AnaerobePub Date : 2026-03-01Epub Date: 2026-01-23DOI: 10.1016/j.anaerobe.2026.103027
Noureddine Bouras , Guendouz Dif , Saïd Belghit , Scott V. Nguyen , Jonathan L. Jacobs , Omrane Toumatia , Sherif S. Ebada , Imen Nouioui
{"title":"Genome-based reclassification of the genus Thermoanaerobacter: taxonomic emendations and new combinations","authors":"Noureddine Bouras , Guendouz Dif , Saïd Belghit , Scott V. Nguyen , Jonathan L. Jacobs , Omrane Toumatia , Sherif S. Ebada , Imen Nouioui","doi":"10.1016/j.anaerobe.2026.103027","DOIUrl":"10.1016/j.anaerobe.2026.103027","url":null,"abstract":"<div><h3>Objective</h3><div>The genus <em>Thermoanaerobacter</em> is comprised of strictly anaerobic, thermophilic, rod-shaped bacteria predominantly isolated from geothermal environments. Due to phylogenetic and taxonomic overlaps among certain species, this study aims to clarify the taxonomic status of key <em>Thermoanaerobacter</em> members through genome-based analyses.</div></div><div><h3>Methods</h3><div>We conducted a comprehensive taxonomic re-evaluation using multiple genomic metrics, including digital DNA-DNA hybridization (dDDH), average nucleotide identity (ANI via FastANI), average amino acid identity (AAI), and percentage of conserved proteins (POCP). These analyses were supported by 16S rRNA gene sequencing and genome-based phylogenomic reconstruction.</div></div><div><h3>Results</h3><div>Genome-based metrics and phylogenomic analyses revealed several taxonomic inconsistencies within the genus. As a result, <em>Thermoanaerobacter thermohydrosulfuricus</em> is redefined to include <em>Thermoanaerobacter ethanolicus</em> subsp. <em>thermohydrosulfuricus</em>, <em>Thermoanaerobacter ethanolicus</em> subsp. <em>siderophilus</em>, <em>Thermoanaerobacter ethanolicus</em> subsp. <em>ethanolicus</em> and <em>Thermoanaerobacter ethanolicus</em> subsp. <em>indiensis</em> under <em>Thermoanaerobacter thermohydrosulfuricus</em> subsp. <em>thermohydrosulfuricus</em> subsp. nov., while <em>Thermoanaerobacter wiegelii</em> is assigned to <em>Thermoanaerobacter thermohydrosulfuricus</em> subsp. <em>wiegelii</em> subsp. nov., comb. nov. <em>Thermoanaerobacter pseudethanolicus</em>, <em>Thermoanaerobacter brockii</em> subsp. <em>finnii</em>, and <em>Thermoanaerobacter brockii</em> subsp. <em>lactiethylicus</em> DSM 9801<sup>T</sup> were reclassified as <em>Thermoanaerobacter brockii</em>. Additionally, <em>Thermoanaerobacter mathranii</em>, <em>Thermoanaerobacter italicus</em>, and <em>Thermoanaerobacter pentosaceus</em> are reclassified as <em>Thermoanaerobacter thermocopriae</em>.</div></div><div><h3>Conclusions</h3><div>This study supports a taxonomic rearrangement within <em>Thermoanaerobacter</em>, refining species boundaries based on robust genomic evidence. The proposed changes enhance the taxonomic resolution and phylogenetic consistency of thermophilic anaerobic bacteria within this genus.</div></div>","PeriodicalId":8050,"journal":{"name":"Anaerobe","volume":"97 ","pages":"Article 103027"},"PeriodicalIF":2.6,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146045954","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
AnaerobePub Date : 2026-03-01Epub Date: 2026-01-30DOI: 10.1016/j.anaerobe.2026.103024
Marion Dutkiewicz , József Sóki , Etienne Ruppé
