Diversity and Prevalence of Clostridium innocuum in the Human Gut Microbiota.
Diversity and Prevalence of Clostridium innocuum in the Human Gut Microbiota.
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梭状芽孢杆菌是厚壁菌门中革兰氏阳性、孢子形成的厌氧菌的多系群，显著影响人体胃肠道的代谢和功能。最近，基于表型和基于16S rRNA基因的差异，将梭状芽孢杆菌分为梭状芽孢杆菌和赤藓菌两大类。虽然梭状芽胞杆菌包括许多众所周知的致病菌，丹毒毛菌仍然相对不明确，特别是关于它们作为病原体与共生菌的作用。尽管被广泛认为是一种共生菌，但无毒梭菌（Clostridium innocuum）最近与各种疾病状态有关。为了进一步了解无毒梭菌的生态和潜在毒力作用，我们对38株无毒梭菌分离株和194个公开的基因组进行了基因组比较。根据菌落形态，我们从健康志愿者（n = 5）的粪便中分离出多个无毒梭菌品种。将我们的分离株的16S rRNA基因与健康个体中公开可获得的微生物群数据集进行比较，表明在人群中无害梭菌的患病率很高（bbb80 %）。核心基因的单核苷酸多态性（SNPs）和平均核苷酸鉴定（ANI）分析显示，在所有可用基因组中存在4个支系（n = 232）。碳水化合物和蛋白质利用途径的研究，包括与碳水化合物激活酶（CAZyme）数据库的比较，证明了种间和种内的差异，并在体外得到进一步证实。综上所述，这些数据表明了无毒梭菌物种的遗传变异，这可能有助于阐明其在人类疾病和健康中的作用。梭状芽胞杆菌是一类医学上重要的厌氧菌，既是共生体又是病原体。最近，出现了一类新的丹毒毛菌，其中包括一些重新分配的梭状芽孢杆菌，包括无芽梭状芽孢杆菌。最近的研究表明，在难辨梭菌无法分离的患者中，无芽梭菌是一种潜在的腹泻病原体。利用基因组和体外比较，本研究试图在健康的人类肠道中表征无害梭菌。我们的分析表明，C. innocuum是一个高度流行和多样化的物种，显示出进化枝特异性的代谢和潜在的毒力差异。总的来说，这项研究是第一次对C. innocuum作为人类肠道居民进行更广泛描述的调查。
Clostridia are a polyphyletic group of Gram-positive, spore-forming anaerobes in the Firmicutes phylum that significantly impact metabolism and functioning of the human gastrointestinal tract. Recently, Clostridia were divided into two separate classes, Clostridia and Erysipelotrichia, based on phenotypic and 16S rRNA gene-based differences. While Clostridia include many well-known pathogenic bacteria, Erysipelotrichia remain relatively uncharacterized, particularly regarding their role as a pathogen versus commensal. Despite wide recognition as a commensal, the erysipelotrichial species Clostridium innocuum has recently been associated with various disease states. To further understand the ecological and potential virulent role of C. innocuum, we conducted a genomic comparison across 38 C. innocuum isolates and 194 publicly available genomes. Based on colony morphology, we isolated multiple C. innocuum cultivars from the feces of healthy human volunteers (n = 5). Comparison of the 16S rRNA gene of our isolates against publicly available microbiota data sets in healthy individuals suggests a high prevalence of C. innocuum across the human population (>80%). Analysis of single nucleotide polymorphisms (SNPs) across core genes and average nucleotide identify (ANI) revealed the presence of four clades among all available genomes (n = 232 total). Investigation of carbohydrate and protein utilization pathways, including comparison against the carbohydrate-activating enzyme (CAZyme) database, demonstrated inter- and intraclade differences that were further substantiated in vitro. Collectively, these data indicate genetic variance within the C. innocuum species that may help clarify its role in human disease and health. IMPORTANCE Clostridia are a group of medically important anaerobes as both commensals and pathogens. Recently, a new class of Erysipelotrichia containing a number of reassigned clostridial species has emerged, including Clostridium innocuum. Recent studies have implicated C. innocuum as a potential causative agent of diarrhea in patients from whom Clostridioides difficile could not be isolated. Using genomic and in vitro comparison, this study sought to characterize C. innocuum in the healthy human gut. Our analyses suggest that C. innocuum is a highly prevalent and diverse species, demonstrating clade-specific differences in metabolism and potential virulence. Collectively, this study is the first investigation into a broader description of C. innocuum as a human gut inhabitant.
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