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Aizpurua O, Dunn RR, Hansen LH, Gilbert MTP, Alberdi A. Field and laboratory guidelines for reliable bioinformatic and statistical analysis of bacterial shotgun metagenomic data. Crit Rev Biotechnol 2024; 44:1164-1182. [PMID: 37731336 DOI: 10.1080/07388551.2023.2254933] [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: 01/24/2023] [Revised: 05/22/2023] [Accepted: 06/27/2023] [Indexed: 09/22/2023]
Abstract
Shotgun metagenomics is an increasingly cost-effective approach for profiling environmental and host-associated microbial communities. However, due to the complexity of both microbiomes and the molecular techniques required to analyze them, the reliability and representativeness of the results are contingent upon the field, laboratory, and bioinformatic procedures employed. Here, we consider 15 field and laboratory issues that critically impact downstream bioinformatic and statistical data processing, as well as result interpretation, in bacterial shotgun metagenomic studies. The issues we consider encompass intrinsic properties of samples, study design, and laboratory-processing strategies. We identify the links of field and laboratory steps with downstream analytical procedures, explain the means for detecting potential pitfalls, and propose mitigation measures to overcome or minimize their impact in metagenomic studies. We anticipate that our guidelines will assist data scientists in appropriately processing and interpreting their data, while aiding field and laboratory researchers to implement strategies for improving the quality of the generated results.
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Affiliation(s)
- Ostaizka Aizpurua
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
| | - Lars H Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - M T P Gilbert
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, NTNU, Trondheim, Norway
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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2
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Togawa N, Yamada R, Aoki Y, Suehiro S, Uchida N, Haseda A, Kagami-Katsuyama H, Honma N, Nishihira J. Improvement of skin condition and intestinal microbiota via Heyndrickxia coagulans SANK70258 intake: A placebo-controlled, randomized, double-blind, parallel-group comparative study. Nutrition 2024; 126:112533. [PMID: 39127017 DOI: 10.1016/j.nut.2024.112533] [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: 04/24/2024] [Revised: 07/04/2024] [Accepted: 07/12/2024] [Indexed: 08/12/2024]
Abstract
OBJECTIVE Heyndrickxia coagulans SANK70258, a representative probiotic, is known for alleviating inflammation caused by cedar pollen, improving the intestinal environment and bowel movements. A previous study on consuming H. coagulans SANK70258 together with galactooligosaccharides showed a trend toward improvement in skin scaliness scores and subjective assessments of skin roughness. However, the effect of H. coagulans SANK70258 alone on the skin remains unclear. Thus, we aimed to re-evaluate the effects of the intake of H. coagulans SANK70258 alone on skin conditions and the intestinal environment through a clinical trial. METHODS This placebo-controlled, double-blind clinical trial involved 80 Japanese women aged 30 to 65 with perceived skin roughness. Participants were divided into placebo and test groups. Over eight weeks, the test group consumed H. coagulans SANK70258, and its effects on skin condition and intestinal health were examined. RESULTS The probiotic group showed significant intestinal improvements, with reduced fecal phenol levels (p = 0.044) and pH (p = 0.022), as well as enhanced skin lightness (L* value) (p = 0.040) and liver function tests. Metabolic analyses revealed decreases in fecal Nε-(carboxymethyl)lysine and plasma hydroxyproline, suggesting skin health benefits. There were also significant improvements in skin scaliness (p = 0.015) and bowel movement frequency (p = 0.032) in subgroup analysis. CONCLUSIONS H. coagulans SANK70258 can improve skin health by improving the intestinal lining. This probiotic reduces the levels of intestinal putrefactive products and advanced glycation end-product levels in feces, suggesting that it may affect not only skin health but also systemic tissues such as the liver.
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Affiliation(s)
- Naoyuki Togawa
- Food & Healthcare Group, Wellness Technology Department, Mitsubishi Chemical Corporation, Yokohama-shi, Japan.
| | - Ryouichi Yamada
- Food & Healthcare Group, Wellness Technology Department, Mitsubishi Chemical Corporation, Yokohama-shi, Japan
| | | | | | | | - Akane Haseda
- Department of Medical Management and Informatics, Hokkaido Information University, Hokkaido, Japan
| | - Hiroyo Kagami-Katsuyama
- Department of Medical Management and Informatics, Hokkaido Information University, Hokkaido, Japan
| | - Naoyuki Honma
- Department of Medical Management and Informatics, Hokkaido Information University, Hokkaido, Japan
| | - Jun Nishihira
- Department of Medical Management and Informatics, Hokkaido Information University, Hokkaido, Japan
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3
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Baba Y, Azuma N, Saito Y, Takahashi K, Matsui R, Takara T. Effect of Intake of Bifidobacteria and Dietary Fiber on Resting Energy Expenditure: A Randomized, Placebo-Controlled, Double-Blind, Parallel-Group Comparison Study. Nutrients 2024; 16:2345. [PMID: 39064788 PMCID: PMC11279889 DOI: 10.3390/nu16142345] [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: 06/09/2024] [Revised: 07/16/2024] [Accepted: 07/19/2024] [Indexed: 07/28/2024] Open
Abstract
Bifidobacterium animalis subsp. lactis GCL2505 in combination with inulin has been shown to have several health benefits, including an improvement in the intestinal microbiota and a reduction in human visceral fat. Previous studies have suggested that the visceral fat reduction of GCL2505 and inulin may be achieved by improving daily energy expenditure. This parallel, placebo-controlled, randomized, double-blind study was conducted to evaluate the effects of GCL2505 and inulin on resting energy expenditure (REE) in overweight or mildly obese Japanese adults (n = 44). Participants ingested 1 × 1010 colony forming units of GCL2505 and 5.0 g of inulin daily for 4 weeks. REE score at week 4 was set as the primary endpoint. At week 4, the REE score of the GCL2505 and inulin group was significantly higher than that of the placebo group, with a difference of 84.4 kcal/day. In addition, fecal bifidobacteria counts were significantly increased in the GCL2505 and inulin group. Our results indicated that the intake of GCL2505 and inulin improves energy balance, which is known to be a major factor of obesity, by modulating the microbiota in the gut. This is the first report to demonstrate the effects of probiotics and dietary fiber on REE in humans.
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Affiliation(s)
- Yuhei Baba
- Dairy Business Division, Ezaki Glico Co., Ltd., 4-6-5 Utajima, Nishiyodogawa-ku, Osaka 555-8502, Japan
| | - Naoki Azuma
- R&D Laboratory, Ezaki Glico Co., Ltd., 4-6-5 Utajima, Nishiyodogawa-ku, Osaka 555-8502, Japan; (N.A.); (Y.S.); (K.T.); (R.M.)
| | - Yasuo Saito
- R&D Laboratory, Ezaki Glico Co., Ltd., 4-6-5 Utajima, Nishiyodogawa-ku, Osaka 555-8502, Japan; (N.A.); (Y.S.); (K.T.); (R.M.)
| | - Kazuma Takahashi
- R&D Laboratory, Ezaki Glico Co., Ltd., 4-6-5 Utajima, Nishiyodogawa-ku, Osaka 555-8502, Japan; (N.A.); (Y.S.); (K.T.); (R.M.)
| | - Risa Matsui
- R&D Laboratory, Ezaki Glico Co., Ltd., 4-6-5 Utajima, Nishiyodogawa-ku, Osaka 555-8502, Japan; (N.A.); (Y.S.); (K.T.); (R.M.)
| | - Tsuyoshi Takara
- Medical Corporation Seishinkai Takara Clinic, 9F Taisei Bldg., 2-3-2 Higashi-gotanda, Shinagawa-ku, Tokyo 142-0022, Japan;
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4
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Mejia EM, Hizon NA, Dueck CE, Lidder R, Daigle J, Wonitowy Q, Medina NG, Mohammed UP, Cox GW, Safronetz D, Hagan M, Strong J, Nichani A, Mulvey MR, Mangat CS. Detection of mpox virus in wastewater provides forewarning of clinical cases in Canadian cities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 933:173108. [PMID: 38729376 DOI: 10.1016/j.scitotenv.2024.173108] [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: 02/09/2024] [Revised: 05/07/2024] [Accepted: 05/07/2024] [Indexed: 05/12/2024]
Abstract
Wastewater-based surveillance (WBS) has shown to be an effective tool in monitoring the spread of SARS-CoV-2 and has helped guide public health actions. Consequently, WBS has expanded to now include the monitoring of mpox virus (MPXV) to contribute to its mitigation efforts. In this study, we demonstrate a unique sample processing and a molecular diagnostic strategy for MPXV detection that can inform on the epidemiological situation of mpox outbreaks through WBS. We conducted WBS for MPXV in 22 Canadian wastewater treatment plants (WWTPs) for 14 weeks. Three MPXV qPCR assays were assessed in this study for the detection of MPXV which include the G2R assays (G2R_WA and G2R_G) developed by the Centers for Disease Control and Prevention (CDC) in 2010, and an in-house-developed assay that we have termed G2R_NML. The G2R_NML assay was designed using reference genomes from the 2022 MPXV outbreak and provides a larger qPCR amplicon size to facilitate Sanger sequencing. Results show that all three assays have similar limits of detection and are able to detect the presence of MPXV in wastewater. The G2R_NML assay produced a significantly greater number of Sanger sequence-confirmed MPXV results compared to the CDC G2R assays. Detection of MPXV was possible where provincial surveillance indicated overall low caseloads, and in some sites forewarning of up to several weeks was observed. Overall, this study proposes that WBS of MPXV provides additional information to help fill knowledge gaps in clinical case-surveillance and is potentially an essential component to the management of mpox.
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Affiliation(s)
- Edgard M Mejia
- Wastewater Surveillance Unit, Bacterial Pathogens, AMR, and Wastewater, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.