{"title":"Beta-lactamases in anaerobic, intestinal bacteria: a narrative review","authors":"Marion Dutkiewicz , József Sóki , Etienne Ruppé","doi":"10.1016/j.anaerobe.2026.103024","DOIUrl":"10.1016/j.anaerobe.2026.103024","url":null,"abstract":"<div><div>Anaerobic bacteria in the human intestinal microbiota play a pivotal role in antibiotic resistance, primarily through the production of β-lactamases. This narrative review explores the diversity of β-lactamases found in intestinal anaerobes, their functional characteristics, and clinical implications. Species of the genus <em>Bacteroides</em> are major producers, harboring enzymes from Ambler classes A (e.g. CepA, CfxA and CblA), B (e.g. CfiA and CcrA) and D (e.g. OXA-347), with activity ranging from cephalosporinases to carbapenemases and oxacillinases. Other gut members, including <em>Clostridioides difficile</em>, <em>Fusobacterium nucleatum</em>, and <em>Acidaminococcus fermentans</em>, also encode specific β-lactamases. These enzymes contribute to microbiota resilience following β-lactam exposure and can protect neighboring bacteria via extracellular degradation. This protective mechanism has inspired therapeutic applications, such as recombinant β-lactamases (ribaxamase, SYN-006) designed to preserve gut integrity during antibiotic therapy. Understanding these intrinsic resistance mechanisms is essential for optimizing antibiotic stewardship and mitigating the spread of resistance genes.</div></div>","PeriodicalId":8050,"journal":{"name":"Anaerobe","volume":"97 ","pages":"Article 103024"},"PeriodicalIF":2.6,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146099575","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
AnaerobePub Date : 2026-03-01Epub Date: 2026-01-23DOI: 10.1016/j.anaerobe.2026.103026
Fredrik Hammarskjöld , Knut Taxbro , Catarina Alkemark , Anneli Hammarskjöld , Cecilia Magnusson , Sara Mernelius
{"title":"Clostridioides difficile infection in patients with COVID-19 pneumonia - Analysis of occurrence and genetic distribution from three intensive care units","authors":"Fredrik Hammarskjöld , Knut Taxbro , Catarina Alkemark , Anneli Hammarskjöld , Cecilia Magnusson , Sara Mernelius","doi":"10.1016/j.anaerobe.2026.103026","DOIUrl":"10.1016/j.anaerobe.2026.103026","url":null,"abstract":"<div><h3>Background</h3><div>The Coronavirus Disease 2019 (COVID-19) pandemic challenged several of the well-known routines to prevent <em>Clostridioides difficile</em> infection (CDI) in intensive care units (ICUs). There are limited data evaluating CDI in ICU patients with COVID-19 pneumonia and acute respiratory distress syndrome. The objective of this study was to determine the occurrence of CDI and possible transmission of <em>C. difficile</em> within three ICUs in patients with COVID-19 pneumonia.</div></div><div><h3>Methods</h3><div>A retrospective analysis was conducted on all patients with confirmed COVID-19 pneumonia treated in the ICU between March 14, 2020 and July 31, 2021. All patients were assessed for the presence of diarrhoea, as well as for positive <em>C. difficile</em> antigen analysis. <em>C. difficile</em> isolates underwent high molecular weight (HMW) typing and whole genome sequencing (WGS) for the assessment of transmission.</div></div><div><h3>Results</h3><div>A total of 343 patients were treated in the ICUs during the study period. Diarrhoea was observed in 219 (63.8 %) patients, and 8 patients (2.3 %) were diagnosed with CDI. No evidence of transmission between patients was seen.</div></div><div><h3>Conclusion</h3><div>This study reveals a low occurrence of CDI in ICU patients with COVID-19 pneumonia. WGS was superior to HMW-typing in evaluating potential transmission.</div></div>","PeriodicalId":8050,"journal":{"name":"Anaerobe","volume":"97 ","pages":"Article 103026"},"PeriodicalIF":2.6,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146045848","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
AnaerobePub Date : 2026-03-01Epub Date: 2026-02-14DOI: 10.1016/j.anaerobe.2026.103033
{"title":"Expression of concern: \"Pyrosequencing study of fecal microflora of autistic and control children\".","authors":"","doi":"10.1016/j.anaerobe.2026.103033","DOIUrl":"https://doi.org/10.1016/j.anaerobe.2026.103033","url":null,"abstract":"","PeriodicalId":8050,"journal":{"name":"Anaerobe","volume":"97 ","pages":"103033"},"PeriodicalIF":2.6,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147466946","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
