiviral activity.
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Affiliation(s)
- Tristan Bepler
- New York Structural Biology Center, New York, NY, United States
| | - Michael D. Barrera
- School of Systems Biology, George Mason University, Manassas, VA, United States
| | - Mary T. Rooney
- Department of Applied Science, William & Mary, Williamsburg, VA, United States
- Department of Chemistry, Hofstra University, Hempstead, NY, United States
| | - Yawei Xiong
- Department of Applied Science, William & Mary, Williamsburg, VA, United States
| | - Huihui Kuang
- New York Structural Biology Center, New York, NY, United States
| | - Evan Goodell
- Department of Applied Science, William & Mary, Williamsburg, VA, United States
| | - Matthew J. Goodwin
- Department of Chemistry, William & Mary, Williamsburg, VA, United States
| | - Elizabeth Harbron
- Department of Chemistry, William & Mary, Williamsburg, VA, United States
| | - Riqiang Fu
- National High Magnetic Field Laboratory, Tallahassee, FL, United States
| | - Mihaela Mihailescu
- Institute for Bioscience and Biotechnology Research, Rockville, MD, United States
| | - Aarthi Narayanan
- Department of Biology, George Mason University, Manassas, VA, United States
| | - Myriam L. Cotten
- Department of Applied Science, William & Mary, Williamsburg, VA, United States
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, United States
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232
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Secaira-Morocho H, Chede A, Gonzalez-de-Salceda L, Garcia-Pichel F, Zhu Q. An evolutionary optimum amid moderate heritability in prokaryotic cell size. Cell Rep 2024; 43:114268. [PMID: 38776226 DOI: 10.1016/j.celrep.2024.114268] [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: 01/04/2024] [Revised: 04/11/2024] [Accepted: 05/08/2024] [Indexed: 05/24/2024] Open
Abstract
We investigate the distribution and evolution of prokaryotic cell size based on a compilation of 5,380 species. Size spans four orders of magnitude, from 100 nm (Mycoplasma) to more than 1 cm (Thiomargarita); however, most species congregate heavily around the mean. The distribution approximates but is distinct from log normality. Comparative phylogenetics suggests that size is heritable, yet the phylogenetic signal is moderate, and the degree of heritability is independent of taxonomic scale (i.e., fractal). Evolutionary modeling indicates the presence of an optimal cell size to which most species gravitate. The size is equivalent to a coccus of 0.70 μm in diameter. Analyses of 1,361 species with sequenced genomes show that genomic traits contribute to size evolution moderately and synergistically. Given our results, scaling theory, and empirical evidence, we discuss potential drivers that may expand or shrink cells around the optimum and propose a stability landscape model for prokaryotic cell size.
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Affiliation(s)
- Henry Secaira-Morocho
- Center for Fundamental and Applied Microbiomics and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Abhinav Chede
- Center for Fundamental and Applied Microbiomics and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Luis Gonzalez-de-Salceda
- Center for Fundamental and Applied Microbiomics and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Ferran Garcia-Pichel
- Center for Fundamental and Applied Microbiomics and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA.
| | - Qiyun Zhu
- Center for Fundamental and Applied Microbiomics and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA.
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233
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Marqués MC, Andreu-Moreno I, Sanjuán R, Elena SF, Geller R. An efficient plasmid-based system for the recovery of recombinant vesicular stomatitis virus encoding foreign glycoproteins. Sci Rep 2024; 14:14644. [PMID: 38918479 PMCID: PMC11199562 DOI: 10.1038/s41598-024-65384-8] [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: 02/28/2024] [Accepted: 06/19/2024] [Indexed: 06/27/2024] Open
Abstract
Viral glycoproteins mediate entry into host cells, thereby dictating host range and pathogenesis. In addition, they constitute the principal target of neutralizing antibody responses, making them important antigens in vaccine development. Recombinant vesicular stomatitis virus (VSV) encoding foreign glycoproteins can provide a convenient and safe surrogate system to interrogate the function, evolution, and antigenicity of viral glycoproteins from viruses that are difficult to manipulate or those requiring high biosafety level containment. However, the production of recombinant VSV can be technically challenging. In this work, we present an efficient and robust plasmid-based system for the production of recombinant VSV encoding foreign glycoproteins. We validate the system using glycoproteins from different viral families, including arenaviruses, coronaviruses, and hantaviruses, as well as highlight their utility for studying the effects of mutations on viral fitness. Overall, the methods described herein can facilitate the study of both native and recombinant VSV encoding foreign glycoproteins and can serve as the basis for the production of VSV-based vaccines.
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Affiliation(s)
- María-Carmen Marqués
- Institute for Integrative Systems Biology (I2SysBio), CSIC-Universitat de València, 46980, Paterna, Valencia, Spain
| | - Iván Andreu-Moreno
- Institute for Integrative Systems Biology (I2SysBio), CSIC-Universitat de València, 46980, Paterna, Valencia, Spain
| | - Rafael Sanjuán
- Institute for Integrative Systems Biology (I2SysBio), CSIC-Universitat de València, 46980, Paterna, Valencia, Spain
| | - Santiago F Elena
- Institute for Integrative Systems Biology (I2SysBio), CSIC-Universitat de València, 46980, Paterna, Valencia, Spain
- The Santa Fe Institute, Santa Fe, NM, 87501, USA
| | - Ron Geller
- Institute for Integrative Systems Biology (I2SysBio), CSIC-Universitat de València, 46980, Paterna, Valencia, Spain.