| | - Nikho A Hizon
- Wastewater Surveillance Unit, Bacterial Pathogens, AMR, and Wastewater, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Codey E Dueck
- Wastewater Surveillance Unit, Bacterial Pathogens, AMR, and Wastewater, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Ravinder Lidder
- Wastewater Surveillance Unit, Bacterial Pathogens, AMR, and Wastewater, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Jade Daigle
- Wastewater Surveillance Unit, Bacterial Pathogens, AMR, and Wastewater, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Quinn Wonitowy
- Wastewater Surveillance Unit, Bacterial Pathogens, AMR, and Wastewater, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Nestor G Medina
- Wastewater Surveillance Unit, Bacterial Pathogens, AMR, and Wastewater, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Umar P Mohammed
- Wastewater Surveillance Unit, Bacterial Pathogens, AMR, and Wastewater, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Graham W Cox
- Wastewater Surveillance Unit, Bacterial Pathogens, AMR, and Wastewater, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - David Safronetz
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada; Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Mable Hagan
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Jim Strong
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada; Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Anil Nichani
- Wastewater Surveillance Unit, Bacterial Pathogens, AMR, and Wastewater, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Michael R Mulvey
- Wastewater Surveillance Unit, Bacterial Pathogens, AMR, and Wastewater, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada; Antimicrobial Resistance Nosocomial Infections, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada; Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Chand S Mangat
- Wastewater Surveillance Unit, Bacterial Pathogens, AMR, and Wastewater, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada; Antimicrobial Resistance Nosocomial Infections, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada; Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
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Isokääntä H, Tomnikov N, Vanhatalo S, Munukka E, Huovinen P, Hakanen AJ, Kallonen T. High-throughput DNA extraction strategy for fecal microbiome studies. Microbiol Spectr 2024; 12:e0293223. [PMID: 38747618 PMCID: PMC11237708 DOI: 10.1128/spectrum.02932-23] [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: 08/09/2023] [Accepted: 04/19/2024] [Indexed: 06/06/2024] Open
Abstract
Microbiome studies are becoming larger in size to detect the potentially small effect that environmental factors have on our gut microbiomes, or that the microbiome has on our health. Therefore, fast and reproducible DNA isolation methods are needed to handle thousands of fecal samples. We used the Chemagic 360 chemistry and Magnetic Separation Module I (MSMI) instrument to compare two sample preservatives and four different pre-treatment protocols to find an optimal method for DNA isolation from thousands of fecal samples. The pre-treatments included bead beating, sample handling in tube and plate format, and proteinase K incubation. The optimal method offers a sufficient yield of high-quality DNA without contamination. Three human fecal samples (adult, senior, and infant) with technical replicates were extracted. The extraction included negative controls (OMNIgeneGUT, DNA/RNA shield fluid, and Chemagic Lysis Buffer 1) to detect cross-contamination and ZymoBIOMICS Gut Microbiome Standard as a positive control to mimic the human gut microbiome and assess sensitivity of the extraction method. All samples were extracted using Chemagic DNA Stool 200 H96 kit (PerkinElmer, Finland). The samples were collected in two preservatives, OMNIgeneGUT and DNA/RNA shield fluid. DNA quantity was measured using Qubit-fluorometer, DNA purity and quality using gel electrophoresis, and taxonomic signatures with 16S rRNA gene-based sequencing with V3V4 and V4 regions. Bead beating increased bacterial diversity. The largest increase was detected in gram-positive genera Blautia, Bifidobacterium, and Ruminococcus. Preservatives showed minor differences in bacterial abundances. The profiles between the V3V4 and V4 regions differed considerably with lower diversity samples. Negative controls showed signs from genera abundant in fecal samples. Technical replicates of the Gut Standard and stool samples showed low variation. The selected isolation protocol included recommended steps from manufacturer as well as bead beating. Bead beating was found to be necessary to detect hard-to-lyse bacteria. The protocol was reproducible in terms of DNA yield among different stool replicates and the ZymoBIOMICS Gut Microbiome Standard. The MSM1 instrument and pre-treatment in a 96-format offered the possibility of automation and handling of large sample collections. Both preservatives were feasible in terms of sample handling and had low variation in taxonomic signatures. The 16S rRNA target region had a high impact on the composition of the bacterial profile. IMPORTANCE Next-generation sequencing (NGS) is a widely used method for determining the composition of the gut microbiota. Due to the differences in the gut microbiota composition between individuals, microbiome studies have expanded into large population studies to maximize detection of small effects on microbe-host interactions. Thus, the demand for a rapid and reliable microbial profiling is continuously increasing, making the optimization of high-throughput 96-format DNA extraction integral for NGS-based downstream applications. However, experimental protocols are prone to bias and errors from sample collection and storage, to DNA extraction, primer selection and sequencing, and bioinformatics analyses. Methodological bias can contribute to differences in microbiome profiles, causing variability across studies and laboratories using different protocols. To improve consistency and confidence of the measurements, the standardization of microbiome analysis methods has been recognized in many fields.
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Affiliation(s)
- Heidi Isokääntä
- Infections and Immunity Unit, Institute of Biomedicine, University of Turku, Turku, Finland
- Centre for Population Health Research, University of Turku, Turku, Finland
| | - Natalie Tomnikov
- Department of Clinical Microbiology, Tyks Laboratories, Turku University Hospital, Turku, Finland
| | - Sanja Vanhatalo
- Infections and Immunity Unit, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Eveliina Munukka
- Clinical Microbiome Bank, Microbe Center, Turku University Hospital and University of Turku, Turku, Finland
- Division of Digestive Surgery and Urology, Turku University Hospital, Turku, Finland
| | - Pentti Huovinen
- Infections and Immunity Unit, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Antti J. Hakanen
- Infections and Immunity Unit, Institute of Biomedicine, University of Turku, Turku, Finland
- Department of Clinical Microbiology, Tyks Laboratories, Turku University Hospital, Turku, Finland
- Clinical Microbiome Bank, Microbe Center, Turku University Hospital and University of Turku, Turku, Finland
| | - Teemu Kallonen
- Infections and Immunity Unit, Institute of Biomedicine, University of Turku, Turku, Finland
- Department of Clinical Microbiology, Tyks Laboratories, Turku University Hospital, Turku, Finland
- Clinical Microbiome Bank, Microbe Center, Turku University Hospital and University of Turku, Turku, Finland
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6
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Fernández-Pato A, Sinha T, Gacesa R, Andreu-Sánchez S, Gois MFB, Gelderloos-Arends J, Jansen DBH, Kruk M, Jaeger M, Joosten LAB, Netea MG, Weersma RK, Wijmenga C, Harmsen HJM, Fu J, Zhernakova A, Kurilshikov A. Choice of DNA extraction method affects stool microbiome recovery and subsequent phenotypic association analyses. Sci Rep 2024; 14:3911. [PMID: 38366085 PMCID: PMC10873414 DOI: 10.1038/s41598-024-54353-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: 06/29/2023] [Accepted: 02/12/2024] [Indexed: 02/18/2024] Open
Abstract
The lack of standardization in the methods of DNA extraction from fecal samples represents the major source of experimental variation in the microbiome research field. In this study, we aimed to compare the metagenomic profiles and microbiome-phenotype associations obtained by applying two commercially available DNA extraction kits: the AllPrep DNA/RNA Mini Kit (APK) and the QIAamp Fast DNA Stool Mini Kit (FSK). Using metagenomic sequencing data available from 745 paired fecal samples from two independent population cohorts, Lifelines-DEEP (LLD, n = 292) and the 500 Functional Genomics project (500FG, n = 453), we confirmed significant differences in DNA yield and the recovered microbial communities between protocols, with the APK method resulting in a higher DNA concentration and microbial diversity. Further, we observed a massive difference in bacterial relative abundances at species-level between the APK and the FSK protocols, with > 75% of species differentially abundant between protocols in both cohorts. Specifically, comparison with a standard mock community revealed that the APK method provided higher accuracy in the recovery of microbial relative abundances, with the absence of a bead-beating step in the FSK protocol causing an underrepresentation of gram-positive bacteria. This heterogeneity in the recovered microbial composition led to remarkable differences in the association with anthropometric and lifestyle phenotypes. The results of this study further reinforce that the choice of DNA extraction method impacts the metagenomic profile of human gut microbiota and highlight the importance of harmonizing protocols in microbiome studies.
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Affiliation(s)
- Asier Fernández-Pato
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
| | - Trishla Sinha
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
| | - Ranko Gacesa
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
| | - Sergio Andreu-Sánchez
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
| | - Milla F Brandao Gois
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
| | - Jody Gelderloos-Arends
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
| | - Dianne B H Jansen
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
| | - Marloes Kruk
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
| | - Martin Jaeger
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Medical Genetics, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Genomics and Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
| | - Hermie J M Harmsen
- Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands.
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7
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Routy B, Jackson T, Mählmann L, Baumgartner CK, Blaser M, Byrd A, Corvaia N, Couts K, Davar D, Derosa L, Hang HC, Hospers G, Isaksen M, Kroemer G, Malard F, McCoy KD, Meisel M, Pal S, Ronai Z, Segal E, Sepich-Poore GD, Shaikh F, Sweis RF, Trinchieri G, van den Brink M, Weersma RK, Whiteson K, Zhao L, McQuade J, Zarour H, Zitvogel L. Melanoma and microbiota: Current understanding and future directions. Cancer Cell 2024; 42:16-34. [PMID: 38157864 PMCID: PMC11096984 DOI: 10.1016/j.ccell.2023.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/04/2023] [Accepted: 12/05/2023] [Indexed: 01/03/2024]
Abstract
Over the last decade, the composition of the gut microbiota has been found to correlate with the outcomes of cancer patients treated with immunotherapy. Accumulating evidence points to the various mechanisms by which intestinal bacteria act on distal tumors and how to harness this complex ecosystem to circumvent primary resistance to immune checkpoint inhibitors. Here, we review the state of the microbiota field in the context of melanoma, the recent breakthroughs in defining microbial modes of action, and how to modulate the microbiota to enhance response to cancer immunotherapy. The host-microbe interaction may be deciphered by the use of "omics" technologies, and will guide patient stratification and the development of microbiota-centered interventions. Efforts needed to advance the field and current gaps of knowledge are also discussed.
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Affiliation(s)
- Bertrand Routy
- University of Montreal Research Center (CRCHUM), Montreal, QC H2X 0A9, Canada; Hematology-Oncology Division, Department of Medicine, Centre Hospitalier de l'Université de Montréal (CHUM), Montreal, QC H2X 3E4, Canada
| | - Tanisha Jackson
- Melanoma Research Alliance, 730 15th Street NW, Washington, DC 20005, USA
| | - Laura Mählmann
- Seerave Foundation, The Seerave Foundation, 35-37 New Street, St Helier, JE2 3RA Jersey, UK
| | | | - Martin Blaser
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ 08854, USA
| | - Allyson Byrd
- Department of Cancer Immunology, Genentech, Inc., South San Francisco, CA 94080, USA
| | | | - Kasey Couts
- Department of Medicine, Division of Medical Oncology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Diwakar Davar
- Department of Medicine and UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Lisa Derosa
- Gustave Roussy Cancer Center, ClinicoBiome, 94805 Villejuif, France; Université Paris Saclay, Faculty of Medicine, 94270 Kremlin Bicêtre, France; Inserm U1015, Equipe Labellisée par la Ligue Contre le Cancer, 94800 Villejuif, France
| | - Howard C Hang
- Departments of Immunology & Microbiology and Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Geke Hospers
- Department of Medical Oncology, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, The Netherlands
| | | | - Guido Kroemer
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université Paris Cité, Sorbonne Université, Inserm U1138, Institut Universitaire de France, 75006 Paris, France; Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, 94905 Villejuif, France; Institut du Cancer Paris CARPEM, Department of Biology, Hôpital Européen Georges Pompidou, AP-HP, 75015 Paris, France
| | - Florent Malard
- Sorbonne Université, Centre de Recherche Saint-Antoine INSERM UMRs938, Service d'Hématologie Clinique et de Thérapie Cellulaire, Hôpital Saint Antoine, AP-HP, Paris, France
| | - Kathy D McCoy
- Department of Physiology & Pharmacology, Snyder Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Marlies Meisel
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA USA; Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, PA USA
| | - Sumanta Pal
- Department of Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Ze'ev Ronai
- Sanford Burnham Prebys Discovery Medical Research Institute, La Jolla, CA 92037, USA
| | - Eran Segal
- Weizmann Institute of Science, Computer Science and Applied Mathematics Department, 234th Herzel st., Rehovot 7610001, Israel
| | - Gregory D Sepich-Poore
- Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Micronoma Inc., San Diego, CA 92121, USA
| | - Fyza Shaikh
- Johns Hopkins School of Medicine, Department of Oncology, Baltimore, MD 21287, USA
| | - Randy F Sweis
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Giorgio Trinchieri
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Marcel van den Brink
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Immunology, Sloan Kettering Institute, New York, NY 10065, USA; Weill Cornell Medical College, New York, NY 10065, USA
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands
| | - Katrine Whiteson
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Liping Zhao
- Department of Biochemistry and Microbiology, New Jersey Institute of Food, Nutrition and Health, Rutgers University, New Brunswick, NY 08901, USA
| | - Jennifer McQuade
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Hassane Zarour
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15232, USA.
| | - Laurence Zitvogel
- Gustave Roussy Cancer Center, ClinicoBiome, 94805 Villejuif, France; Université Paris Saclay, Faculty of Medicine, 94270 Kremlin Bicêtre, France; Inserm U1015, Equipe Labellisée par la Ligue Contre le Cancer, 94800 Villejuif, France; Center of Clinical Investigations in Biotherapies of Cancer (CICBT), Gustave Roussy, 94805 Villejuif, France.