AnaerobePub Date : 2026-03-01Epub Date: 2025-11-29DOI: 10.1016/j.anaerobe.2025.103017
Slim Hmidi , Sophie Edouard , Jérémy Delerce , Aurélia Caputo , Carine Couderc , Simon Robinne , Pierre-Edouard Fournier , Anthony Levasseur , Hervé Chaudet , Nadim Cassir
{"title":"MALDI-TOF mass spectrometry coupled with machine learning: an accurate tool to detect toxigenic Clostridioides difficile strains","authors":"Slim Hmidi , Sophie Edouard , Jérémy Delerce , Aurélia Caputo , Carine Couderc , Simon Robinne , Pierre-Edouard Fournier , Anthony Levasseur , Hervé Chaudet , Nadim Cassir","doi":"10.1016/j.anaerobe.2025.103017","DOIUrl":"10.1016/j.anaerobe.2025.103017","url":null,"abstract":"<div><h3>Purpose</h3><div><em>Clostridioides difficile</em> infection (CDI) is one of the most common healthcare-associated infections, causing significant morbidity and mortality. A CDI diagnosis involves a clinical assessment and laboratory testing. This study aimed to evaluate the effectiveness of MALDI-TOF mass spectrometry in identifying toxigenic <em>C. difficile</em> strains.</div></div><div><h3>Methods</h3><div>From May 2019 to March 2024, all clinical samples received for <em>C. difficile</em> and toxins testing by PCR were also tested by culture under anaerobic conditions. At least one MALDI-TOF spectrum was used to identify all the <em>C. difficile</em> strains that were isolated. Whole genome sequencing was then performed to characterise the <em>C. difficile</em> isolates by searching for toxin genes. Machine learning and deep learning algorithms were used to distinguish between toxigenic and non-toxigenic <em>C. difficile</em> strains.</div></div><div><h3>Results</h3><div>A total of 389 <em>C. difficile</em> strains, isolated from the stools of 315 patients, were analyzed. Of these, 249 were toxigenic (225 ToxA + B + CDT−, 22 ToxA + B + CDT+, and 2 ToxA−B + CDT+), and 140 were non-toxigenic (ToxA−B−CDT−). The support vector machine algorithm produced the most accurate results (91.5 % accuracy and a κ value of 0.831) with high sensitivity (93.1 %) and specificity (90 %), as well as high positive and negative predictive values (PPV of 90.3 % and NPV of 92.3 %, respectively). The random forest algorithm demonstrated accuracies as high as 87.7 %.</div></div><div><h3>Conclusions</h3><div>Supervised machine learning paves the way for inexpensive and easy-to-use alternative methods that enable the use of MALDI-TOF MS to recognise toxigenic and non-toxigenic <em>C. difficile</em> strains.</div></div>","PeriodicalId":8050,"journal":{"name":"Anaerobe","volume":"97 ","pages":"Article 103017"},"PeriodicalIF":2.6,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145653480","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
AnaerobePub Date : 2026-03-01Epub Date: 2026-02-12DOI: 10.1016/j.anaerobe.2026.103032
Ana Cláudia Norte , Miguel A. Carretero , Luís P. da Silva , Gregorio Moreno-Rueda , Jorge Garrido-Bautista , Francisco Javier Zamora-Camacho , Mar Comas , Fernando Gómez-Ramirez , Catarina Rato , Jaime A. Ramos , Afonso Rocha , El-Mustapha Laghzaoui , Rodrigo Megía-Palma , Emilio Civantos , M. Sofia Núncio , Isabel Lopes de Carvalho , Volker Fingerle , Gabriele Margos