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234
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Hu H, Zhang P, Liu F, Pan S. Regulations of Citrus Pectin Oligosaccharide on Cholesterol Metabolism: Insights from Integrative Analysis of Gut Microbiota and Metabolites. Nutrients 2024; 16:2002. [PMID: 38999750 PMCID: PMC11243408 DOI: 10.3390/nu16132002] [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: 03/21/2024] [Revised: 04/25/2024] [Accepted: 05/04/2024] [Indexed: 07/14/2024] Open
Abstract
(1) Background: Recently, academic studies are demonstrating that the cholesterol-lowering effects of pectin oligosaccharides (POSs) are correlated to intestinal flora. However, the mechanisms of POS on cholesterol metabolisms are limited, and the observations of intestinal flora are lacking integrative analyses. (2) Aim and methods: To reveal the regulatory mechanisms of POS on cholesterol metabolism via an integrative analysis of the gut microbiota, the changes in gut microbiota structure and metabolite composition after POS addition were investigated using Illumina MiSeq sequencing and non-targeted metabolomics through in vitro gut microbiota fermentation. (3) Results: The composition of fecal gut flora was adjusted positively by POS. POS increased the abundances of the cholesterol-related bacterial groups Bacteroidetes, Bifidobacterium and Lactobacillus, while it decreased conditional pathogenic Escherichia coli and Enterococcus, showing good prebiotic activities. POS changed the composition of gut microbiota fermentation metabolites (P24), causing significant changes in 221 species of fermentation metabolites in a non-targeted metabolomics analysis and promoting the production of short-chain fatty acids. The abundances of four types of cholesterol metabolism-related metabolites (adenosine monophosphate, cyclic adenosine monophosphate, guanosine and butyrate) were significantly higher in the P24 group than those in the control group without POS addition. (4) Conclusion: The abovementioned results may explain the hypocholesterolemic effects of POS and promotion effects on cholesterol efflux of P24. These findings indicated that the potential regulatory mechanisms of citrus POS on cholesterol metabolism are modulated by cholesterol-related gut microbiota and specific metabolites.
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Affiliation(s)
- Haijuan Hu
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Peipei Zhang
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Fengxia Liu
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Siyi Pan
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
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Stege PB, Schokker D, Harders F, Kar SK, Stockhofe N, Perricone V, Rebel JMJ, de Jong IC, Bossers A. Diet-induced changes in the jejunal microbiota of developing broilers reduce the abundance of Enterococcus hirae and Enterococcus faecium. BMC Genomics 2024; 25:627. [PMID: 38910254 PMCID: PMC11193906 DOI: 10.1186/s12864-024-10496-8] [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: 02/12/2024] [Accepted: 06/05/2024] [Indexed: 06/25/2024] Open
Abstract
Modern broiler breeds allow for high feed efficiency and rapid growth, which come at a cost of increased susceptibility to pathogens and disease. Broiler growth rate, feed efficiency, and health are affected by the composition of the gut microbiota, which in turn is influenced by diet. In this study, we therefore assessed how diet composition can affect the broiler jejunal gut microbiota. A total of 96 broiler chickens were divided into four diet groups: control, coated butyrate supplementation, medium-chain fatty acid supplementation, or a high-fibre low-protein content. Diet groups were sub-divided into age groups (4, 12 and 33 days of age) resulting in groups of 8 broilers per diet per age. The jejunum content was used for metagenomic shotgun sequencing to determine the microbiota taxonomic composition at species level. The composed diets resulted in a total of 104 differentially abundant bacterial species. Most notably were the butyrate-induced changes in the jejunal microbiota of broilers 4 days post-hatch, resulting in the reduced relative abundance of mainly Enterococcus faecium (-1.8 l2fc, Padj = 9.9E-05) and the opportunistic pathogen Enterococcus hirae (-2.9 l2fc, Padj = 2.7E-08), when compared to the control diet. This effect takes place during early broiler development, which is critical for broiler health, thus exemplifying the importance of how diet can influence the microbiota composition in relation to broiler health. Future studies should therefore elucidate how diet can be used to promote a beneficial microbiota in the early stages of broiler development.
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Affiliation(s)
- Paul B Stege
- Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, Netherlands.
| | - Dirkjan Schokker
- Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, Netherlands
| | - Frank Harders
- Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, Netherlands
| | - Soumya K Kar
- Wageningen Livestock Research, Wageningen University and Research, Wageningen, Netherlands
| | - Norbert Stockhofe
- Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, Netherlands
| | - Vera Perricone
- Department of Veterinary Medicine and Animal Science, University of Milan, Milan, Italy
| | - Johanna M J Rebel
- Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, Netherlands
| | - Ingrid C de Jong
- Wageningen Livestock Research, Wageningen University and Research, Wageningen, Netherlands
| | - Alex Bossers
- Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, Netherlands
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236
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Lu C, Zou T, Liu Q, Huang X. Twenty-nine newly sequenced genomes and a comprehensive genome dataset for the insect endosymbiont Buchnera. Sci Data 2024; 11:673. [PMID: 38909040 PMCID: PMC11193766 DOI: 10.1038/s41597-024-03537-0] [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: 12/17/2023] [Accepted: 06/17/2024] [Indexed: 06/24/2024] Open
Abstract
Most phloem-feeding insects face nutritional deficiency and rely on their intracellular symbionts to provide nutrients, and most of endosymbiont genomes have undergone reduction. However, the study of genome reduction processes of endosymbionts has been constrained by the limited availability of genome data from different insect lineages. The obligate relationship between aphids and Buchnera aphidicola (hereafter Buchnera) makes them a classic model for studying insect-endosymbiont interaction. Here, we report 29 newly sequenced Buchnera genomes from 11 aphid subfamilies, and a comprehensive dataset based on 90 Buchnera genomes from 14 aphid subfamilies. The dataset shows a significant genomic difference of Buchnera among different aphid lineages. The dataset exhibits a more balanced distribution of Buchnera (from 14 aphid subfamilies) genome sizes, ranging from 400 kb to 600 kb, which can illustrate the genome reduction process of Buchnera. The new genome data provide valuable insights into the microevolutionary processes leading to genomic reduction of insect endosymbionts.