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8
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Rintarhat P, Cho YJ, Koh H, Park S, Lee EJ, Lim H, Noh J, Lee DW, Jung WH. Assessment of DNA extraction methods for human gut mycobiome analysis. ROYAL SOCIETY OPEN SCIENCE 2024; 11:231129. [PMID: 38204788 PMCID: PMC10776226 DOI: 10.1098/rsos.231129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 12/11/2023] [Indexed: 01/12/2024]
Abstract
The gut mycobiome plays an important role in the health and disease of the human gut, but its exact function is still under investigation. While there is a wealth of information available on the bacterial community of the human gut microbiome, research on the fungal community is still relatively limited. In particular, technical methodologies for mycobiome analysis, especially the DNA extraction method for human faecal samples, varied in different studies. In the current study, two commercial kits commonly used in DNA extraction, the QIAamp® Fast DNA Stool Mini Kit and DNeasy PowerSoil Pro Kit, and one manual method, the International Human Microbiome Standards Protocol Q, were compared. Furthermore, the effectiveness of two different bead-beating machines, the Mini-Beadbeater-16 and FastPrep-24TM 5G, was compared in parallel. A mock fungal community with a known composition of fungal strains was also generated and included to compare different DNA extraction methods. Our results suggested that the method using the DNeasy PowerSoil Pro Kit and Mini-Beadbeater-16 provides the best results to extract DNA from human faecal samples. Based on our data, we propose a standard operating procedure for DNA extraction from human faecal samples for mycobiome analysis.
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Affiliation(s)
- Piyapat Rintarhat
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Korea
| | - Yong-Joon Cho
- Department of Molecular Bioscience, Kangwon National University, Chuncheon 24341, Korea
| | - Hong Koh
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Sowon Park
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Eun Joo Lee
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Hyeji Lim
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Jihye Noh
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Dong-Woo Lee
- Department of Biotechnology, Yonsei University, Seoul, Korea
| | - Won Hee Jung
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Korea
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9
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Azuma N, Saito Y, Nishijima T, Aoki R, Nishihira J. Effect of daily ingestion of Bifidobacterium and dietary fiber on vascular endothelial function: a randomized, double-blind, placebo-controlled, parallel-group comparison study. Biosci Biotechnol Biochem 2023; 88:86-96. [PMID: 37849220 DOI: 10.1093/bbb/zbad148] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 10/10/2023] [Indexed: 10/19/2023]
Abstract
Bifidobacterium animalis subsp. lactis GCL2505 (GCL2505) improves the intestinal microbiota and reduces human visceral fat. This randomized, double-blind, placebo-controlled, parallel-group study was conducted to examine the effects of inulin, a prebiotic dietary fiber, and GCL2505 on vascular endothelial function in healthy subjects (n = 60). The test drink contained 2.0 g/100 g inulin and 1.0 × 1010 colony-forming units/100 g GCL2505 and was consumed daily for 12 weeks. Flow-mediated dilation was set as the primary endpoint. Subgroup analysis of vascular endothelial function demonstrated a significant increase in the change of flow-mediated dilation (%) from weeks 0 to 12 in the GCL2505 and inulin group (n = 24) compared with the placebo group (n = 23), while an improving trend in low-density lipoprotein cholesterol and plasminogen activator inhibitor-1 were confirmed. Our results indicated that the test drink had a positive effect on vascular endothelial function and related blood parameters.
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Affiliation(s)
- Naoki Azuma
- R&D Laboratory, Ezaki Glico Co., Ltd., Osaka, Japan
| | - Yasuo Saito
- R&D Laboratory, Ezaki Glico Co., Ltd., Osaka, Japan
| | - Tomohiko Nishijima
- Mechanism-based Research Laboratory, Ezaki Glico Co., Ltd., Osaka, Japan
| | - Ryo Aoki
- Mechanism-based Research Laboratory, Ezaki Glico Co., Ltd., Osaka, Japan
| | - Jun Nishihira
- Department of Medical Management and Informatics, Hokkaido Information University, Hokkaido, Japan
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10
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Baba Y, Saito Y, Kadowaki M, Azuma N, Tsuge D. Effect of Continuous Ingestion of Bifidobacteria and Inulin on Reducing Body Fat: A Randomized, Double-Blind, Placebo-Controlled, Parallel-Group Comparison Study. Nutrients 2023; 15:5025. [PMID: 38140284 PMCID: PMC10745352 DOI: 10.3390/nu15245025] [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: 11/02/2023] [Revised: 11/22/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
Bifidobacterium animalis subsp. lactis GCL2505 has been shown to have several positive health effects, including improved defecation frequency and reduced visceral fat. It is known that combined intake of GCL2505 and inulin increases the total number of bifidobacteria compared with ingestion of GCL2505 alone. This randomized, double-blind, placebo-controlled, parallel-group study was conducted to confirm that consumption of GCL2505 and inulin reduces abdominal fat (n = 120). Participants consumed a test beverage containing 1 × 1010 colony-forming units of GCL2505 per 100 g and 2.0 g of inulin per 100 g for 12 weeks. A change in the visceral fat area (VFA) was set as the primary endpoint. There were significant reductions in VFA and total fat area. The intervention significantly increased the total number of bifidobacteria and affected the levels of several lipid markers. Regression analysis of bifidobacteria and measured parameters showed that total bifidobacteria correlated with VFA and body mass index (BMI), while endogenous bifidobacteria and Bifidobacterium animalis subsp. lactis correlated only with BMI, suggesting that increases in both contributed to the decrease in VFA. These results suggest that combined intake of GCL2505 and inulin improves the intestinal environment and reduces abdominal fat in association with the SCFA-mediated pathway.
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Affiliation(s)
- Yuhei Baba
- Dairy Business Division, Ezaki Glico Co., Ltd., 4-6-5 Utajima, Nishiyodogawa-Ku, Osaka 555-8502, Japan
| | - Yasuo Saito
- R&D Laboratory, Ezaki Glico Co., Ltd., 4-6-5 Utajima, Nishiyodogawa-Ku, Osaka 555-8502, Japan; (Y.S.); (M.K.); (N.A.)
| | - Mei Kadowaki
- R&D Laboratory, Ezaki Glico Co., Ltd., 4-6-5 Utajima, Nishiyodogawa-Ku, Osaka 555-8502, Japan; (Y.S.); (M.K.); (N.A.)
| | - Naoki Azuma
- R&D Laboratory, Ezaki Glico Co., Ltd., 4-6-5 Utajima, Nishiyodogawa-Ku, Osaka 555-8502, Japan; (Y.S.); (M.K.); (N.A.)
| | - Daisuke Tsuge
- Shinagawa Season Terrace Health Care Clinic, Shinagawa Season Terrace (5F), 1-2-70 Konan, Minato-Ku, Tokyo 108-0075, Japan;
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11
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Sekiguchi Y, Teramoto K, Tourlousse DM, Ohashi A, Hamajima M, Miura D, Yamada Y, Iwamoto S, Tanaka K. A large-scale genomically predicted protein mass database enables rapid and broad-spectrum identification of bacterial and archaeal isolates by mass spectrometry. Genome Biol 2023; 24:257. [PMID: 38049850 PMCID: PMC10696839 DOI: 10.1186/s13059-023-03096-4] [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: 03/30/2023] [Accepted: 10/24/2023] [Indexed: 12/06/2023] Open
Abstract
MALDI-TOF MS-based microbial identification relies on reference spectral libraries, which limits the screening of diverse isolates, including uncultured lineages. We present a new strategy for broad-spectrum identification of bacterial and archaeal isolates by MALDI-TOF MS using a large-scale database of protein masses predicted from nearly 200,000 publicly available genomes. We verify the ability of the database to identify microorganisms at the species level and below, achieving correct identification for > 90% of measured spectra. We further demonstrate its utility by identifying uncultured strains from mouse feces with metagenomics, allowing the identification of new strains by customizing the database with metagenome-assembled genomes.
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Affiliation(s)
- Yuji Sekiguchi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), AIST Tsukuba Central 6, Ibaraki, 305-8566, Japan.
| | | | - Dieter M Tourlousse
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), AIST Tsukuba Central 6, Ibaraki, 305-8566, Japan
| | - Akiko Ohashi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), AIST Tsukuba Central 6, Ibaraki, 305-8566, Japan
| | - Mayu Hamajima
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), AIST Tsukuba Central 6, Ibaraki, 305-8566, Japan
| | - Daisuke Miura
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), AIST Tsukuba Central 6, Ibaraki, 305-8566, Japan
| | - Yoshihiro Yamada
- Koichi Tanaka Mass Spectrometry Research Laboratory, Shimadzu Corporation, Kyoto, Japan
| | - Shinichi Iwamoto
- Koichi Tanaka Mass Spectrometry Research Laboratory, Shimadzu Corporation, Kyoto, Japan
| | - Koichi Tanaka
- Koichi Tanaka Mass Spectrometry Research Laboratory, Shimadzu Corporation, Kyoto, Japan
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12
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Afonso CL, Afonso AM. Next-Generation Sequencing for the Detection of Microbial Agents in Avian Clinical Samples. Vet Sci 2023; 10:690. [PMID: 38133241 PMCID: PMC10747646 DOI: 10.3390/vetsci10120690] [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: 10/13/2023] [Revised: 11/24/2023] [Accepted: 11/29/2023] [Indexed: 12/23/2023] Open
Abstract
Direct-targeted next-generation sequencing (tNGS), with its undoubtedly superior diagnostic capacity over real-time PCR (RT-PCR), and direct-non-targeted NGS (ntNGS), with its higher capacity to identify and characterize multiple agents, are both likely to become diagnostic methods of choice in the future. tNGS is a rapid and sensitive method for precise characterization of suspected agents. ntNGS, also known as agnostic diagnosis, does not require a hypothesis and has been used to identify unsuspected infections in clinical samples. Implemented in the form of multiplexed total DNA metagenomics or as total RNA sequencing, the approach produces comprehensive and actionable reports that allow semi-quantitative identification of most of the agents present in respiratory, cloacal, and tissue samples. The diagnostic benefits of the use of direct tNGS and ntNGS are high specificity, compatibility with different types of clinical samples (fresh, frozen, FTA cards, and paraffin-embedded), production of nearly complete infection profiles (viruses, bacteria, fungus, and parasites), production of "semi-quantitative" information, direct agent genotyping, and infectious agent mutational information. The achievements of NGS in terms of diagnosing poultry problems are described here, along with future applications. Multiplexing, development of standard operating procedures, robotics, sequencing kits, automated bioinformatics, cloud computing, and artificial intelligence (AI) are disciplines converging toward the use of this technology for active surveillance in poultry farms. Other advances in human and veterinary NGS sequencing are likely to be adaptable to avian species in the future.
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13
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Pinnell LJ, Young JD, Thompson TW, Wolfe CA, Bryant TC, Nair MN, Richeson JT, Morley PS. Establishing the link between microbial communities in bovine liver abscesses and the gastrointestinal tract. Anim Microbiome 2023; 5:58. [PMID: 37986094 PMCID: PMC10662489 DOI: 10.1186/s42523-023-00278-0] [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: 05/19/2023] [Accepted: 10/27/2023] [Indexed: 11/22/2023] Open
Abstract
BACKGROUND Liver abscesses (LAs) are one of the most common and important problems faced by the beef industry. The most efficacious method for the prevention of LAs in North America is through dietary inclusion of low doses of antimicrobial drugs such as tylosin, but the mechanisms by which this treatment prevents LAs are not fully understood. LAs are believed to result from mucosal barrier dysfunction in the gastrointestinal tract (GIT) allowing bacterial translocation to the liver via the portal vein, yet differences in the GIT microbiome of cattle with and without LAs have not been explored. Here, we characterized microbial communities from LAs, rumen, ileum, and colon from the same cattle for the first time. RESULTS Results demonstrate that tylosin supplementation was associated with differences in microbial community structure in the rumen and small intestine, largely because of differences in the predominance of Clostridia. Importantly, we show for the first time that microbial communities from multiple LAs in one animal's liver are highly similar, suggesting that abscesses found at different locations in the liver may originate from a localized source in the GIT (rather than disparate locations). A large portion of abscesses were dominated by microbial taxa that were most abundant in the hindgut. Further, we identified taxa throughout the GIT that were differentially abundant between animals with and without liver abscesses. Bifidobacterium spp.-a bacteria commonly associated with a healthy GIT in several species-were more abundant in the rumen and ileum of animals without LAs compared to those with LAs. CONCLUSIONS Together these results provide the first direct comparison of GIT and LA microbial communities within the same animal, add considerable evidence to the hypothesis that some LA microbial communities arise from the hindgut, and suggest that barrier dysfunction throughout the GIT may be the underlying cause of LA formation in cattle.