{"title":"Vertebrate host or tick vector? Which is to blame for Borrelia lusitaniae population structure?","authors":"Ana Cláudia Norte , Miguel A. Carretero , Luís P. da Silva , Gregorio Moreno-Rueda , Jorge Garrido-Bautista , Francisco Javier Zamora-Camacho , Mar Comas , Fernando Gómez-Ramirez , Catarina Rato , Jaime A. Ramos , Afonso Rocha , El-Mustapha Laghzaoui , Rodrigo Megía-Palma , Emilio Civantos , M. Sofia Núncio , Isabel Lopes de Carvalho , Volker Fingerle , Gabriele Margos","doi":"10.1016/j.anaerobe.2026.103032","DOIUrl":"10.1016/j.anaerobe.2026.103032","url":null,"abstract":"<div><h3>Objective</h3><div><em>Borrelia lusitaniae</em> is a lizard-associated spirochaete which shows highly genetically structured populations in western Europe. Our objective was to assess whether selective forces acting on the <em>Ixodes</em> tick vector or the reservoir lizard, <em>Psammodromus algirus</em>, shaped its population structure.</div></div><div><h3>Methods</h3><div>We collected ticks feeding on <em>P. algirus</em> in the Iberian Peninsula and north Africa, and genetically characterized <em>B. lusitaniae</em>, the infected ticks, and the vertebrate host.</div></div><div><h3>Results</h3><div>The goeBURST analysis on seven MLST <em>B. lusitaniae</em> genes identified two main clusters: one from central Europe and other from north Africa and Portugal (south of Tagus river), with some connections between the north Tagus populations in central Spain and north African ones. The <em>Ixodes</em> sp. nuclear gene <em>trospA</em> did not entirely correspond with the <em>B. lusitaniae</em> population structure. The <em>P. algirus</em>'s phylogeny based on the ND4 mitochondrial gene also did not show lineage distinctions between north and south Tagus.</div></div><div><h3>Conclusion</h3><div>Both the clustering of <em>B. lusitaniae</em> lineages from this region together with those of south Portugal and north Africa, and the presence of ticks belonging to different <em>trospA</em> clades, suggests Central Spain, a contact area between lineages of <em>P. algirus,</em> as pivotal in the phylogeography of the host, its ticks and <em>Borrelia</em>.</div></div>","PeriodicalId":8050,"journal":{"name":"Anaerobe","volume":"97 ","pages":"Article 103032"},"PeriodicalIF":2.6,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146197260","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
AnaerobePub Date : 2026-03-01Epub Date: 2026-02-05DOI: 10.1016/j.anaerobe.2026.103030
Nabiha B. Remmani , Zineb S. Harous , Rand Q. Alzaidy , Shahd A. Ahmednour , Hiroshi Egusa , Sameh S.M. Soliman
{"title":"The role of Fusobacterium nucleatum in the pathogenesis of endometriosis: A microbial and microenvironmental perspective","authors":"Nabiha B. Remmani , Zineb S. Harous , Rand Q. Alzaidy , Shahd A. Ahmednour , Hiroshi Egusa , Sameh S.M. Soliman","doi":"10.1016/j.anaerobe.2026.103030","DOIUrl":"10.1016/j.anaerobe.2026.103030","url":null,"abstract":"<div><div>Endometriosis is a chronic, inflammatory gynecological condition characterized by the ectopic growth of endometrial-like tissue, with an unclear etiology and limited treatment efficacy. Recent studies implicate the oral and gut commensal bacterium <em>Fusobacterium nucleatum</em> in the pathogenesis of endometriosis, with uterine colonization reported in up to 64% of affected women. This review highlights the potential role of <em>F. nucleatum</em> in disease progression, particularly through its metabolic activation within the endometrial microenvironment. We explore the contribution of key bacterial metabolites (formate, lactate, and hydrogen sulfide), proteins (FadA and Fap2), and lipids (oxidized LDL, lysophosphatidylcholines, and saturated fatty acids) to inflammation, immune evasion, and epithelial–mesenchymal transition (EMT), features that overlap with tumor biology. The review also investigates the preferential triggers of <em>F. nucleatum</em> translocation into the endometrium. Host factors such as hypoxia, estrogen dominance, and retrograde menstruation appear to create a permissive microenvironment that potentially facilitates <em>F. nucleatum</em> colonization and virulence. While current therapeutic strategies largely neglect microbial involvement, emerging approaches including targeted antimicrobials, probiotics, immunomodulators, and microenvironmental modulation offer promising avenues for microbiome-informed endometriosis management. This narrative review also underscores the urgent need for longitudinal, <em>in vivo</em> studies to characterize the relationship between the oral, gut, and endometrial microbiomes and their impact on disease onset and progression.