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Affiliation(s)
- Congcong Lu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Tianmin Zou
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Qian Liu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaolei Huang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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237
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Hick E, Suárez M, Rey A, Mantecón L, Fernández N, Solís G, Gueimonde M, Arboleya S. Personalized Nutrition with Banked Human Milk for Early Gut Microbiota Development: In Pursuit of the Perfect Match. Nutrients 2024; 16:1976. [PMID: 38999725 PMCID: PMC11243202 DOI: 10.3390/nu16131976] [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: 05/23/2024] [Revised: 06/17/2024] [Accepted: 06/19/2024] [Indexed: 07/14/2024] Open
Abstract
The correct initial colonization and establishment of the gut microbiota during the early stages of life is a key step, with long-lasting consequences throughout the entire lifespan of the individual. This process is affected by several perinatal factors; among them, feeding mode is known to have a critical role. Breastfeeding is the optimal nutrition for neonates; however, it is not always possible, especially in cases of prematurity or early pathology. In such cases, most commonly babies are fed with infant formulas in spite of the official nutritional and health international organizations' recommendation on the use of donated human milk through milk banks for these cases. However, donated human milk still does not totally match maternal milk in terms of infant growth and gut microbiota development. The present review summarizes the practices of milk banks and hospitals regarding donated human milk, its safety and quality, and the health outcomes in infants fed with donated human milk. Additionally, we explore different alternatives to customize pasteurized donated human milk with the aim of finding the perfect match between each baby and banked milk for promoting the establishment of a beneficial gut microbiota from the early stages of life.
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Affiliation(s)
- Emilia Hick
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (IPLA-CSIC), 33300 Villaviciosa, Spain
| | - Marta Suárez
- Pediatrics Service, Central University Hospital of Asturias (HUCA-SESPA), 33011 Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - Alejandra Rey
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (IPLA-CSIC), 33300 Villaviciosa, Spain
| | - Laura Mantecón
- Pediatrics Service, Central University Hospital of Asturias (HUCA-SESPA), 33011 Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - Nuria Fernández
- Pediatrics Service, University Hospital of Cabueñes (CAB-SESPA), 33394 Gijón, Spain
| | - Gonzalo Solís
- Pediatrics Service, Central University Hospital of Asturias (HUCA-SESPA), 33011 Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - Miguel Gueimonde
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (IPLA-CSIC), 33300 Villaviciosa, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - Silvia Arboleya
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (IPLA-CSIC), 33300 Villaviciosa, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
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238
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Liu H, Li J, Guan C, Gao W, Li Y, Wang J, Yang Y, Du Y. Endometriosis is a disease of immune dysfunction, which could be linked to microbiota. Front Genet 2024; 15:1386411. [PMID: 38974388 PMCID: PMC11227297 DOI: 10.3389/fgene.2024.1386411] [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: 02/15/2024] [Accepted: 05/29/2024] [Indexed: 07/09/2024] Open
Abstract
Background: Endometriosis, characterized by extrauterine endometrial tissue, leads to irregular bleeding and pelvic pain. Menstrual retrograde theory suggests fragments traverse fallopian tubes, causing inflammation and scar tissue. Prevalent among infertile women, risk factors include fewer pregnancies, delayed childbirth, irregular cycles, and familial predisposition. Treatments, medication, and surgery entail side effects. Studies link gut microbiota alterations to endometriosis, necessitating research to establish causation. We used Mendelian randomization to investigate the potential link between endometriosis and gut microbiota through genetic variants. Methods: Two-sample Mendelian randomization analyzed gut microbiota's potential causal effects on endometriosis. Instrumental variables, robustly associated with exposures, leveraged GWAS data from MiBioGen for gut microbiota and FinnGen R8 release for endometriosis. SNPs strongly associated with exposures were instrumental variables. Rigorous assessments ensured SNP impact scrutiny on endometriosis. Results: At the genus level, Anaerotruncus, Desulfovibrio, Haemophilus, and Holdemania showed causal association with endometriosis. Specific gut microbiota exhibited causal effects on different endometriosis stages. Holdemania and Ruminococcaceae UCG002 exerted reversible, stage-specific impacts. Conclusion: Mendelian randomization provides evidence for the causal link between specific gut microbiotas and endometriosis, emphasizing the pivotal role of gut microbiota dysbiosis. Modulating gut microbiota emerges as a promising strategy for preventing and treating endometriosis.
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Affiliation(s)
- Hongyan Liu
- Department of Family Planning, The Second Hospital of Tianjin Medical University, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Junxia Li
- Department of Family Planning, The Second Hospital of Tianjin Medical University, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Chenchen Guan
- Department of Family Planning, The Second Hospital of Tianjin Medical University, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Wenjie Gao
- Department of Family Planning, The Second Hospital of Tianjin Medical University, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Yan Li
- Department of Family Planning, The Second Hospital of Tianjin Medical University, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Jianmei Wang
- Department of Family Planning, The Second Hospital of Tianjin Medical University, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Yang Yang
- Department of Family Planning, The Second Hospital of Tianjin Medical University, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Yongrui Du
- Department of Family Planning, The Second Hospital of Tianjin Medical University, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
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239
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Brenchley JM, Serrano-Villar S. From dysbiosis to defense: harnessing the gut microbiome in HIV/SIV therapy. MICROBIOME 2024; 12:113. [PMID: 38907315 PMCID: PMC11193286 DOI: 10.1186/s40168-024-01825-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 04/26/2024] [Indexed: 06/23/2024]
Abstract
BACKGROUND Although the microbiota has been extensively associated with HIV pathogenesis, the majority of studies, particularly those using omics techniques, are largely correlative and serve primarily as a basis for hypothesis generation. Furthermore, most have focused on characterizing the taxonomic composition of the bacterial component, often overlooking other levels of the microbiome. The intricate mechanisms by which the microbiota influences immune responses to HIV are still poorly understood. Interventional studies on gut microbiota provide a powerful tool to test the hypothesis of whether we can harness the microbiota to improve health outcomes in people with HIV. RESULTS Here, we review the multifaceted role of the gut microbiome in HIV/SIV disease progression and its potential as a therapeutic target. We explore the complex interplay between gut microbial dysbiosis and systemic inflammation, highlighting the potential for microbiome-based therapeutics to open new avenues in HIV management. These include exploring the efficacy of probiotics, prebiotics, fecal microbiota transplantation, and targeted dietary modifications. We also address the challenges inherent in this research area, such as the difficulty in inducing long-lasting microbiome alterations and the complexities of study designs, including variations in probiotic strains, donor selection for FMT, antibiotic conditioning regimens, and the hurdles in translating findings into clinical practice. Finally, we speculate on future directions for this rapidly evolving field, emphasizing the need for a more granular understanding of microbiome-immune interactions, the development of personalized microbiome-based therapies, and the application of novel technologies to identify potential therapeutic agents. CONCLUSIONS Our review underscores the importance of the gut microbiome in HIV/SIV disease and its potential as a target for innovative therapeutic strategies.