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Affiliation(s)
- Lee J Pinnell
- Veterinary Education, Research, and Outreach Program, Texas A&M University, Canyon, TX, 79015, USA
| | - J Daniel Young
- Department of Agricultural Sciences, West Texas A&M University, Canyon, TX, 79015, USA
| | - Tyler W Thompson
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Cory A Wolfe
- Veterinary Education, Research, and Outreach Program, Texas A&M University, Canyon, TX, 79015, USA
| | - Tony C Bryant
- Five Rivers Cattle Feeding, Johnstown, CO, 80534, USA
| | - Mahesh N Nair
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - John T Richeson
- Department of Agricultural Sciences, West Texas A&M University, Canyon, TX, 79015, USA
| | - Paul S Morley
- Veterinary Education, Research, and Outreach Program, Texas A&M University, Canyon, TX, 79015, USA.
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14
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Yang Y, Deng Y, Liu L, Yin X, Xu X, Wang D, Zhang T. Establishing reference material for the quest towards standardization in environmental microbial metagenomic studies. WATER RESEARCH 2023; 245:120641. [PMID: 37748344 DOI: 10.1016/j.watres.2023.120641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 09/02/2023] [Accepted: 09/15/2023] [Indexed: 09/27/2023]
Abstract
Breakthroughs in DNA-based technologies, especially in metagenomic sequencing, have drastically enhanced researchers' ability to explore environmental microbiome and the associated interplays within. However, as new methodologies are being actively developed for improvements in different aspects, metagenomic workflows become diversified and heterogeneous. Through a single-variable control approach, we quantified the microbial profiling variations arising from 6 common technical variables associated with metagenomic workflows for both simple and complex samples. The incurred variations were constantly the lowest in replicates of DNA isolation and DNA sequencing library construction. Different DNA extraction kits often caused the highest variation among all the tested variables. Additionally, sequencing run batch was an important source of variability for targeted platforms. As such, the development of an environmental reference material for complex environmental samples could be beneficial in benchmarking accrued non-biological variability within and between protocols and insuring reliable and reproducible sequencing outputs immediately upstream of bioinformatic analysis. To develop an environment reference material, sequencing of a well-homogenized environmental sample composed of activated sludge was performed using different pre-analytical assays in replications. In parallel, a certified mock community was processed and sequenced. Assays were ranked based on the reconstruction of the theoretical mock community profile. The reproducibility of the best-performing assay and the microbial profile of the reference material were further ascertained. We propose the adoption of our complex environmental reference material, which could reflect the degree of diversity in environmental microbiome studies, to facilitate accurate, reproducible, and comparable environmental metagenomics-based studies.
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Affiliation(s)
- Yu Yang
- Department of Civil Engineering, Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, The University of Hong Kong, Hong Kong, China
| | - Yu Deng
- Department of Civil Engineering, Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, The University of Hong Kong, Hong Kong, China
| | - Lei Liu
- Department of Civil Engineering, Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, The University of Hong Kong, Hong Kong, China
| | - Xiaole Yin
- Department of Civil Engineering, Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, The University of Hong Kong, Hong Kong, China
| | - Xiaoqing Xu
- Department of Civil Engineering, Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, The University of Hong Kong, Hong Kong, China
| | - Dou Wang
- Department of Civil Engineering, Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, The University of Hong Kong, Hong Kong, China
| | - Tong Zhang
- Department of Civil Engineering, Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, The University of Hong Kong, Hong Kong, China; School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Sassoon Road, Hong Kong SAR, China; Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau SAR, China.
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15
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Azuma N, Mawatari T, Saito Y, Tsukamoto M, Sampei M, Iwama Y. Effect of Continuous Ingestion of Bifidobacteria and Dietary Fiber on Improvement in Cognitive Function: A Randomized, Double-Blind, Placebo-Controlled Trial. Nutrients 2023; 15:4175. [PMID: 37836458 PMCID: PMC10574581 DOI: 10.3390/nu15194175] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 09/25/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
Bifidobacterium animalis subsp. lactis GCL2505 has been shown to have some positive effects on health, including improved defecation frequency and reduced visceral fat. These effects are thought to be due to GCL2505's unique ability to reach the intestine in a viable form and proliferate after a single intake. This leads to an increased number of intestinal bifidobacteria. This randomized, double-blind, placebo-controlled, parallel-group study was conducted to confirm that intake of GCL2505 and inulin (a prebiotic) improve cognitive function (n = 80). Participants consumed test drinks containing 1 × 1010 colony-forming units of GCL2505 per 100 g and 2.0 g of inulin per 100 g for 12 weeks. The change in cognitive function assessment scores was set as the primary endpoint. There were significant improvements in scores in the neurocognitive index domain, which is an assessment of overall cognitive function, in addition to overall attention, cognitive flexibility, and executive function domains. The intervention significantly increased the number of fecal bifidobacteria and affected the levels of several inflammatory markers. These results suggest that intake of GCL2505 and inulin improves cognitive function by improving the intestinal environment and alleviating inflammation.
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Affiliation(s)
- Naoki Azuma
- R&D Laboratory, Ezaki Glico Co., Ltd., 4-6-5, Utajima, Nishiyodogawa-Ku, Osaka 555-8502, Japan; (T.M.); (Y.S.); (M.T.); (M.S.)
| | - Takashi Mawatari
- R&D Laboratory, Ezaki Glico Co., Ltd., 4-6-5, Utajima, Nishiyodogawa-Ku, Osaka 555-8502, Japan; (T.M.); (Y.S.); (M.T.); (M.S.)
| | - Yasuo Saito
- R&D Laboratory, Ezaki Glico Co., Ltd., 4-6-5, Utajima, Nishiyodogawa-Ku, Osaka 555-8502, Japan; (T.M.); (Y.S.); (M.T.); (M.S.)
| | - Masashi Tsukamoto
- R&D Laboratory, Ezaki Glico Co., Ltd., 4-6-5, Utajima, Nishiyodogawa-Ku, Osaka 555-8502, Japan; (T.M.); (Y.S.); (M.T.); (M.S.)
| | - Masatoshi Sampei
- R&D Laboratory, Ezaki Glico Co., Ltd., 4-6-5, Utajima, Nishiyodogawa-Ku, Osaka 555-8502, Japan; (T.M.); (Y.S.); (M.T.); (M.S.)
| | - Yoshitaka Iwama
- Nihonbashi Cardiology Clinic, Kyodo Bldg. #201, 13-4 Nihonbashi Kodenmacho, Chuo-Ku, Tokyo 103-0001, Japan;
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16
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Sinclair J, West NP, Cox AJ. Comparison of four DNA extraction methods for 16s rRNA microbiota profiling of human faecal samples. BMC Res Notes 2023; 16:169. [PMID: 37568179 PMCID: PMC10422837 DOI: 10.1186/s13104-023-06451-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 08/08/2023] [Indexed: 08/13/2023] Open
Abstract
OBJECTIVE Growth in large population-based studies assessing contributions of the gut microbiota to health and disease requires high-throughput sample processing and analysis methods. This study assessed the impact that modifications to a commercially available magnetic bead based, semi-automated DNA extraction kit had on determination of microbial composition, relative to an established in-house method involving a combination of mechanical and chemical lysis. DNA was extracted from faecal samples from healthy adults (n = 12; 34-69 years), microbial composition was determined by V3-V4 16s rRNA sequencing and compared between extraction methods. RESULTS Diversity metrics did not differ between extraction methods. Differences in the relative abundance of key phyla, including a significantly lower abundance of the Firmicutes (p = 0.004) and higher relative abundance of the Bacteroidetes (p = 0.005) and Proteobacteria (p = 0.008) phyla were noted where the DNA extraction did not include additional chemical and mechanical lysis. Principal coordinate analysis of family and genera level data also suggested a potential for sample pre-processing to impact microbial composition. Observations of the potential for skewed microbial composition profiles from samples prepared using a semi-automated DNA extraction kit without additional sample pre-processing highlights a need for consideration of standardisation of methodological approaches to increase the comparability of microbial compositional data.
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Affiliation(s)
- James Sinclair
- Menzies Health Institute Queensland, Griffith University, Parklands Drive, Southport, QLD 4215 Australia
| | - Nicholas P West
- Menzies Health Institute Queensland, Griffith University, Parklands Drive, Southport, QLD 4215 Australia
- School of Pharmacy and Medical Sciences, Griffith University, Parklands Drive, Southport, QLD 4215 Australia
| | - Amanda J Cox
- Menzies Health Institute Queensland, Griffith University, Parklands Drive, Southport, QLD 4215 Australia
- School of Pharmacy and Medical Sciences, Griffith University, Parklands Drive, Southport, QLD 4215 Australia
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17
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Fukuoka H, Tourlousse DM, Ohashi A, Suzuki S, Nakagawa K, Ozawa M, Ishibe A, Endo I, Sekiguchi Y. Elucidating colorectal cancer-associated bacteria through profiling of minimally perturbed tissue-associated microbiota. Front Cell Infect Microbiol 2023; 13:1216024. [PMID: 37593761 PMCID: PMC10432157 DOI: 10.3389/fcimb.2023.1216024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 07/07/2023] [Indexed: 08/19/2023] Open
Abstract
Sequencing-based interrogation of gut microbiota is a valuable approach for detecting microbes associated with colorectal cancer (CRC); however, such studies are often confounded by the effect of bowel preparation. In this study, we evaluated the viability of identifying CRC-associated mucosal bacteria through centimeter-scale profiling of the microbiota in tumors and adjacent noncancerous tissue from eleven patients who underwent colonic resection without preoperative bowel preparation. High-throughput 16S rRNA gene sequencing revealed that differences between on- and off-tumor microbiota varied considerably among patients. For some patients, phylotypes affiliated with genera previously implicated in colorectal carcinogenesis, as well as genera with less well-understood roles in CRC, were enriched in tumor tissue, whereas for other patients, on- and off-tumor microbiota were very similar. Notably, the enrichment of phylotypes in tumor-associated mucosa was highly localized and no longer apparent even a few centimeters away from the tumor. Through short-term liquid culturing and metagenomics, we further generated more than one-hundred metagenome-assembled genomes, several representing bacteria that were enriched in on-tumor samples. This is one of the first studies to analyze largely unperturbed mucosal microbiota in tissue samples from the resected colons of unprepped CRC patients. Future studies with larger cohorts are expected to clarify the causes and consequences of the observed variability in the emergence of tumor-localized microbiota among patients.
