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Tannock GW. Understanding the gut microbiota by considering human evolution: a story of fire, cereals, cooking, molecular ingenuity, and functional cooperation. Microbiol Mol Biol Rev 2024; 88:e0012722. [PMID: 38126754 PMCID: PMC10966955 DOI: 10.1128/mmbr.00127-22] [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] [Indexed: 12/23/2023] Open
Abstract
SUMMARYThe microbial community inhabiting the human colon, referred to as the gut microbiota, is mostly composed of bacterial species that, through extensive metabolic networking, degrade and ferment components of food and human secretions. The taxonomic composition of the microbiota has been extensively investigated in metagenomic studies that have also revealed details of molecular processes by which common components of the human diet are metabolized by specific members of the microbiota. Most studies of the gut microbiota aim to detect deviations in microbiota composition in patients relative to controls in the hope of showing that some diseases and conditions are due to or exacerbated by alterations to the gut microbiota. The aim of this review is to consider the gut microbiota in relation to the evolution of Homo sapiens which was heavily influenced by the consumption of a nutrient-dense non-arboreal diet, limited gut storage capacity, and acquisition of skills relating to mastering fire, cooking, and cultivation of cereal crops. The review delves into the past to gain an appreciation of what is important in the present. A holistic view of "healthy" microbiota function is proposed based on the evolutionary pathway shared by humans and gut microbes.
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Affiliation(s)
- Gerald W. Tannock
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
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Yuan C, Xu W, Zhao C, Gao W, Wu G. Case Report: Detection of Treponema phagedenis in cerebrospinal fluid of a neurosyphilis patient by metagenomic next-generation sequencing. Front Cell Infect Microbiol 2023; 13:1218049. [PMID: 37712061 PMCID: PMC10497860 DOI: 10.3389/fcimb.2023.1218049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 08/11/2023] [Indexed: 09/16/2023] Open
Abstract
Treponema phagedenis, a human commensal spirochete, has been reported world-wide as a key factor in the pathogenesis of bovine digital dermatitis. Here we report a case of T. phagedenis sequence detection in the cerebrospinal fluid (CSF) of a patient. The patient was diagnosed with neurosyphilis, and T. phagedenis was detected as the only microorganism in his CSF by metagenomic sequencing. The patient went through a round of penicillin therapy previously (2.4 million units of Benzathine Penicillin intramuscularly once a week for three weeks) that did not resolve the symptoms; after the diagnosis of neurosyphilis he was treated with Penicillin G Sodium 4.0 million units q4h intravenous for 14 days then his symptoms resolved. To the best of our knowledge, T. phagedenis has never been reported to be detected in a human's CSF before. This was also the first time it was detected by metagenomic next-generation sequencing. We propose that more etiological tests should be performed including culture and sequencing for more patients with syphilis, which will contribute to a deeper understanding of the pathogenicity of the spirochete.
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Affiliation(s)
- Chenyan Yuan
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing, Jiangsu, China
- Department of Laboratory Medicine, Medical School of Southeast University, Nanjing, Jiangsu, China
| | - Wei Xu
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing, Jiangsu, China
- Department of Laboratory Medicine, Medical School of Southeast University, Nanjing, Jiangsu, China
| | - Chenggui Zhao
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing, Jiangsu, China
- Department of Laboratory Medicine, Medical School of Southeast University, Nanjing, Jiangsu, China
| | - Wei Gao
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing, Jiangsu, China
- Department of Laboratory Medicine, Medical School of Southeast University, Nanjing, Jiangsu, China
| | - Guoqiu Wu
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing, Jiangsu, China
- Department of Laboratory Medicine, Medical School of Southeast University, Nanjing, Jiangsu, China
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Southeast University, Nanjing, Jiangsu, China
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Carter MM, Olm MR, Merrill BD, Dahan D, Tripathi S, Spencer SP, Yu FB, Jain S, Neff N, Jha AR, Sonnenburg ED, Sonnenburg JL. Ultra-deep sequencing of Hadza hunter-gatherers recovers vanishing gut microbes. Cell 2023; 186:3111-3124.e13. [PMID: 37348505 PMCID: PMC10330870 DOI: 10.1016/j.cell.2023.05.046] [Citation(s) in RCA: 44] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 02/12/2023] [Accepted: 05/26/2023] [Indexed: 06/24/2023]
Abstract
The gut microbiome modulates immune and metabolic health. Human microbiome data are biased toward industrialized populations, limiting our understanding of non-industrialized microbiomes. Here, we performed ultra-deep metagenomic sequencing on 351 fecal samples from the Hadza hunter-gatherers of Tanzania and comparative populations in Nepal and California. We recovered 91,662 genomes of bacteria, archaea, bacteriophages, and eukaryotes, 44% of which are absent from existing unified datasets. We identified 124 gut-resident species vanishing in industrialized populations and highlighted distinct aspects of the Hadza gut microbiome related to in situ replication rates, signatures of selection, and strain sharing. Industrialized gut microbes were found to be enriched in genes associated with oxidative stress, possibly a result of microbiome adaptation to inflammatory processes. This unparalleled view of the Hadza gut microbiome provides a valuable resource, expands our understanding of microbes capable of colonizing the human gut, and clarifies the extensive perturbation induced by the industrialized lifestyle.