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Affiliation(s)
- Jason M Brenchley
- Barrier Immunity Section, Lab of Viral Diseases, NIAID, NIH, Bethesda, MA, USA.
| | - Sergio Serrano-Villar
- Department of Infectious Diseases, Hospital Universitario Ramon y Cajal, IRYCIS and CIBERInfec, Madrid, Spain.
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240
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Liang Y, Dikow RB, Su X, Wen J, Ren Z. Comparative genomics of the primary endosymbiont Buchnera aphidicola in aphid hosts and their coevolutionary relationships. BMC Biol 2024; 22:137. [PMID: 38902723 PMCID: PMC11188193 DOI: 10.1186/s12915-024-01934-w] [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: 05/04/2023] [Accepted: 05/28/2024] [Indexed: 06/22/2024] Open
Abstract
BACKGROUND Coevolution between modern aphids and their primary obligate, bacterial endosymbiont, Buchnera aphidicola, has been previously reported at different classification levels based on molecular phylogenetic analyses. However, the Buchnera genome remains poorly understood within the Rhus gall aphids. RESULTS We assembled the complete genome of the endosymbiont Buchnera in 16 aphid samples, representing 13 species in all six genera of Rhus gall aphids by shotgun genome skimming method. We compared the newly assembled genomes with those from GenBank to comprehensively investigate patterns of coevolution between the bacteria Buchnera and their aphid hosts. Buchnera genomes were mostly collinear, and the pan-genome contained 684 genes, in which the core genome contained 256 genes with some lineages having large numbers of tandem gene duplications. There has been substantial gene-loss in each Buchnera lineage. We also reconstructed the phylogeny for Buchnera and their host aphids, respectively, using 72 complete genomes of Buchnera, along with the complete mitochondrial genomes and three nuclear genes of 31 corresponding host aphid accessions. The cophylogenetic test demonstrated significant coevolution between these two partner groups at individual, species, generic, and tribal levels. CONCLUSIONS Buchnera exhibits very high levels of genomic sequence divergence but relative stability in gene order. The relationship between the symbionts Buchnera and its aphid hosts shows a significant coevolutionary pattern and supports complexity of the obligate symbiotic relationship.
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Affiliation(s)
- Yukang Liang
- School of Life Science and Shanxi Key Laboratory of Nucleic Acid Biopesticides, Shanxi University, 92 Wucheng Rd, Taiyuan Shanxi, 030006, China
| | - Rebecca B Dikow
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, 600 Maryland Avenue SW, Washington, DC, 20024, USA
| | - Xu Su
- School of Geography and Life Science, Qinghai Normal University, 38 Wusixi Road, Xining, 810008, China
| | - Jun Wen
- Department of Botany, National Museum of Natural History, Smithsonian Institution, MRC-166, Washington, DC, 20013-7012, USA.
| | - Zhumei Ren
- School of Life Science and Shanxi Key Laboratory of Nucleic Acid Biopesticides, Shanxi University, 92 Wucheng Rd, Taiyuan Shanxi, 030006, China.
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241
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Wang Y, Zhang Z, Chen Q, Chen T. Simultaneous application of oral and intravaginal probiotics for Helicobacter pylori and its antibiotic-therapy-induced vaginal dysbacteriosis. NPJ Biofilms Microbiomes 2024; 10:49. [PMID: 38902244 PMCID: PMC11190290 DOI: 10.1038/s41522-024-00521-9] [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: 07/19/2023] [Accepted: 06/07/2024] [Indexed: 06/22/2024] Open
Abstract
Helicobacter pylori is a prevalent bacterial pathogen globally, implicated in various gastrointestinal disorders. Current recommended antibiotic therapies for H. pylori infection have been proven to be therapeutically insufficient, with low eradication rates and high recurrence rates. Emerging evidence suggests that antibiotic therapy for H. pylori can lead to gastrointestinal and subsequent vaginal dysbiosis, posing challenges for conventional antibiotic approaches. Thus, this article proposes a novel probiotic therapy involving simultaneous oral and intra-vaginal probiotic administration alongside antibiotics for H. pylori treatment, aiming to enhance eradication rates and mitigate dysbiosis. We begin by providing an overview of gastrointestinal and vaginal microbiota and their interconnectedness through the vagina-gut axis. We then review the efficacy of current antibiotic regimens for H. pylori and discuss how antibiotic treatment impacts the vaginal microenvironment. To explore the feasibility of this approach, we evaluate the effectiveness of oral and intra-vaginal probiotics in restoring normal microbiota in the gastrointestinal and vaginal tracts, respectively. Additionally, we analyze the direct mechanisms by which oral and intra-vaginal probiotics act on their respective tracts and discuss potential cross-tract mechanisms. Considering the potential synergistic therapeutic effects of probiotics in both the gastrointestinal and vaginal tracts, dual-channel probiotic therapy holds promise as a more effective approach for H. pylori eradication and dysbiosis mitigation, presenting a novel concept in the collaborative treatment of gastrointestinal and genital disorders.