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Affiliation(s)
- Hironori Fukuoka
- Department of Gastroenterological Surgery, Yokohama City University Hospital, Yokohama, Japan
| | - Dieter M. Tourlousse
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Akiko Ohashi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Shinsuke Suzuki
- Department of Surgery, Fujisawa Shonandai Hospital, Fujisawa, Japan
| | - Kazuya Nakagawa
- Department of Gastroenterological Surgery, Yokohama City University Hospital, Yokohama, Japan
| | - Mayumi Ozawa
- Department of Gastroenterological Surgery, Yokohama City University Hospital, Yokohama, Japan
| | - Atsushi Ishibe
- Department of Gastroenterological Surgery, Yokohama City University Hospital, Yokohama, Japan
| | - Itaru Endo
- Department of Gastroenterological Surgery, Yokohama City University Hospital, Yokohama, Japan
| | - Yuji Sekiguchi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
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18
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Elie C, Perret M, Hage H, Sentausa E, Hesketh A, Louis K, Fritah-Lafont A, Leissner P, Vachon C, Rostaing H, Reynier F, Gervasi G, Saliou A. Comparison of DNA extraction methods for 16S rRNA gene sequencing in the analysis of the human gut microbiome. Sci Rep 2023; 13:10279. [PMID: 37355726 PMCID: PMC10290636 DOI: 10.1038/s41598-023-33959-6] [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: 10/21/2022] [Accepted: 04/21/2023] [Indexed: 06/26/2023] Open
Abstract
The gut microbiome is widely analyzed using high-throughput sequencing, such as 16S rRNA gene amplicon sequencing and shotgun metagenomic sequencing (SMS). DNA extraction is known to have a large impact on the metagenomic analyses. The aim of this study was to compare DNA extraction protocols for 16S sequencing. In that context, four commonly used DNA extraction methods were compared for the analysis of the gut microbiota. Commercial versions were evaluated against modified protocols using a stool preprocessing device (SPD, bioMérieux) upstream DNA extraction. Stool samples from nine healthy volunteers and nine patients with a Clostridium difficile infection were extracted with all protocols and 16S sequenced. Protocols were ranked using wet- and dry-lab criteria, including quality controls of the extracted genomic DNA, alpha-diversity, accuracy using a mock community of known composition and repeatability across technical replicates. SPD improved overall efficiency of three of the four tested protocols compared with their commercial version, in terms of DNA extraction yield, sample alpha-diversity, and recovery of Gram-positive bacteria. The best overall performance was obtained for the S-DQ protocol, SPD combined with the DNeasy PowerLyser PowerSoil protocol from QIAGEN. Based on this evaluation, we strongly believe that the use of such stool preprocessing device improves both the standardization and the quality of the DNA extraction in the human gut microbiome studies.
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Affiliation(s)
- Céline Elie
- BIOASTER, Microbiology Research Institute, 40 avenue Tony Garnier, 69007, Lyon, France
| | - Magali Perret
- BIOASTER, Microbiology Research Institute, 40 avenue Tony Garnier, 69007, Lyon, France
| | - Hayat Hage
- BIOASTER, Microbiology Research Institute, 40 avenue Tony Garnier, 69007, Lyon, France
| | - Erwin Sentausa
- BIOASTER, Microbiology Research Institute, 40 avenue Tony Garnier, 69007, Lyon, France
| | - Amy Hesketh
- BIOASTER, Microbiology Research Institute, 40 avenue Tony Garnier, 69007, Lyon, France
| | - Karen Louis
- BIOASTER, Microbiology Research Institute, 40 avenue Tony Garnier, 69007, Lyon, France
| | - Asmaà Fritah-Lafont
- BIOASTER, Microbiology Research Institute, 40 avenue Tony Garnier, 69007, Lyon, France
| | - Philippe Leissner
- BIOASTER, Microbiology Research Institute, 40 avenue Tony Garnier, 69007, Lyon, France
| | - Carole Vachon
- bioMérieux, 5 Rue des Berges, 38000, Grenoble, France
| | | | - Frédéric Reynier
- BIOASTER, Microbiology Research Institute, 40 avenue Tony Garnier, 69007, Lyon, France
| | - Gaspard Gervasi
- bioMérieux, 376 Chemin de l'Orme, 69280, Marcy-l'Étoile, France
| | - Adrien Saliou
- BIOASTER, Microbiology Research Institute, 40 avenue Tony Garnier, 69007, Lyon, France.
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Wang Y, Zhang R, Pu Y, Wang D, Wang Y, Wu X, Pan Y, Luo C, Zhao G, Quan Z, Zheng Y. Sample Collection, DNA Extraction, and Library Construction Protocols of the Human Microbiome Studies in the International Human Phenome Project. PHENOMICS (CHAM, SWITZERLAND) 2023; 3:300-308. [PMID: 37325707 PMCID: PMC10260709 DOI: 10.1007/s43657-023-00097-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 01/09/2023] [Accepted: 01/12/2023] [Indexed: 06/17/2023]
Abstract
The human microbiome plays a crucial role in human health. In the past decade, advances in high-throughput sequencing technologies and analytical software have significantly improved our knowledge of the human microbiome. However, most studies concerning the human microbiome did not provide repeatable protocols to guide the sample collection, handling, and processing procedures, which impedes obtaining valid and timely microbial taxonomic and functional results. This protocol provides detailed operation methods of human microbial sample collection, DNA extraction, and library construction for both the amplicon sequencing-based measurements of the microbial samples from the human nasal cavity, oral cavity, and skin, as well as the shotgun metagenomic sequencing-based measurements of the human stool samples among adult participants. This study intends to develop practical procedure standards to improve the reproducibility of microbiota profiling of human samples. Supplementary Information The online version contains supplementary material available at 10.1007/s43657-023-00097-y.
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Affiliation(s)
- Yetong Wang
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, and School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai, 200433 China
| | - Ruyi Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai, 200433 China
| | - Yanni Pu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, and School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai, 200433 China
| | - Danqi Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai, 200433 China
| | - Yanren Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai, 200433 China
| | - Xuemei Wu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, and School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai, 200433 China
| | - Yujie Pan
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, and School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai, 200433 China
| | - Chen Luo
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, and School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai, 200433 China
| | - Guoping Zhao
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, and School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai, 200433 China
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
| | - Zhexue Quan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai, 200433 China
| | - Yan Zheng
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, and School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai, 200433 China
- Department of Cardiology, Shanghai Institute of Cardiovascular Disease, Zhongshan Hospital, Fudan University, 1609 Xietu Road, Shanghai, 200032 China
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20
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Nam NN, Do HDK, Loan Trinh KT, Lee NY. Metagenomics: An Effective Approach for Exploring Microbial Diversity and Functions. Foods 2023; 12:foods12112140. [PMID: 37297385 DOI: 10.3390/foods12112140] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/21/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
Various fields have been identified in the "omics" era, such as genomics, proteomics, transcriptomics, metabolomics, phenomics, and metagenomics. Among these, metagenomics has enabled a significant increase in discoveries related to the microbial world. Newly discovered microbiomes in different ecologies provide meaningful information on the diversity and functions of microorganisms on the Earth. Therefore, the results of metagenomic studies have enabled new microbe-based applications in human health, agriculture, and the food industry, among others. This review summarizes the fundamental procedures on recent advances in bioinformatic tools. It also explores up-to-date applications of metagenomics in human health, food study, plant research, environmental sciences, and other fields. Finally, metagenomics is a powerful tool for studying the microbial world, and it still has numerous applications that are currently hidden and awaiting discovery. Therefore, this review also discusses the future perspectives of metagenomics.
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Affiliation(s)
- Nguyen Nhat Nam
- Biotechnology Center, School of Agriculture and Aquaculture, Tra Vinh University, Tra Vinh City 87000, Vietnam
| | - Hoang Dang Khoa Do
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ward 13, District 04, Ho Chi Minh City 72820, Vietnam
| | - Kieu The Loan Trinh
- Department of BioNano Technology, Gachon University 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 13120, Republic of Korea
| | - Nae Yoon Lee
- Department of BioNano Technology, Gachon University 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 13120, Republic of Korea
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Yang Y, Deng Y, Shi X, Liu L, Yin X, Zhao W, Li S, Yang C, Zhang T. QMRA of beach water by Nanopore sequencing-based viability-metagenomics absolute quantification. WATER RESEARCH 2023; 235:119858. [PMID: 36931186 DOI: 10.1016/j.watres.2023.119858] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 02/28/2023] [Accepted: 03/07/2023] [Indexed: 06/18/2023]
Abstract
The majority of the current regulatory practices for routine monitoring of beach water quality rely on the culture-based enumeration of faecal indicator bacteria (FIB) to develop criteria for promoting the general public's health. To address the limitations of culture methods and the arguable reliability of FIB in indicating health risks, we developed a Nanopore metagenomic sequencing-based viable cell absolute quantification workflow to rapidly and accurately estimate a broad range of microbes in beach waters by a combination of propidium monoazide (PMA) and cellular spike-ins. Using the simple synthetic bacterial communities mixed with viable and heat-killed cells, we observed near-complete relic DNA removal by PMA with minimal disturbance to the composition of viable cells, demonstrating the feasibility of PMA treatment in profiling viable cells by Nanopore sequencing. On a simple mock community comprised of 15 prokaryotic species, our results showed high accordance between the expected and estimated concentrations, suggesting the accuracy of our method in absolute quantification. We then further assessed the accuracy of our method for counting viable Escherichia coli and Vibrio spp. in beach waters by comparing to culture-based method, which were also in high agreement. Furthermore, we demonstrated that 1 Gb sequences obtained within 2 h would be sufficient to quantify a species having a concentration of ≥ 10 cells/mL in beach waters. Using our viability-resolved quantification workflow to assess the microbial risk of the beach water, we conducted (1) screening-level quantitative microbial risk assessment (QMRA) to investigate human illness risk and site-specific risk patterns that might guide risk management efforts and (2) metagenomics-based resistome risk assessment to evaluate another layer of risk caused by difficult illness treatment due to antimicrobial resistance (AMR). In summary, our metagenomic workflow for the rapid absolute quantification of viable bacteria demonstrated its great potential in paving new avenues toward holistic microbial risk assessment.
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Affiliation(s)
- Yu Yang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China; State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong, China
| | - Yu Deng
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Xianghui Shi
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Lei Liu
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Xiaole Yin
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Wanwan Zhao
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Shuxian Li
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Chao Yang
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China.
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China; State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong, China; Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau SAR, China.
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22
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Kool J, Tymchenko L, Shetty SA, Fuentes S. Reducing bias in microbiome research: Comparing methods from sample collection to sequencing. Front Microbiol 2023; 14:1094800. [PMID: 37065158 PMCID: PMC10101209 DOI: 10.3389/fmicb.2023.1094800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 02/22/2023] [Indexed: 04/01/2023] Open
Abstract
BackgroundMicrobiota profiles are strongly influenced by many technical aspects that impact the ability of researchers to compare results. To investigate and identify potential biases introduced by technical variations, we compared several approaches throughout the entire workflow of a microbiome study, from sample collection to sequencing, using commercially available mock communities (from bacterial strains as well as from DNA) and multiple human fecal samples, including a large set of positive controls created as a random mix of several participant samples.MethodsHuman fecal material was sampled, and aliquots were used to test two commercially available stabilization solutions (OMNIgene·GUT and Zymo Research) in comparison to samples frozen immediately upon collection. In addition, the methodology for DNA extraction, input of DNA, or the number of PCR cycles were analyzed. Furthermore, to investigate the potential batch effects in DNA extraction, sequencing, and barcoding, we included 139 positive controls.ResultsSamples preserved in both the stabilization buffers limited the overgrowth of Enterobacteriaceae when compared to unpreserved samples stored at room temperature (RT). These stabilized samples stored at RT were different from immediately frozen samples, where the relative abundance of Bacteroidota was higher and Actinobacteriota and Firmicutes were lower. As reported previously, the method used for cell disruption was a major contributor to variation in microbiota composition. In addition, a high number of cycles during PCR lead to an increase in contaminants detected in the negative controls. The DNA extraction had a significant impact on the microbial composition, also observed with the use of different Illumina barcodes during library preparation and sequencing, while no batch effect was observed in replicate runs.ConclusionOur study reaffirms the importance of the mechanical cell disruption method and immediate frozen storage as critical aspects in fecal microbiota studies. A comparison of storage conditions revealed that the bias was limited in RT samples preserved in stabilization systems, and these may be a suitable compromise when logistics are challenging due to the size or location of a study. Moreover, to reduce the effect of contaminants in fecal microbiota profiling studies, we suggest the use of ~125 pg input DNA and 25 PCR cycles as optimal parameters during library preparation.
