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Di Gesù CM, Matz LM, Fultz R, Bolding IJ, Buffington SA. Monospecies probiotic preparation and administration with downstream analysis of sex-specific effects on gut microbiome composition in mice. STAR Protoc 2023; 4:102386. [PMID: 37379217 PMCID: PMC10331592 DOI: 10.1016/j.xpro.2023.102386] [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: 02/06/2023] [Revised: 04/16/2023] [Accepted: 05/25/2023] [Indexed: 06/30/2023] Open
Abstract
Dysbiosis of the gut microbiome is implicated in the growing burden of non-communicable chronic diseases, including neurodevelopmental disorders, and both preclinical and clinical studies highlight the potential for precision probiotic therapies in their prevention and treatment. Here, we present an optimized protocol for the preparation and administration of Limosilactobacillus reuteri MM4-1A (ATCC-PTA-6475) to adolescent mice. We also describe steps for performing downstream analysis of metataxonomic sequencing data with careful assessment of sex-specific effects on microbiome composition and structure. For complete details on the use and execution of this protocol, please refer to Di Gesù et al.1.
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Affiliation(s)
- Claudia M Di Gesù
- Department of Neurobiology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; Department of Biomedicine, Neuroscience and Advanced Diagnostics (BIND), University of Palermo, 90127 Palermo, Italy
| | - Lisa M Matz
- Department of Neurobiology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Robert Fultz
- Department of Neurobiology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Ian J Bolding
- Department of Neurobiology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Shelly A Buffington
- Department of Neurobiology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; Sealy Center for Microbiome Research, The University of Texas Medical Branch, Galveston, TX 77555, USA.
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2
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Radaic A, Shamir ER, Jones K, Villa A, Garud NR, Tward AD, Kamarajan P, Kapila YL. Specific Oral Microbial Differences in Proteobacteria and Bacteroidetes Are Associated with Distinct Sites When Moving from Healthy Mucosa to Oral Dysplasia-A Microbiome and Gene Profiling Study and Focused Review. Microorganisms 2023; 11:2250. [PMID: 37764094 PMCID: PMC10534919 DOI: 10.3390/microorganisms11092250] [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: 07/18/2023] [Revised: 08/24/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
Oral potentially malignant disorders (OPMDs) are a group of conditions that carry a risk of oral squamous cell carcinoma (OSCC) development. Recent studies indicate that periodontal disease-associated pathogenic bacteria may play a role in the transition from healthy mucosa to dysplasia and to OSCC. Yet, the microbial signatures associated with the transition from healthy mucosa to dysplasia have not been established. To characterize oral microbial signatures at these different sites, we performed a 16S sequencing analysis of both oral swab and formalin-fixed, paraffin-embedded tissue (FFPE) samples. We collected oral swabs from healthy mucosa (from healthy patients), histologically normal mucosa adjacent to dysplasia, and low-grade oral dysplasia. Additionally, FFPE samples from histologically normal mucosa adjacent to OSCC, plus low grade and high-grade oral dysplasia samples were also collected. The collected data demonstrate significant differences in the alpha and beta microbial diversities of different sites in oral mucosa, dysplasia, and OSCC, as well as increased dissimilarities within these sites. We found that the Proteobacteria phyla abundance increased, concurrent with a progressive decrease in the Firmicutes phyla abundance, as well as altered levels of Enterococcus cecorum, Fusobacterium periodonticum, Prevotella melaninogenica, and Fusobacterium canifelinum when moving from healthy to diseased sites. Moreover, the swab sample analysis indicates that the oral microbiome may be altered in areas that are histologically normal, including in mucosa adjacent to dysplasia. Furthermore, trends in specific microbiome changes in oral swab samples preceded those in the tissues, signifying early detection opportunities for clinical diagnosis. In addition, we evaluated the gene expression profile of OSCC cells (HSC-3) infected with either P. gingivalis, T. denticola, F. nucelatum, or S. sanguinis and found that the three periodontopathogens enrich genetic processes related to cancer progression, including skin keratinization/cornification, while the commensal enriched processes related to RNA processing and adhesion. Finally, we reviewed the dysplasia microbiome literature and found a significant decrease in commensal bacteria, such as the Streptococci genus, and a simultaneous increase in pathogenic bacteria, mainly Bacteroidetes phyla and Fusobacterium genus. These findings suggest that features of the oral microbiome can serve as novel biomarkers for dysplasia and OSCC disease progression.
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Affiliation(s)
- Allan Radaic
- School of Dentistry, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA; (A.R.); (P.K.)