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Affiliation(s)
- Yufan Wang
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330006, China
- Queen Mary School, Jiangxi Medical College, Nanchang University, Nanchang, 330031, China
- National Engineering Research Centre for Bioengineering Drugs and Technologies, Institute of Translational Medicine, Jiangxi Medical College, Nanchang University, Nanchang, 330031, China
| | - Zhenyu Zhang
- Department of Gastroenterology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China.
| | - Qi Chen
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330006, China.
| | - Tingtao Chen
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330006, China.
- National Engineering Research Centre for Bioengineering Drugs and Technologies, Institute of Translational Medicine, Jiangxi Medical College, Nanchang University, Nanchang, 330031, China.
- School of Pharmacy, Jiangxi Medical College, Nanchang University, Nanchang, 330031, China.
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242
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Seif El-Din MM, Hagras M, Mayhoub AS. Phenylthiazoles with potent & optimum selectivity toward Clostridium difficile. RSC Med Chem 2024; 15:1991-2001. [PMID: 38911156 PMCID: PMC11187570 DOI: 10.1039/d4md00164h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 03/21/2024] [Indexed: 06/25/2024] Open
Abstract
Clostridium difficile (C. difficile) is one of the most threatening bacteria globally, causing high mortality and morbidity in humans and animals, and is considered a public health threat that requires urgent and aggressive action. Interruption of the human gut microbiome and the development of antibiotic resistance urgently require development and synthesis of effective alternative antibiotics with minimal effects on the normal gut microbial flora. In this study, cyclization of the aminoguanidine head to the thiazole nucleus while maintaining its other pharmacophoric features leads to selective targeting of Clostridioides difficile as shown in the graphical abstract. The most promising compound, 5, was significantly more efficient than vancomycin and metronidazole against six strains of C. diff with MIC values as low as 0.030 μg mL-1. Additionally, compound 5 was superior to vancomycin and metronidazole, showing no inhibition toward nine tested strains of the normal human gut microbiota (>64 μg mL-1). The high safety profile of compound 5 was also observed with two cell lines HRT-18 and Vero cells.
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Affiliation(s)
- Mahmoud M Seif El-Din
- University of Science and Technology, Nanoscience Program, Zewail City of Science and Technology Ahmed Zewail Street Giza Egypt
| | - Mohamed Hagras
- Department of Pharmaceutical Organic Chemistry, College of Pharmacy, Al-Azhar University Cairo Egypt
| | - Abdelrahman S Mayhoub
- University of Science and Technology, Nanoscience Program, Zewail City of Science and Technology Ahmed Zewail Street Giza Egypt
- Department of Pharmaceutical Organic Chemistry, College of Pharmacy, Al-Azhar University Cairo Egypt
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243
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Grundmann CO, Guzman J, Vilcinskas A, Pupo MT. The insect microbiome is a vast source of bioactive small molecules. Nat Prod Rep 2024; 41:935-967. [PMID: 38411238 DOI: 10.1039/d3np00054k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Covering: September 1964 to June 2023Bacteria and fungi living in symbiosis with insects have been studied over the last sixty years and found to be important sources of bioactive natural products. Not only classic producers of secondary metabolites such as Streptomyces and other members of the phylum Actinobacteria but also numerous bacteria from the phyla Proteobacteria and Firmicutes and an impressive array of fungi (usually pathogenic) serve as the source of a structurally diverse number of small molecules with important biological activities including antimicrobial, cytotoxic, antiparasitic and specific enzyme inhibitors. The insect niche is often the exclusive provider of microbes producing unique types of biologically active compounds such as gerumycins, pederin, dinactin, and formicamycins. However, numerous insects still have not been described taxonomically, and in most cases, the study of their microbiota is completely unexplored. In this review, we present a comprehensive survey of 553 natural products produced by microorganisms isolated from insects by collating and classifying all the data according to the type of compound (rather than the insect or microbial source). The analysis of the correlations among the metadata related to insects, microbial partners, and their produced compounds provides valuable insights into the intricate dynamics between insects and their symbionts as well as the impact of their metabolites on these relationships. Herein, we focus on the chemical structure, biosynthesis, and biological activities of the most relevant compounds.
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Affiliation(s)
| | - Juan Guzman
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
| | - Andreas Vilcinskas
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
- Institute for Insect Biotechnology, Justus-Liebig-University, Giessen, Germany
| | - Mônica Tallarico Pupo
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil.
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244
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Lange E, Kranert L, Krüger J, Benndorf D, Heyer R. Microbiome modeling: a beginner's guide. Front Microbiol 2024; 15:1368377. [PMID: 38962127 PMCID: PMC11220171 DOI: 10.3389/fmicb.2024.1368377] [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: 01/10/2024] [Accepted: 05/27/2024] [Indexed: 07/05/2024] Open
Abstract
Microbiomes, comprised of diverse microbial species and viruses, play pivotal roles in human health, environmental processes, and biotechnological applications and interact with each other, their environment, and hosts via ecological interactions. Our understanding of microbiomes is still limited and hampered by their complexity. A concept improving this understanding is systems biology, which focuses on the holistic description of biological systems utilizing experimental and computational methods. An important set of such experimental methods are metaomics methods which analyze microbiomes and output lists of molecular features. These lists of data are integrated, interpreted, and compiled into computational microbiome models, to predict, optimize, and control microbiome behavior. There exists a gap in understanding between microbiologists and modelers/bioinformaticians, stemming from a lack of interdisciplinary knowledge. This knowledge gap hinders the establishment of computational models in microbiome analysis. This review aims to bridge this gap and is tailored for microbiologists, researchers new to microbiome modeling, and bioinformaticians. To achieve this goal, it provides an interdisciplinary overview of microbiome modeling, starting with fundamental knowledge of microbiomes, metaomics methods, common modeling formalisms, and how models facilitate microbiome control. It concludes with guidelines and repositories for modeling. Each section provides entry-level information, example applications, and important references, serving as a valuable resource for comprehending and navigating the complex landscape of microbiome research and modeling.