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Affiliation(s)
- Jolanda Kool
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Liza Tymchenko
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Sudarshan A. Shetty
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
- Department of Medical Microbiology and Infection Prevention, Virology and Immunology Research Group, University Medical Center Groningen, Groningen, Netherlands
| | - Susana Fuentes
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
- *Correspondence: Susana Fuentes
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23
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Fu S, Wang R, Xu Z, Zhou H, Qiu Z, Shen L, Yang Q. Metagenomic sequencing combined with flow cytometry facilitated a novel microbial risk assessment framework for bacterial pathogens in municipal wastewater without cultivation. IMETA 2023; 2:e77. [PMID: 38868349 PMCID: PMC10989823 DOI: 10.1002/imt2.77] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 12/05/2022] [Accepted: 12/07/2022] [Indexed: 06/14/2024]
Abstract
A workflow that combined metagenomic sequencing with flow cytometry was developed. The absolute abundance of pathogens was accurately estimated in mock communities and real samples. Metagenome-assembled genomes binned from metagenomic data set is robust in phylogenetic analysis and virulence profiling.
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Affiliation(s)
- Songzhe Fu
- Key Laboratory of Environment Controlled Aquaculture (KLECA), Ministry of EducationDalian Ocean UniversityDalianChina
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of EducationNorthwest UniversityXi'anChina
| | - Rui Wang
- Key Laboratory of Environment Controlled Aquaculture (KLECA), Ministry of EducationDalian Ocean UniversityDalianChina
| | - Zheng Xu
- Shenzhen Yantian District People's HospitalShenzhenChina
- Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhenChina
| | - Huiwen Zhou
- College of Life Science and HealthNortheastern UniversityShenyangChina
| | - Zhiguang Qiu
- School of Environment and Energy, Shenzhen Graduate SchoolPeking UniversityShenzhenChina
| | - Lixin Shen
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of EducationNorthwest UniversityXi'anChina
| | - Qian Yang
- Center for Microbial Ecology and Technology (CMET)Ghent UniversityGentBelgium
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24
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Morita H, Kano C, Ishii C, Kagata N, Ishikawa T, Hirayama A, Uchiyama Y, Hara S, Nakamura T, Fukuda S. Bacteroides uniformis and its preferred substrate, α-cyclodextrin, enhance endurance exercise performance in mice and human males. SCIENCE ADVANCES 2023; 9:eadd2120. [PMID: 36696509 PMCID: PMC9876546 DOI: 10.1126/sciadv.add2120] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Although gut microbiota has been linked to exercise, whether alterations in the abundance of specific bacteria improve exercise performance remains ambiguous. In a cross-sectional study involving 25 male long-distance runners, we found a correlation between Bacteroides uniformis abundance in feces and the 3000-m race time. In addition, we administered flaxseed lignan or α-cyclodextrin as a test tablet to healthy, active males who regularly exercised in a randomized, double-blind, placebo-controlled study to increase B. uniformis in the gut (UMIN000033748). The results indicated that α-cyclodextrin supplementation improved human endurance exercise performance. Moreover, B. uniformis administration in mice increased swimming time to exhaustion, cecal short-chain fatty acid concentrations, and the gene expression of enzymes associated with gluconeogenesis in the liver while decreasing hepatic glycogen content. These findings indicate that B. uniformis enhances endurance exercise performance, which may be mediated by facilitating hepatic endogenous glucose production.
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Affiliation(s)
- Hiroto Morita
- Core Technology Laboratories, Asahi Quality & Innovations Ltd., 1-1-21, Midori, Moriya, Ibaraki 302-0106, Japan
| | - Chie Kano
- Core Technology Laboratories, Asahi Quality & Innovations Ltd., 1-1-21, Midori, Moriya, Ibaraki 302-0106, Japan
| | - Chiharu Ishii
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka-shi, Yamagata 997-0052, Japan
| | - Noriko Kagata
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka-shi, Yamagata 997-0052, Japan
| | - Takamasa Ishikawa
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka-shi, Yamagata 997-0052, Japan
| | - Akiyoshi Hirayama
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka-shi, Yamagata 997-0052, Japan
| | - Yoshihide Uchiyama
- Aoyama Gakuin University Track and Field Club, Aoyama Gakuin University, 4-4-25 Shibuya, Shibuya-ku, Tokyo 150-8366, Japan
- School of International Politics, Economics and Communication, Aoyama Gakuin University, 4-4-25 Shibuya, Shibuya-ku, Tokyo 150-8366, Japan
| | - Susumu Hara
- Aoyama Gakuin University Track and Field Club, Aoyama Gakuin University, 4-4-25 Shibuya, Shibuya-ku, Tokyo 150-8366, Japan
- School of Global Studies and Collaboration, Aoyama Gakuin University, 4-4-25 Shibuya, Shibuya-ku, Tokyo 150-8366, Japan
| | - Teppei Nakamura
- Core Technology Laboratories, Asahi Quality & Innovations Ltd., 1-1-21, Midori, Moriya, Ibaraki 302-0106, Japan
| | - Shinji Fukuda
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka-shi, Yamagata 997-0052, Japan
- Gut Environmental Design Group, Kanagawa Institute of Industrial Science and Technology, 3-25-13 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa 210-0821, Japan
- Transborder Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba-shi, Ibaraki 305-8575, Japan
- Laboratory for Regenerative Microbiology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan
- Corresponding author.
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Fekete EE, Figeys D, Zhang X. Microbiota-directed biotherapeutics: considerations for quality and functional assessment. Gut Microbes 2023; 15:2186671. [PMID: 36896938 PMCID: PMC10012963 DOI: 10.1080/19490976.2023.2186671] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/11/2023] Open
Abstract
Mounting evidence points to causative or correlative roles of gut microbiome in the development of a myriad of diseases ranging from gastrointestinal diseases, metabolic diseases to neurological disorders and cancers. Consequently, efforts have been made to develop and apply therapeutics targeting the human microbiome, in particular the gut microbiota, for treating diseases and maintaining wellness. Here we summarize the current development of gut microbiota-directed therapeutics with a focus on novel biotherapeutics, elaborate the need of advanced -omics approaches for evaluating the microbiota-type biotherapeutics, and discuss the clinical and regulatory challenges. We also discuss the development and potential application of ex vivo microbiome assays and in vitro intestinal cellular models in this context. Altogether, this review aims to provide a broad view of promises and challenges of the emerging field of microbiome-directed human healthcare.
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Affiliation(s)
- Emily Ef Fekete
- Regulatory Research Division, Centre for Oncology, Radiopharmaceuticals and Research, Biologic and Radiopharmaceutical Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, Canada
| | - Daniel Figeys
- School of Pharmaceutical Sciences, Faculty of Medicine, University of Ottawa, Ottawa, Canada.,Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Xu Zhang
- Regulatory Research Division, Centre for Oncology, Radiopharmaceuticals and Research, Biologic and Radiopharmaceutical Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, Canada.,School of Pharmaceutical Sciences, Faculty of Medicine, University of Ottawa, Ottawa, Canada
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Intestinal Microbiota: The Driving Force behind Advances in Cancer Immunotherapy. Cancers (Basel) 2022; 14:cancers14194796. [PMID: 36230724 PMCID: PMC9564057 DOI: 10.3390/cancers14194796] [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: 08/24/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 11/17/2022] Open
Abstract
Simple Summary Despite the great achievements of cancer immunotherapy in a variety of tumors, tumor heterogeneity and drug resistance still plague patients and clinical researchers. In particular, the occurrence of immune-related adverse events forces patients to discontinue cancer immunotherapy. Therefore, it is urgent to optimize cancer immunotherapy and improve the efficacy of immunotherapy. With the iteration of sequencing technology, the microbiome, as the second set of genomes in the body, has been proven to be involved in immunity and metabolism. More and more studies are gradually shifting the perspective to the intestinal microbiota and cancer immunotherapy. The intestinal microbiota reactivates and modulates immune cells in immunotherapy and is expected to become a biomarker for predicting immune efficacy. Targeting to improve the intestinal microbiota can enhance anti-tumor immunity. This advantage is beneficial to control related adverse symptoms and expand the beneficiary population of cancer immunotherapy. This finding can help clinicians comprehensively evaluate the effect of tumor screening and tumor treatment. Therefore, the innovative combination of gut microbiota and cancer immunotherapy is expected to be an active strategy to enhance individualized immune responses. Abstract In recent years, cancer immunotherapy has become a breakthrough method to solve solid tumors. It uses immune checkpoint inhibitors to interfere with tumor immune escape to coordinate anti-tumor therapy. However, immunotherapy has an individualized response rate. Moreover, immune-related adverse events and drug resistance are still urgent issues that need to be resolved, which may be attributed to the immune imbalance caused by immune checkpoint inhibitors. Microbiome research has fully revealed the metabolic-immune interaction relationship between the microbiome and the host. Surprisingly, sequencing technology further proved that intestinal microbiota could effectively intervene in tumor immunotherapy and reduce the incidence of adverse events. Therefore, cancer immunotherapy under the intervention of intestinal microbiota has innovatively broadened the anti-tumor landscape and is expected to become an active strategy to enhance individualized responses.
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Flint A, Laidlaw A, Li L, Raitt C, Rao M, Cooper A, Weedmark K, Carrillo C, Tamber S. Choice of DNA extraction method affects detection of bacterial taxa from retail chicken breast. BMC Microbiol 2022; 22:230. [PMID: 36180850 PMCID: PMC9524001 DOI: 10.1186/s12866-022-02650-7] [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: 04/30/2022] [Accepted: 09/14/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sequence-based methods for the detection of bacteria such as 16S rRNA amplicon sequencing and metagenomics can provide a comprehensive view of the bacterial microbiome of food. These methods rely on the detection of gene sequences to indicate the presence of viable bacteria. This indirect form of detection can be prone to experimental artefacts. Sample handling and processing are key sources of variation that require standard approaches. Extracting sufficient quantities of high quality DNA from food matrices is challenging because target bacterial species are usually minor components of the microbiota and foods contain an array of compounds that are inhibitory to downstream DNA applications. Here, three DNA extraction methods are compared for their ability to extract high quality bacterial DNA from retail chicken breast rinses, with or without enrichment. Method performance was assessed by comparing ease of use, DNA yield, DNA quality, PCR amplicon yield, and the detection of bacterial taxa by 16S rRNA amplicon sequencing. RESULTS All three DNA extraction methods yielded DNA of sufficient quantity and quality to perform quantitative PCR and 16S rRNA amplicon sequencing. The extraction methods differed in ease of use, with the two commercial kits (PowerFood, PowerSoil) offering considerable time and cost savings over a hybrid method that used laboratory reagents for lysis and commercial column based kits for further purification. Bacterial richness as determined by 16S rRNA amplicon sequencing was similar across the three DNA extraction methods. However, differences were noted in the relative abundance of bacterial taxa, with significantly higher abundance of Gram-positive genera detected in the DNA samples prepared using the PowerFood DNA extraction kit. CONCLUSION The choice of DNA extraction method can affect the detection of bacterial taxa by 16S rRNA amplicon sequencing in chicken meat rinses. Investigators should be aware of this procedural bias and select methods that are fit for the purposes of their investigation.