- School of Dentistry, University of California, San Francisco (UCSF), San Francisco, CA 94143, USA; (K.J.); (A.V.)
| | - Eliah R. Shamir
- School of Medicine, University of California, San Francisco (UCSF), San Francisco, CA 94143, USA; (E.R.S.); (A.D.T.)
- Genentech, Inc., South San Francisco, CA 94080, USA
| | - Kyle Jones
- School of Dentistry, University of California, San Francisco (UCSF), San Francisco, CA 94143, USA; (K.J.); (A.V.)
- Genentech, Inc., South San Francisco, CA 94080, USA
| | - Alessandro Villa
- School of Dentistry, University of California, San Francisco (UCSF), San Francisco, CA 94143, USA; (K.J.); (A.V.)
- Miami Cancer Institute, Baptist Health South Florida, Miami, FL 33176, USA
| | - Nandita R. Garud
- College of Life Sciences, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA;
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Aaron D. Tward
- School of Medicine, University of California, San Francisco (UCSF), San Francisco, CA 94143, USA; (E.R.S.); (A.D.T.)
| | - Pachiyappan Kamarajan
- School of Dentistry, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA; (A.R.); (P.K.)
- School of Dentistry, University of California, San Francisco (UCSF), San Francisco, CA 94143, USA; (K.J.); (A.V.)
| | - Yvonne L. Kapila
- School of Dentistry, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA; (A.R.); (P.K.)
- School of Dentistry, University of California, San Francisco (UCSF), San Francisco, CA 94143, USA; (K.J.); (A.V.)
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Shang S, Zhu J, Liu X, Wang W, Dai T, Wang L, Li B. The Impacts of Fecal Microbiota Transplantation from Same Sex on the Symptoms of Ulcerative Colitis Patients. Pol J Microbiol 2023; 72:247-268. [PMID: 37725892 PMCID: PMC10508974 DOI: 10.33073/pjm-2023-025] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 06/08/2023] [Indexed: 09/21/2023] Open
Abstract
We aimed to compare the clinical efficacy of fecal microbiota transplantation (FMT) from the same sex on ulcerative colitis (UC) patients. A total of 272 UC patients were selected in the prospective clinical study, which incorporated four distinct groups, each comprising male and female patients, who were either receiving FMT or placebo, respectively. FMT was performed by sending the gut microbiota of healthy female or male adolescents to the same gender patients via gastroscope three times (one time/three weeks), and a placebo was used with an equal volume of saline. Abdominal pain, diarrhea, thick bloody stool, intestinal mucosal lesion, and Mayo scores were measured. Self-rating anxiety scale (SAS) and self-rating depression scale (SDS) were evaluated. The changes of intestinal flora were detected by the 16S rRNA sequencing. FMT reduced the scores of diarrhea, abdominal pain, mucosal lesion, and Mayo, SAS, and SDS in UC patients compared to the placebo group (p < 0.05). Clostridiales and Desulfovibrionaceae were dominant in gut microbiota from male patients and were reduced after FMT. Meanwhile, the abundance of Prevotella, Lactobacillus, and Bifidobacterium was increased in the male group. Female patients had a higher abundance of Escherichia-Shigella, Desulfovibrionaceae, and Staphylococcaceae before FMT, and it was reduced after FMT. Meanwhile, the abundance of Porphyromonadaceae, Prevotella, Lactobacillus, and Bifidobacterium was increased in the female group. There were no significant changes for the species in the corresponding placebo groups. FMT improved the UC symptoms of male and female patients, which may be associated with different gut microbiota changes.