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Affiliation(s)
- Emanuel Lange
- Multidimensional Omics Data Analysis, Department for Bioanalytics, Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany
- Graduate School Digital Infrastructure for the Life Sciences, Bielefeld Institute for Bioinformatics Infrastructure (BIBI), Faculty of Technology, Bielefeld University, Bielefeld, Germany
| | - Lena Kranert
- Institute for Automation Engineering, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Jacob Krüger
- Engineering of Software-Intensive Systems, Department of Mathematics and Computer Science, Eindhoven University of Technology, Eindhoven, Netherlands
| | - Dirk Benndorf
- Applied Biosciences and Bioprocess Engineering, Anhalt University of Applied Sciences, Köthen, Germany
| | - Robert Heyer
- Multidimensional Omics Data Analysis, Department for Bioanalytics, Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany
- Graduate School Digital Infrastructure for the Life Sciences, Bielefeld Institute for Bioinformatics Infrastructure (BIBI), Faculty of Technology, Bielefeld University, Bielefeld, Germany
- Multidimensional Omics Data Analysis, Faculty of Technology, Bielefeld University, Bielefeld, Germany
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Kolp MR, de Anda Acosta Y, Brewer W, Nichols HL, Goldstein EB, Tallapragada K, Parker BJ. Pathogen-microbiome interactions and the virulence of an entomopathogenic fungus. Appl Environ Microbiol 2024; 90:e0229323. [PMID: 38786361 PMCID: PMC11218631 DOI: 10.1128/aem.02293-23] [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: 12/20/2023] [Accepted: 05/03/2024] [Indexed: 05/25/2024] Open
Abstract
Bacteria shape interactions between hosts and fungal pathogens. In some cases, bacteria associated with fungi are essential for pathogen virulence. In other systems, host-associated microbiomes confer resistance against fungal pathogens. We studied an aphid-specific entomopathogenic fungus called Pandora neoaphidis in the context of both host and pathogen microbiomes. Aphids host several species of heritable bacteria, some of which confer resistance against Pandora. We first found that spores that emerged from aphids that harbored protective bacteria were less virulent against subsequent hosts and did not grow on plate media. We then used 16S amplicon sequencing to study the bacterial microbiome of fungal mycelia and spores during plate culturing and host infection. We found that the bacterial community is remarkably stable in culture despite dramatic changes in pathogen virulence. Last, we used an experimentally transformed symbiont of aphids to show that Pandora can acquire host-associated bacteria during infection. Our results uncover new roles for bacteria in the dynamics of aphid-pathogen interactions and illustrate the importance of the broader microbiological context in studies of fungal pathogenesis. IMPORTANCE Entomopathogenic fungi play important roles in the population dynamics of many insect species. Understanding the factors shaping entomopathogen virulence is critical for agricultural management and for the use of fungi in pest biocontrol. We show that heritable bacteria in aphids, which confer protection to their hosts against fungal entomopathogens, influence virulence against subsequent hosts. Aphids reproduce asexually and are typically surrounded by genetically identical offspring, and thus these effects likely shape the dynamics of fungal disease in aphid populations. Furthermore, fungal entomopathogens are known to rapidly lose virulence in lab culture, complicating their laboratory use. We show that this phenomenon is not driven by changes in the associated bacterial microbiome. These results contribute to our broader understanding of the aphid model system and shed light on the biology of the Entomophthorales-an important but understudied group of fungi.
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Affiliation(s)
- Matthew R. Kolp
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
- Richard A. Gillespie College of Veterinary Medicine, Lincoln Memorial University, Harrogate, Tennessee, USA
| | | | - William Brewer
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Holly L. Nichols
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | | | - Keertana Tallapragada
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, USA
| | - Benjamin J. Parker
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
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246
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Baek HJ, Kim KS, Kwoen M, Park ES, Lee HJ, Park KU. Saliva assay: a call for methodological standardization. J Periodontal Implant Sci 2024; 54:54.e13. [PMID: 39058348 DOI: 10.5051/jpis.2304180209] [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: 11/08/2023] [Revised: 02/08/2024] [Accepted: 02/18/2024] [Indexed: 07/28/2024] Open
Abstract
The oral cavity provides an ideal environment for microorganisms, including bacteria, viruses, and fungi, to flourish. Increasing attention has been focused on the connection between the oral microbiome and both oral and systemic diseases, spurring active research into the collection and analysis of specimens for healthcare purposes. Among the various methods for analyzing the oral microbiome, saliva analysis is especially prominent. Saliva samples, which can be collected non-invasively, provide information on the systemic health and oral microbiome composition of an individual. This review was performed to evaluate the current state of the relevant research through an examination of the literature and to suggest an appropriate assay method for investigating the oral microbiome. We analyzed articles published in English in SCI(E) journals after January 1, 2000, ultimately selecting 53 articles for review. Articles were identified through keyword searches in the PubMed, Embase, Cochrane, Web of Science, and CINAHL databases. Three experienced researchers conducted full-text assessments following title and abstract screening to select appropriate papers. Subsequently, they organized and analyzed the desired data. Our review revealed that most studies utilized unstimulated saliva samples for oral microbiome analysis. Of the 53 studies examined, 29 identified relationships between the oral microbiome and various diseases, such as oral disease, Behçet disease, cancer, and oral lichen planus. However, the studies employed diverse methods of collection and analysis, which compromised the reliability and accuracy of the findings. To address the limitations caused by methodological inconsistencies, a standardized saliva assay should be established.
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Affiliation(s)
- Hyeong-Jin Baek
- Department of Periodontology, Section of Dentistry, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Keun-Suh Kim
- Department of Periodontology, Section of Dentistry, Seoul National University Bundang Hospital, Seongnam, Korea
| | - MinJeong Kwoen
- Department of Periodontology, Section of Dentistry, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Eun-Sun Park
- Medical Library, College of Medicine, Seoul National University, Seoul, Korea
| | - Hyo-Jung Lee
- Department of Periodontology, Section of Dentistry, Seoul National University Bundang Hospital, Seongnam, Korea.
| | - Kyoung-Un Park
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seongnam, Korea.