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Affiliation(s)
- Annika Flint
- Bureau of Microbial Hazards Health Canada, 251 Sir Frederick Banting Driveway, A.L. 2204E, Ottawa, ON, K1A 0K9, Canada
| | - Anna Laidlaw
- Bureau of Microbial Hazards Health Canada, 251 Sir Frederick Banting Driveway, A.L. 2204E, Ottawa, ON, K1A 0K9, Canada
| | - Leo Li
- Bureau of Microbial Hazards Health Canada, 251 Sir Frederick Banting Driveway, A.L. 2204E, Ottawa, ON, K1A 0K9, Canada
| | - Courtney Raitt
- Bureau of Microbial Hazards Health Canada, 251 Sir Frederick Banting Driveway, A.L. 2204E, Ottawa, ON, K1A 0K9, Canada
| | - Mary Rao
- Bureau of Microbial Hazards Health Canada, 251 Sir Frederick Banting Driveway, A.L. 2204E, Ottawa, ON, K1A 0K9, Canada
| | - Ashley Cooper
- Canadian Food Inspection Agency, 960 Carling Road, Ottawa, ON, K1A 0Z2, Canada
| | - Kelly Weedmark
- Bureau of Microbial Hazards Health Canada, 251 Sir Frederick Banting Driveway, A.L. 2204E, Ottawa, ON, K1A 0K9, Canada
| | - Catherine Carrillo
- Canadian Food Inspection Agency, 960 Carling Road, Ottawa, ON, K1A 0Z2, Canada
| | - Sandeep Tamber
- Bureau of Microbial Hazards Health Canada, 251 Sir Frederick Banting Driveway, A.L. 2204E, Ottawa, ON, K1A 0K9, Canada.
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Matthewman C, Narin A, Huston H, Hopkins CE. Systems to model the personalized aspects of microbiome health and gut dysbiosis. Mol Aspects Med 2022; 91:101115. [PMID: 36104261 DOI: 10.1016/j.mam.2022.101115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 08/03/2022] [Indexed: 01/17/2023]
Abstract
The human gut microbiome is a complex and dynamic microbial entity that interacts with the environment and other parts of the body including the brain, heart, liver, and immune system. These multisystem interactions are highly conserved from invertebrates to humans, however the complexity and diversity of human microbiota compositions often yield a context that is unique to each individual. Yet commonalities remain across species, where a healthy gut microbiome will be rich in symbiotic commensal biota while an unhealthy gut microbiota will be experiencing abnormal blooms of pathobiont bacteria. In this review we discuss how omics technologies can be applied in a personalized approach to understand the microbial crosstalk and microbial-host interactions that affect the delicate balance between eubiosis and dysbiosis in an individual gut microbiome. We further highlight the strengths of model organisms in identifying and characterizing these conserved synergistic and/or pathogenic host-microbe interactions. And finally, we touch upon the growing area of personalized therapeutic interventions targeting gut microbiome.
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Chen J, Wang Y, Shi Y, Liu Y, Wu C, Luo Y. Association of Gut Microbiota With Intestinal Ischemia/Reperfusion Injury. Front Cell Infect Microbiol 2022; 12:962782. [PMID: 35903197 PMCID: PMC9314564 DOI: 10.3389/fcimb.2022.962782] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 06/14/2022] [Indexed: 11/13/2022] Open
Abstract
Intestinal ischemia/reperfusion (II/R) is a common acute and critical condition in clinical practice with a high mortality rate. However, there is still a lack of effective prevention and treatment measures for II/R injury. The role of the gut microbiota in II/R has attracted widespread attention. Recent evidence has demonstrated that the gut microbiota plays a pivotal role in the occurrence, development, and prognosis of II/R. Therefore, maintaining the homeostasis of gut microbiota and its metabolites may be a potential strategy for the treatment of II/R. This review focuses on the importance of crosstalk between the gastrointestinal ecosystem and II/R to highlight II/R-induced gut microbiota signatures and potential applications of microbial-based therapies in II/R. This will also provide potentially effective biomarkers for the prediction, diagnosis and treatment of II/R.
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Affiliation(s)
- Jingyi Chen
- Department of Anesthesiology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
- *Correspondence: Jingyi Chen, ; Yanrong Luo, ; Chengyi Wu,
| | - Yu Wang
- Department of Anesthesiology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Yongxia Shi
- Department of Surgical Nursing, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Yongpan Liu
- Department of Anesthesiology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Chengyi Wu
- Department of Anesthesiology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
- *Correspondence: Jingyi Chen, ; Yanrong Luo, ; Chengyi Wu,
| | - Yanrong Luo
- Physical Examination Center, Shiyan Hospital of Integrated Traditional and Western Medicine, Shiyan, China
- *Correspondence: Jingyi Chen, ; Yanrong Luo, ; Chengyi Wu,
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Schmidt A, Schneider C, Decker P, Hohberg K, Römbke J, Lehmitz R, Bálint M. Shotgun metagenomics of soil invertebrate communities reflects taxonomy, biomass, and reference genome properties. Ecol Evol 2022; 12:e8991. [PMID: 35784064 PMCID: PMC9170594 DOI: 10.1002/ece3.8991] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 05/11/2022] [Accepted: 05/17/2022] [Indexed: 12/03/2022] Open
Abstract
Metagenomics - shotgun sequencing of all DNA fragments from a community DNA extract - is routinely used to describe the composition, structure, and function of microorganism communities. Advances in DNA sequencing and the availability of genome databases increasingly allow the use of shotgun metagenomics on eukaryotic communities. Metagenomics offers major advances in the recovery of biomass relationships in a sample, in comparison to taxonomic marker gene-based approaches (metabarcoding). However, little is known about the factors which influence metagenomics data from eukaryotic communities, such as differences among organism groups, the properties of reference genomes, and genome assemblies.We evaluated how shotgun metagenomics records composition and biomass in artificial soil invertebrate communities at different sequencing efforts. We generated mock communities of controlled biomass ratios from 28 species from all major soil mesofauna groups: mites, springtails, nematodes, tardigrades, and potworms. We shotgun sequenced these communities and taxonomically assigned them with a database of over 270 soil invertebrate genomes.We recovered over 95% of the species, and observed relatively high false-positive detection rates. We found strong differences in reads assigned to different taxa, with some groups (e.g., springtails) consistently attracting more hits than others (e.g., enchytraeids). Original biomass could be predicted from read counts after considering these taxon-specific differences. Species with larger genomes, and with more complete assemblies, consistently attracted more reads than species with smaller genomes. The GC content of the genome assemblies had no effect on the biomass-read relationships. Results were similar among different sequencing efforts.The results show considerable differences in taxon recovery and taxon specificity of biomass recovery from metagenomic sequence data. The properties of reference genomes and genome assemblies also influence biomass recovery, and they should be considered in metagenomic studies of eukaryotes. We show that low- and high-sequencing efforts yield similar results, suggesting high cost-efficiency of metagenomics for eukaryotic communities. We provide a brief roadmap for investigating factors which influence metagenomics-based eukaryotic community reconstructions. Understanding these factors is timely as accessibility of DNA sequencing and momentum for reference genomes projects show a future where the taxonomic assignment of DNA from any community sample becomes a reality.
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Affiliation(s)
- Alexandra Schmidt
- Senckenberg Biodiversity Climate Research CenterFrankfurt am MainGermany
- Biology DepartmentJ.W. Goethe UniversityFrankfurt am MainGermany
- Loewe Center for Translational Biodiversity Genomics (LOEWE‐TBG)Frankfurt am MainGermany
- Limnological Institute (Environmental Genomics)University of KonstanzKonstanzGermany
| | - Clément Schneider
- Loewe Center for Translational Biodiversity Genomics (LOEWE‐TBG)Frankfurt am MainGermany
- Soil Zoology DepartmentSenckenberg Museum of Natural History GörlitzGörlitzGermany
| | - Peter Decker
- Loewe Center for Translational Biodiversity Genomics (LOEWE‐TBG)Frankfurt am MainGermany
- Blumenstr. 5GörlitzGermany
| | - Karin Hohberg
- Loewe Center for Translational Biodiversity Genomics (LOEWE‐TBG)Frankfurt am MainGermany
- Soil Zoology DepartmentSenckenberg Museum of Natural History GörlitzGörlitzGermany
| | - Jörg Römbke
- ECT Oekotoxikologie GmbHFlörsheim am MainGermany
| | - Ricarda Lehmitz
- Loewe Center for Translational Biodiversity Genomics (LOEWE‐TBG)Frankfurt am MainGermany
- Soil Zoology DepartmentSenckenberg Museum of Natural History GörlitzGörlitzGermany
| | - Miklós Bálint
- Senckenberg Biodiversity Climate Research CenterFrankfurt am MainGermany
- Loewe Center for Translational Biodiversity Genomics (LOEWE‐TBG)Frankfurt am MainGermany
- Institute for Insect BiotechnologyJustus Liebig UniversityGießenGermany
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Koorakula R, Ghanbari M, Schiavinato M, Wegl G, Dohm JC, Domig KJ. Storage media and RNA extraction approaches substantially influence the recovery and integrity of livestock fecal microbial RNA. PeerJ 2022; 10:e13547. [PMID: 35694379 PMCID: PMC9186325 DOI: 10.7717/peerj.13547] [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: 06/29/2021] [Accepted: 05/16/2022] [Indexed: 01/17/2023] Open
Abstract
Background There is growing interest in understanding gut microbiome dynamics, to increase the sustainability of livestock production systems and to better understand the dynamics that regulate antibiotic resistance genes (i.e., the resistome). High-throughput sequencing of RNA transcripts (RNA-seq) from microbial communities (metatranscriptome) allows an unprecedented opportunity to analyze the functional and taxonomical dynamics of the expressed microbiome and emerges as a highly informative approach. However, the isolation and preservation of high-quality RNA from livestock fecal samples remains highly challenging. This study aimed to determine the impact of the various sample storage and RNA extraction strategies on the recovery and integrity of microbial RNA extracted from selected livestock (chicken and pig) fecal samples. Methods Fecal samples from pigs and chicken were collected from conventional slaughterhouses. Two different storage buffers were used at two different storage temperatures. The extraction of total RNA was done using four different commercially available kits and RNA integrity/quality and concentration were measured using a Bioanalyzer 2100 system with RNA 6000 Nano kit (Agilent, Santa Clara, CA, USA). In addition, RT-qPCR was used to assess bacterial RNA quality and the level of host RNA contamination. Results The quantity and quality of RNA differed by sample type (i.e., either pig or chicken) and most significantly by the extraction kit, with differences in the extraction method resulting in the least variability in pig feces samples and the most variability in chicken feces. Considering a tradeoff between the RNA yield and the RNA integrity and at the same time minimizing the amount of host RNA in the sample, a combination of storing the fecal samples in RNALater at either 4 °C (for 24 h) or -80 °C (up to 2 weeks) with extraction with PM kit (RNEasy Power Microbiome Kit) had the best performance for both chicken and pig samples. Conclusion Our findings provided a further emphasis on using a consistent methodology for sample storage, duration as well as a compatible RNA extraction approach. This is crucial as the impact of these technical steps can be potentially large compared with the real biological variability to be explained in microbiome and resistome studies.