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Affiliation(s)
- Shu Shang
- Department of Endoscopic Diagnosis and Treatment Center, Shenyang Fifth People's Hospital, Shenyang, China
| | - Jian Zhu
- Department of Anorectal, Shenyang Fifth People's Hospital, Shenyang, China
| | - Xi Liu
- Department of Endoscopic Diagnosis and Treatment Center, Shenyang Fifth People's Hospital, Shenyang, China
| | - Wei Wang
- Department of Endoscopic Diagnosis and Treatment Center, Shenyang Fifth People's Hospital, Shenyang, China
| | - Tingting Dai
- Department of Endoscopic Diagnosis and Treatment Center, Shenyang Fifth People's Hospital, Shenyang, China
| | - Li Wang
- Zhuoyuan Health Human Microbiology Research Laboratory, Institute of Advanced Technology, University of Science and Technology of China, Hefei, China
| | - Baojun Li
- Department of Dean, Shenyang Fifth People's Hospital, Shenyang, China
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Chukhlovin AB, Dudurich VV, Kusakin AV, Polev DE, Ermachenko ED, Aseev MV, Zakharov YA, Eismont YA, Danilov LG, Glotov OS. Evaluation of Gut Microbiota in Healthy Persons and Type 1 Diabetes Mellitus Patients in North-Western Russia. Microorganisms 2023; 11:1813. [PMID: 37512985 PMCID: PMC10385534 DOI: 10.3390/microorganisms11071813] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 07/05/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
Bacterial microbiota in stool may vary over a wide range, depending on age, nutrition, etc. The purpose of our work was to discriminate phyla and genera of intestinal bacteria and their biodiversity within a healthy population (North-Western Russia) compared to the patients with type 1 diabetes mellitus (T1DM). The study group included 183 healthy persons 2 to 53 years old (a mean of 26.5±1.0 years old), and 41 T1DM patients (mean age 18.2±1.8 years old). The disease onset was at 11±1.5 years, with a T1DM experience of 7±1.5 years. Total DNA was isolated from the stool samples, and sequencing libraries were prepared by amplifying the V3-V4 region of the 16S rRNA gene sequenced by Illumina MiSeq. Bioinformatic processing of NGS databases was adapted for microbiota evalutaion. Despite the broad scatter, the biological diversity for bacterial microbiota expressed as the Shannon index was significantly increased from younger to older ages in the comparison group, higher in adult healthy persons, with a trend for decrease in the Actinomycetota phylum which includes Bifidobacterium longum species. Similar but non-significant age trends were noted in the T1DM group. Concordant with the Bacillota prevalence in stool samples of diabetic patients, some anaerobic bacteria (Faecalibacteria, Lachnospira and Ruminococcae, Roseburia) were enriched in the T1DM microbiome against controls. Hence, correction of microbiota for Ruminococcus and Lachnospiraceae requires future search for new probiotics. Lower abundance of Actinomycetota and Bifidobacter in T1DM suggests potential usage of Bifidobacter-based probiotics in this cohort.
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Affiliation(s)
- Alexei B Chukhlovin
- R.M.Gorbacheva Memorial Institute of Oncology, Hematology and Transplantation, Pavlov First Saint Petersburg State Medical University, 197022 St. Petersburg, Russia
- Pediatric Research and Clinical Center for Infectious Diseases, 197022 St. Petersburg, Russia
| | | | - Aleksey V Kusakin
- R.M.Gorbacheva Memorial Institute of Oncology, Hematology and Transplantation, Pavlov First Saint Petersburg State Medical University, 197022 St. Petersburg, Russia
- Pediatric Research and Clinical Center for Infectious Diseases, 197022 St. Petersburg, Russia
- SCAMT Institute, ITMO University, 191002 St. Petersburg, Russia
| | | | | | | | - Yuri A Zakharov
- Canadian Institute for Regenerative Medicine, Toronto, ON M5G OA3, Canada
| | - Yuri A Eismont
- R.M.Gorbacheva Memorial Institute of Oncology, Hematology and Transplantation, Pavlov First Saint Petersburg State Medical University, 197022 St. Petersburg, Russia
- Pediatric Research and Clinical Center for Infectious Diseases, 197022 St. Petersburg, Russia
- Serbalab Laboratory, 199106 St. Petersburg, Russia
| | - Lavrentii G Danilov
- Department of Genetics and Biotechnology, Saint-Petersburg State University, Universitetskaya Nab. 7/9, 199034 St. Petersburg, Russia
| | - Oleg S Glotov
- Pediatric Research and Clinical Center for Infectious Diseases, 197022 St. Petersburg, Russia
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Shetty SA, Kool J, Fuentes S. A tool to assess the mock community samples in 16S rRNA gene-based microbiota profiling studies. MICROBIOME RESEARCH REPORTS 2023; 2:14. [PMID: 38047277 PMCID: PMC10688813 DOI: 10.20517/mrr.2022.18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/24/2023] [Accepted: 04/17/2023] [Indexed: 12/05/2023]
Abstract
Inclusion and investigation of technical controls in microbiome sequencing studies is important for understanding technical biases and errors. Here, we present chkMocks, a general R-based tool that allows researchers to compare the composition of mock communities that are processed along with samples to their theoretical composition. A visual comparison between experimental and theoretical community composition and their correlation is provided for researchers to assess the quality of their sample processing workflows.
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Affiliation(s)
- Sudarshan A. Shetty
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, Bilthoven 3721 MA, Netherlands
- Department of Medical Microbiology and Infection Prevention, Virology and Immunology Research Group, University Medical Center Groningen, Hanzeplein 1, Groningen 9713 GZ, Netherlands
| | - Jolanda Kool
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, Bilthoven 3721 MA, Netherlands
| | - Susana Fuentes
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, Bilthoven 3721 MA, Netherlands
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