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247
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Pearman WS, Duffy GA, Gemmell NJ, Morales SE, Fraser CI. Long-distance movement dynamics shape host microbiome richness and turnover. FEMS Microbiol Ecol 2024; 100:fiae089. [PMID: 38857884 PMCID: PMC11212666 DOI: 10.1093/femsec/fiae089] [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: 10/06/2023] [Revised: 05/22/2024] [Accepted: 06/08/2024] [Indexed: 06/12/2024] Open
Abstract
Host-associated microbial communities are shaped by host migratory movements. These movements can have contrasting impacts on microbiota, and understanding such patterns can provide insight into the ecological processes that contribute to community diversity. Furthermore, long-distance movements to new environments are anticipated to occur with increasing frequency due to host distribution shifts resulting from climate change. Understanding how hosts transport their microbiota with them could be of importance when examining biological invasions. Although microbial community shifts are well-documented, the underlying mechanisms that lead to the restructuring of these communities remain relatively unexplored. Using literature and ecological simulations, we develop a framework to elucidate the major factors that lead to community change. We group host movements into two types-regular (repeated/cyclical migratory movements, as found in many birds and mammals) and irregular (stochastic/infrequent movements that do not occur on a cyclical basis, as found in many insects and plants). Ecological simulations and prior research suggest that movement type and frequency, alongside environmental exposure (e.g. internal/external microbiota) are key considerations for understanding movement-associated community changes. From our framework, we derive a series of testable hypotheses, and suggest means to test them, to facilitate future research into host movement and microbial community dynamics.
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Affiliation(s)
- William S Pearman
- Department of Marine Science, University of Otago, 310 Castle St, Dunedin 9016, New Zealand
- Department of Anatomy, School of Biomedical Sciences, University of Otago, 270 Great King Street, Dunedin 9016, New Zealand
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, 720 Cumberland St, Dunedin 9016, New Zealand
| | - Grant A Duffy
- Department of Marine Science, University of Otago, 310 Castle St, Dunedin 9016, New Zealand
| | - Neil J Gemmell
- Department of Anatomy, School of Biomedical Sciences, University of Otago, 270 Great King Street, Dunedin 9016, New Zealand
| | - Sergio E Morales
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, 720 Cumberland St, Dunedin 9016, New Zealand
| | - Ceridwen I Fraser
- Department of Marine Science, University of Otago, 310 Castle St, Dunedin 9016, New Zealand
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248
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Cherubini A, Della Torre S, Pelusi S, Valenti L. Sexual dimorphism of metabolic dysfunction-associated steatotic liver disease. Trends Mol Med 2024:S1471-4914(24)00135-7. [PMID: 38890029 DOI: 10.1016/j.molmed.2024.05.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 05/22/2024] [Accepted: 05/23/2024] [Indexed: 06/20/2024]
Abstract
Metabolic dysfunction-associated steatotic liver disease (MASLD) is the most common chronic liver condition. MASLD is a sexually dimorphic condition, with its development and progression influenced by sex chromosomes and hormones. Estrogens typically protect against, whereas androgens promote, MASLD. Therapeutic approaches for a sex-specific personalized medicine include estrogen replacement, androgen blockers, and novel drugs targeting hormonal pathways. However, the interactions between hormonal factors and inherited genetic variation impacts MASLD risk, necessitating more tailored therapies. Understanding sex disparities and the role of estrogens could improve MASLD interventions and management, whereas clinical trials addressing sex differences are crucial for advancing personalized treatment. This review explores the underappreciated impact of sexual dimorphism in MASLD and discusses the potential therapeutic application of sex-related hormones.
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Affiliation(s)
- Alessandro Cherubini
- Department of Transfusion Medicine, Precision Medicine Lab, Biological Resource Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Sara Della Torre
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, 20133 Milan, Italy
| | - Serena Pelusi
- Department of Transfusion Medicine, Precision Medicine Lab, Biological Resource Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Luca Valenti
- Department of Transfusion Medicine, Precision Medicine Lab, Biological Resource Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy; Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy.
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249
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Zhou L, Hu P, Xie J, Li J, Guo C, Yang Z. Influence of Endogenous Bacteria on Behavioral Responses in Leptocybe invasa: An Analysis of mVOCs. INSECTS 2024; 15:455. [PMID: 38921169 PMCID: PMC11203816 DOI: 10.3390/insects15060455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/16/2024] [Accepted: 06/14/2024] [Indexed: 06/27/2024]
Abstract
Microorganisms within insects play a vital role in maintaining the basal physiological functions of the insects, with olfactory signals as critical components of insect survival strategies. Leptocybe invasa (L. invasa), an invasive alien pest inflicting significant damage to eucalyptus trees, harbors a rich and varied bacterial community within its body. However, the impact of its endogenous bacteria and their microbial Volatile Organic Compounds (mVOCs) on the behavioral preferences of L. invasa remains unexplored to date. This study focused on nine cultivable and dominant endogenous bacterial strains within L. invasa. Using a Y-tube olfactometer, we investigated the behavioral responses of female L. invasa to the mVOCs emitted by these bacteria. Concurrently, gas chromatography-mass spectrometry (GC-MS) was employed to quantify the mVOCs produced by these endogenous bacteria. Our findings revealed that Staphylococcus sp. exhibited the highest attractiveness of L. invasa, whereas Microbacterium sp. and E. cloacae exerted the most significant avoidance effects. The analysis of the mVOCs further highlighted the significance of aldehyde compounds, notably 2,3,6-trichlorobenzaldehyde, and alkane compounds, such as eicosane, in mediating the repellency and attraction effects. These results contribute to a deeper understanding of the invasion mechanism of L. invasa and provide a scientific basis for developing novel biopesticides or elicitors.