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Affiliation(s)
- Raju Koorakula
- University of Natural Resources and Life Sciences, Vienna, Department of Food Science and Technology, Institute of Food Science, Vienna, Austria,Competence Centre for Feed and Food Quality, Safety and Innovation (FFoQSI), Tulln an der Donau, Lower Austria, Austria
| | | | - Matteo Schiavinato
- University of Natural Resources and Life Sciences, Vienna, Department of Biotechnology, Institute of Computational Biology, Vienna, Austria
| | | | - Juliane C. Dohm
- University of Natural Resources and Life Sciences, Vienna, Department of Biotechnology, Institute of Computational Biology, Vienna, Austria
| | - Konrad J. Domig
- University of Natural Resources and Life Sciences, Vienna, Department of Food Science and Technology, Institute of Food Science, Vienna, Austria
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Fukui M, Asakuma H, Horiuchi H, Takii H, Yoshioka M, Hinode D. Oral care tablet containing kiwifruit powder affects tongue coating microbiome. Clin Exp Dent Res 2022; 8:721-728. [PMID: 35579104 PMCID: PMC9209808 DOI: 10.1002/cre2.591] [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: 02/18/2022] [Revised: 04/27/2022] [Accepted: 05/01/2022] [Indexed: 11/21/2022] Open
Abstract
Objectives Tongue coating, a kind of biofilm formed on the tongue dorsum, is the cause of various clinical conditions, such as oral halitosis and periodontal diseases, because Fusobacterium nucleatum acts as a bridge between other oral bacteria and periodontopathogenic bacteria in biofilm formation. Our previous clinical study revealed that taking oral care tablets containing kiwifruit powder significantly reduced not only tongue‐coating index and volatile sulfur compounds but also total bacteria and F. nucleatum in tongue coating. In this study, we analyzed the microbiome of tongue coating samples obtained before and after oral care tablets intake to clarify whether this tablet is a useful tool for daily tongue care. Methods Thirty‐two healthy young adults were enrolled, and a crossover clinical trial was conducted. We instructed subjects to remove tongue coating by tongue brush for intervention I, to keep the oral care tablet containing kiwifruit powder on the tongue dorsum and to let it dissolve naturally for intervention II. Microbial DNA was isolated from the collected tongue coating samples in each subject, then 16S rRNA next‐generation sequencing, operational taxonomic unit clustering, and statistical analysis were performed. Results The microbiome analysis revealed that the oral care tablet in intervention II prompted a significant change in the tongue microbiota composition, a significant reduction in the relative abundance of Prevotella and Porphyromonas, and an increase in Firmicutes/Bacteroidetes ratio when compared to that in intervention I. Conclusion These results suggested that the oral care tablet might contribute to the improvement of the oral condition due to its good influence on the tongue coating microbiome.
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Affiliation(s)
- Makoto Fukui
- Department of Hygiene and Oral Health Science, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan
| | - Hiroki Asakuma
- Applied Research Laboratory, Ezaki Glico Co., Ltd., Osaka, Japan
| | - Hiroko Horiuchi
- Applied Research Laboratory, Ezaki Glico Co., Ltd., Osaka, Japan
| | - Hiroshi Takii
- Research Promotion and Management Office, Ezaki Glico Co., Ltd., Osaka, Japan
| | - Masami Yoshioka
- Faculty of Health and Welfare, Tokushima Bunri University, Tokushima, Japan
| | - Daisuke Hinode
- Department of Hygiene and Oral Health Science, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan
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Characterization and Demonstration of Mock Communities as Control Reagents for Accurate Human Microbiome Community Measurements. Microbiol Spectr 2022; 10:e0191521. [PMID: 35234490 PMCID: PMC8941912 DOI: 10.1128/spectrum.01915-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Standardization and quality assurance of microbiome community analysis by high-throughput DNA sequencing require widely accessible and well-characterized reference materials. Here, we report on newly developed DNA and whole-cell mock communities to serve as control reagents for human gut microbiota measurements by shotgun metagenomics and 16S rRNA gene amplicon sequencing. The mock communities were formulated as near-even blends of up to 20 bacterial species prevalent in the human gut, span a wide range of genomic guanine-cytosine (GC) contents, and include multiple strains with Gram-positive type cell walls. Through a collaborative study, we carefully characterized the mock communities by shotgun metagenomics, using previously developed standardized protocols for DNA extraction and sequencing library construction. Further, we validated fitness of the mock communities for revealing technically meaningful differences among protocols for DNA extraction and metagenome/16S rRNA gene amplicon library construction. Finally, we used the mock communities to reveal varying performance of metagenome-based taxonomic profilers and the impact of trimming and filtering of sequencing reads on observed species profiles. The latter showed that aggressive preprocessing of reads may result in substantial GC-dependent bias and should thus be carefully evaluated to minimize unintended effects on species abundances. Taken together, the mock communities are expected to support a myriad of applications that rely on well-characterized control reagents, ranging from evaluation and optimization of methods to assessment of reproducibility in interlaboratory studies and routine quality control. IMPORTANCE Application of high-throughput DNA sequencing has greatly accelerated human microbiome research and its translation into new therapeutic and diagnostic capabilities. Microbiome community analyses results can, however, vary considerably across studies or laboratories, and establishment of measurement standards to improve accuracy and reproducibility has become a priority. The here-developed mock communities, which are available from the NITE Biological Resource Center (NBRC) at the National Institute of Technology and Evaluation (NITE, Japan), provide well-characterized control reagents that allow users to judge the accuracy of their measurement results. Widespread and consistent adoption of the mock communities will improve reproducibility and comparability of microbiome community analyses, thereby supporting and accelerating human microbiome research and development.
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Takeuchi H, Yoshikane Y, Takenaka H, Kimura A, Islam JM, Matsuda R, Okamoto A, Hashimoto Y, Yano R, Yamaguchi K, Sato S, Ishizuka S. Health Effects of Drinking Water Produced from Deep Sea Water: A Randomized Double-Blind Controlled Trial. Nutrients 2022; 14:nu14030581. [PMID: 35276942 PMCID: PMC8839038 DOI: 10.3390/nu14030581] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/15/2022] [Accepted: 01/20/2022] [Indexed: 02/05/2023] Open
Abstract
Global trends focus on a balanced intake of foods and beverages to maintain health. Drinking water (MIU; hardness = 88) produced from deep sea water (DSW) collected offshore of Muroto, Japan, is considered healthy. We previously reported that the DSW-based drinking water (RDSW; hardness = 1000) improved human gut health. The aim of this randomized double-blind controlled trial was to assess the effects of MIU on human health. Volunteers were assigned to MIU (n = 41) or mineral water (control) groups (n = 41). Participants consumed 1 L of either water type daily for 12 weeks. A self-administered questionnaire was administered, and stool and urine samples were collected throughout the intervention. We measured the fecal biomarkers of nine short-chain fatty acids (SCFAs) and secretory immunoglobulin A (sIgA), as well as urinary isoflavones. In the MIU group, concentrations of three major SCFAs and sIgA increased postintervention. MIU intake significantly affected one SCFA (butyric acid). The metabolic efficiency of daidzein-to-equol conversion was significantly higher in the MIU group than in the control group throughout the intervention. MIU intake reflected the intestinal environment through increased production of three major SCFAs and sIgA, and accelerated daidzein-to-equol metabolic conversion, suggesting the beneficial health effects of MIU.
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Affiliation(s)
- Hiroaki Takeuchi
- Department of Medical Laboratory Sciences, Health and Sciences, International University of Health and Welfare Graduate School, 4-3 Kouzunomori, Narita-City 286-8686, Chiba, Japan; (A.K.); (J.M.I.); (R.M.); (A.O.); (Y.H.); (R.Y.); (K.Y.); (S.S.)
- Correspondence: ; Tel.: +81-476-20-7762
| | - Yu Yoshikane
- Department of Human Living Sciences, Notre Dame Seishin University, 2-16-9 Ifuku-cho, Kita-ku, Okayama-city 700-8516, Okayama, Japan;
| | - Hirotsugu Takenaka
- DyDo-T Beverage Co. Ltd., 1310-1 Hanechou-ko, Muroto-City 781-6741, Kochi, Japan;
| | - Asako Kimura
- Department of Medical Laboratory Sciences, Health and Sciences, International University of Health and Welfare Graduate School, 4-3 Kouzunomori, Narita-City 286-8686, Chiba, Japan; (A.K.); (J.M.I.); (R.M.); (A.O.); (Y.H.); (R.Y.); (K.Y.); (S.S.)
| | - Jahirul Md. Islam
- Department of Medical Laboratory Sciences, Health and Sciences, International University of Health and Welfare Graduate School, 4-3 Kouzunomori, Narita-City 286-8686, Chiba, Japan; (A.K.); (J.M.I.); (R.M.); (A.O.); (Y.H.); (R.Y.); (K.Y.); (S.S.)
| | - Reimi Matsuda
- Department of Medical Laboratory Sciences, Health and Sciences, International University of Health and Welfare Graduate School, 4-3 Kouzunomori, Narita-City 286-8686, Chiba, Japan; (A.K.); (J.M.I.); (R.M.); (A.O.); (Y.H.); (R.Y.); (K.Y.); (S.S.)
| | - Aoi Okamoto
- Department of Medical Laboratory Sciences, Health and Sciences, International University of Health and Welfare Graduate School, 4-3 Kouzunomori, Narita-City 286-8686, Chiba, Japan; (A.K.); (J.M.I.); (R.M.); (A.O.); (Y.H.); (R.Y.); (K.Y.); (S.S.)
| | - Yusuke Hashimoto
- Department of Medical Laboratory Sciences, Health and Sciences, International University of Health and Welfare Graduate School, 4-3 Kouzunomori, Narita-City 286-8686, Chiba, Japan; (A.K.); (J.M.I.); (R.M.); (A.O.); (Y.H.); (R.Y.); (K.Y.); (S.S.)
| | - Rie Yano
- Department of Medical Laboratory Sciences, Health and Sciences, International University of Health and Welfare Graduate School, 4-3 Kouzunomori, Narita-City 286-8686, Chiba, Japan; (A.K.); (J.M.I.); (R.M.); (A.O.); (Y.H.); (R.Y.); (K.Y.); (S.S.)
| | - Koichi Yamaguchi
- Department of Medical Laboratory Sciences, Health and Sciences, International University of Health and Welfare Graduate School, 4-3 Kouzunomori, Narita-City 286-8686, Chiba, Japan; (A.K.); (J.M.I.); (R.M.); (A.O.); (Y.H.); (R.Y.); (K.Y.); (S.S.)
| | - Shouichi Sato
- Department of Medical Laboratory Sciences, Health and Sciences, International University of Health and Welfare Graduate School, 4-3 Kouzunomori, Narita-City 286-8686, Chiba, Japan; (A.K.); (J.M.I.); (R.M.); (A.O.); (Y.H.); (R.Y.); (K.Y.); (S.S.)
| | - Satoshi Ishizuka
- Center for Regional Sustainability and Innovation, Kochi University, 2-17-47 Asakurahonmachi, Kochi-City 780-8073, Kochi, Japan;
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Habitual Dietary Intake Affects the Altered Pattern of Gut Microbiome by Acarbose in Patients with Type 2 Diabetes. Nutrients 2021; 13:nu13062107. [PMID: 34205413 PMCID: PMC8235473 DOI: 10.3390/nu13062107] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/16/2021] [Accepted: 06/16/2021] [Indexed: 02/07/2023] Open
Abstract
The aim of this research was to reveal the characteristics of gut microbiome altered by acarbose intervention in Japanese patients with type 2 diabetes (T2D) and its possible association with habitual dietary intake. Eighteen patients with T2D were administered acarbose for four weeks. The abundances of two major phyla, namely Actinobacteria and Bacteroidetes, were reciprocally changed accompanied by the acarbose intervention. There were also significant changes in the abundances of ten genera, including the greater abundance of Bifidobacterium, Eubacterium, and Lactobacillus and the lower abundance of Bacteroides in the group after the intervention than that before the intervention. Hierarchical clustering of habitual dietary intake was performed based on the pattern of changes in the gut microbiota and were classified into distinct three clusters. Cluster I consisted of sucrose, cluster II mainly included fat intake, and cluster III mainly included carbohydrate intake. Moreover, the amount of change in Faecalibacterium was positively correlated with the intake of rice, but negatively correlated with the intake of bread. The intake of potato was negatively correlated with the amount of change in Akkermansia and Subdoligranulum. Acarbose altered the composition of gut microbiome in Japanese patients with T2D, which might be linked to the habitual dietary intake.
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