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Affiliation(s)
- Matthew M Carter
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Matthew R Olm
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Bryan D Merrill
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Dylan Dahan
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Surya Tripathi
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Sean P Spencer
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Feiqiao B Yu
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Sunit Jain
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Norma Neff
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Aashish R Jha
- Genetic Heritage Group, Program in Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Erica D Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA.
| | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Center for Human Microbiome Studies, Stanford University School of Medicine, Stanford, CA 94304, USA.
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Munson E, Carroll KC. Update on Accepted Novel Bacterial Isolates Derived from Human Clinical Specimens and Taxonomic Revisions Published in 2020 and 2021. J Clin Microbiol 2023; 61:e0028222. [PMID: 36533910 PMCID: PMC9879126 DOI: 10.1128/jcm.00282-22] [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] [Indexed: 12/23/2022] Open
Abstract
A number of factors, including microbiome analyses and the increased utilization of whole-genome sequencing in the clinical microbiology laboratory, has contributed to the explosion of novel prokaryotic species discovery, as well as bacterial taxonomy revision. This review attempts to summarize such changes relative to human clinical specimens that occurred in 2020 and 2021, per primary publication in the International Journal of Systematic and Evolutionary Microbiology or acceptance on Validation Lists published by the International Journal of Systematic and Evolutionary Microbiology. Of particular significance among valid and effectively published taxa within the past 2 years were novel Corynebacterium spp., coagulase-positive staphylococci, Pandoraea spp., and members of family Yersiniaceae. Noteworthy taxonomic revisions include those within the Bacillus and Lactobacillus genera, family Staphylococcaceae (including unifications of subspecies designations to species level taxa), Elizabethkingia spp., and former members of Clostridium spp. and Bacteroides spp. Revisions within the Brucella genus have the potential to cause deleterious effects unless the relevance of such changes is properly communicated by microbiologists to stakeholders in clinical practice, infection prevention, and public health.
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Affiliation(s)
- Erik Munson
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
| | - Karen C. Carroll
- Division of Medical Microbiology, Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Lee SA, Kim M, Kim HS, Ahn CY. Extra benefit of microalgae in raw piggery wastewater treatment: pathogen reduction. MICROBIOME 2022; 10:142. [PMID: 36045433 PMCID: PMC9429445 DOI: 10.1186/s40168-022-01339-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 07/28/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Monitoring microbial communities especially focused on pathogens in newly developed wastewater treatment systems is recommended for public health. Thus, we investigated the microbial community shift in a pilot-scale microalgal treatment system for piggery wastewater. RESULTS Microalgae showed reasonable removal efficiencies for COD and ammonia, resulting in higher transparency of the final effluent. Metagenome and microbial diversity analyses showed that heterotrophic microalgal cultivation barely changed the bacterial community; however, the mixotrophic microalgal cultivation induced a sudden change. In addition, an evaluation of risk groups (RGs) of bacteria showed that raw piggery wastewater included abundant pathogens, and the microalgal treatment of the raw piggery wastewater decreased the RG2 pathogens by 63%. However, co-cultivation of microalgae and the most dominant RG2 pathogen, Oligella, showed no direct effects between them. CONCLUSIONS Thus, a microbial interaction network was constructed to elucidate algae-bacteria interrelationships, and the decrease in Oligella was indirectly connected with microalgal growth via Brevundimonas, Sphingopyxis, and Stenotrophomonas. In a validation test, 3 among 4 connecting bacterial strains exhibited inhibition zones against Oligella. Therefore, we showed that microalgal wastewater treatment causes a decrease in RG2 bacteria, which is an indirect impact of microalgae associated with bacteria. Video abstract.
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Affiliation(s)
- Sang-Ah Lee
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
- Environmental Safety Group, Korea Institute of Science and Technology (KIST) Europe, 66123, Saarbrücken, Germany
| | - Minsik Kim
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Hee-Sik Kim
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Chi-Yong Ahn
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
- Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, 34113, Republic of Korea.
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Merrill BD, Carter MM, Olm MR, Dahan D, Tripathi S, Spencer SP, Yu B, Jain S, Neff N, Jha AR, Sonnenburg ED, Sonnenburg JL. Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Microbes.. [PMID: 36238714 PMCID: PMC9558438 DOI: 10.1101/2022.03.30.486478] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The gut microbiome is a key modulator of immune and metabolic health. Human microbiome data is biased towards industrialized populations, providing limited understanding of the distinct and diverse non-industrialized microbiomes. Here, we performed ultra-deep metagenomic sequencing and strain cultivation on 351 fecal samples from the Hadza, hunter-gatherers in Tanzania, and comparative populations in Nepal and California. We recover 94,971 total genomes of bacteria, archaea, bacteriophages, and eukaryotes, 43% of which are absent from existing unified datasets. Analysis of in situ growth rates, genetic pN/pS signatures, high-resolution strain tracking, and 124 gut-resident species vanishing in industrialized populations reveals differentiating dynamics of the Hadza gut microbiome. Industrialized gut microbes are enriched in genes associated with oxidative stress, possibly a result of microbiome adaptation to inflammatory processes. This unparalleled view of the Hadza gut microbiome provides a valuable resource that expands our understanding of microbes capable of colonizing the human gut and clarifies the extensive perturbation brought on by the industrialized lifestyle.
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