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Affiliation(s)
- Leming Zhou
- Guangxi Colleges and Universities Key Laboratory for Cultivation and Utilization of Subtropical Forest Plantation, Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning 530004, China; (L.Z.); (P.H.); (J.X.); (J.L.)
| | - Ping Hu
- Guangxi Colleges and Universities Key Laboratory for Cultivation and Utilization of Subtropical Forest Plantation, Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning 530004, China; (L.Z.); (P.H.); (J.X.); (J.L.)
| | - Jinting Xie
- Guangxi Colleges and Universities Key Laboratory for Cultivation and Utilization of Subtropical Forest Plantation, Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning 530004, China; (L.Z.); (P.H.); (J.X.); (J.L.)
| | - Junjue Li
- Guangxi Colleges and Universities Key Laboratory for Cultivation and Utilization of Subtropical Forest Plantation, Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning 530004, China; (L.Z.); (P.H.); (J.X.); (J.L.)
| | - Chunhui Guo
- Ecological Environment Monitoring and Scientific Research Center, Yellow River Basin Ecology and Environment Administration, Ministry of Ecology and Environment, Zhengzhou 450004, China
| | - Zhengde Yang
- Guangxi Colleges and Universities Key Laboratory for Cultivation and Utilization of Subtropical Forest Plantation, Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning 530004, China; (L.Z.); (P.H.); (J.X.); (J.L.)
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250
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Chu Y, Zhang X, Zuo L, Wang X, Shi Y, Liu L, Zhou L, Kang J, Li B, Cheng W, Du S, Sun Z. Establishment of a multi-strategy platform for quality control and quality markers screen of Mailuoshutong pill. J Pharm Biomed Anal 2024; 243:116070. [PMID: 38428246 DOI: 10.1016/j.jpba.2024.116070] [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: 01/08/2024] [Revised: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 03/03/2024]
Abstract
Thromboangiitis obliterans (TAO) is a non-atherosclerotic segmental inflammatory occlusive disease with a high recurrence rate, high disability rate, difficulty to cure, and poor prognosis. It has been clinically proven that Mailuoshutong pill (MLSTP) is an effective traditional Chinese medicine for treating TAO. As MLSTP contains hundreds of chemical components, the quality control of which is a challenge in the development of reliable quality evaluation metrics. This study aimed to evaluate the quality uniformity of MLSTP by establishing a multi-strategy platform. In the present study, the key targets and signaling pathways of MLSTP treating TAO were predicted by network pharmacology. It was further shown by in vivo validation experiments that MLSTP exerted therapeutic effects on TAO by modulating the PI3K-AKT signaling pathway, VEGF signaling pathway, and HIF-1 signaling pathway. In addition, UPLC fingerprints of MLSTP were established and screened for potential Q-markers of MLSTP in combination with network pharmacology results. Six components, including chlorogenic acid, liquiritin, paeoniflorin, calycosin-7-glucoside, berberine, and formononetin, were selected as potential quality markers (Q-markers) in MLSTP. Finally, the quantitative analysis of multi-components by single marker (QAMS) method was established to quantitatively analyze the six potential Q-markers, and the results were consistent with those obtained by the external standard method (ESM). Taken together, the multi-strategy platform established in this study would be conducive to the Q-markers screening and quality control of MLSTP, improving the quality standard of MLSTP and providing favorable assurance for the clinical management of TAO.
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Affiliation(s)
- Yaojuan Chu
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Henan Engineering Research Center of Clinical Mass Spectrometry for Precision Medicine, Zhengzhou Key Laboratory of Clinical Mass Spectrometry, Zhengzhou 450052, China
| | - Xiangyu Zhang
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Henan Engineering Research Center of Clinical Mass Spectrometry for Precision Medicine, Zhengzhou Key Laboratory of Clinical Mass Spectrometry, Zhengzhou 450052, China; Department of Pharmacy, the Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Lihua Zuo
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Henan Engineering Research Center of Clinical Mass Spectrometry for Precision Medicine, Zhengzhou Key Laboratory of Clinical Mass Spectrometry, Zhengzhou 450052, China
| | - Xiaobao Wang
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Henan Engineering Research Center of Clinical Mass Spectrometry for Precision Medicine, Zhengzhou Key Laboratory of Clinical Mass Spectrometry, Zhengzhou 450052, China
| | - Yingying Shi
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Henan Engineering Research Center of Clinical Mass Spectrometry for Precision Medicine, Zhengzhou Key Laboratory of Clinical Mass Spectrometry, Zhengzhou 450052, China
| | - Liwei Liu
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Henan Engineering Research Center of Clinical Mass Spectrometry for Precision Medicine, Zhengzhou Key Laboratory of Clinical Mass Spectrometry, Zhengzhou 450052, China
| | - Lin Zhou
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Henan Engineering Research Center of Clinical Mass Spectrometry for Precision Medicine, Zhengzhou Key Laboratory of Clinical Mass Spectrometry, Zhengzhou 450052, China
| | - Jian Kang
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Henan Engineering Research Center of Clinical Mass Spectrometry for Precision Medicine, Zhengzhou Key Laboratory of Clinical Mass Spectrometry, Zhengzhou 450052, China
| | - Bing Li
- State Key Laboratory of Common Technology of Traditional Chinese Medicine and Pharmaceuticals, Lunan Pharmaceutical Group Co., Ltd., Linyi 276000, China
| | - Wenbo Cheng
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215000, China
| | - Shuzhang Du
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Henan Engineering Research Center of Clinical Mass Spectrometry for Precision Medicine, Zhengzhou Key Laboratory of Clinical Mass Spectrometry, Zhengzhou 450052, China.
| | - Zhi Sun
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Henan Engineering Research Center of Clinical Mass Spectrometry for Precision Medicine, Zhengzhou Key Laboratory of Clinical Mass Spectrometry, Zhengzhou 450052, China.
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