</div></div>","PeriodicalId":8050,"journal":{"name":"Anaerobe","volume":"97 ","pages":"Article 103030"},"PeriodicalIF":2.6,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146130963","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
AnaerobePub Date : 2026-03-01Epub Date: 2026-01-27DOI: 10.1016/j.anaerobe.2026.103022
Jason R. Barash , Susan P. Sambol , Andrew M. Skinner , Stuart Johnson , Dale N. Gerding
{"title":"Clostridioides difficile colonization of Twin Patients Recovering From Infant Botulism","authors":"Jason R. Barash , Susan P. Sambol , Andrew M. Skinner , Stuart Johnson , Dale N. Gerding","doi":"10.1016/j.anaerobe.2026.103022","DOIUrl":"10.1016/j.anaerobe.2026.103022","url":null,"abstract":"<div><h3>Objectives</h3><div>The prevalence of <em>Clostridioides difficile</em> co-colonization of 107 California patients with suspect infant botulism (IB) was studied over a two-year period. One set of twins with lab-confirmed IB and <em>C. difficile</em> co-colonization was followed longitudinally and their isolated <em>C. difficile</em> was typed by restriction endonuclease analysis (REA).</div></div><div><h3>Methods</h3><div>Stool specimens sent to California Department of Public Health for routine IB diagnostic testing were cultured for <em>C. botulinum</em> and <em>C. difficile.</em> After diagnostic testing identified twin IB patients, their stools collected at weekly and monthly intervals were cultured to determine duration of <em>C. botulinum</em> and <em>C. difficile</em> co-colonization until three consecutive specimens were culture negative for each organism.</div></div><div><h3>Results</h3><div>Twins X and Y were colonized by <em>C. botulinum</em> for a duration of nearly three and four months, followed by <em>C. difficile</em> for eight and seven months, respectively. Continuous colonization by <em>C. difficile</em> was identified in each twin as <em>C. botulinum</em> colonization was waning. They sequentially shared four identical REA types, three toxigenic and one non-toxigenic, including epidemic strain type J9. Neither twin developed <em>C. difficile</em> illness and colonization ceased spontaneously in each.</div></div><div><h3>Conclusions</h3><div><em>C. difficile</em> co-colonization of laboratory-confirmed IB patients is infrequently encountered. IB in both twins was followed by asymptomatic <em>C. difficile</em> colonization. Risk factors for their respective co-colonization remain unknown, including if previous illness with IB was a potential contributing factor. Although the environmental source of the colonizing strains was not determined, this study highlights the ability of <em>C. difficile</em> to spread to close contacts and persist in the infant intestinal microbiome.</div></div>","PeriodicalId":8050,"journal":{"name":"Anaerobe","volume":"97 ","pages":"Article 103022"},"PeriodicalIF":2.6,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146073555","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Advances in Clostridioides difficile research: Insights from the 8th International C. difficile symposium (ICDS 2024)","authors":"Sandra Janezic , Marcela Krutova , Gayatri Vedantam","doi":"10.1016/j.anaerobe.2026.103031","DOIUrl":"10.1016/j.anaerobe.2026.103031","url":null,"abstract":"","PeriodicalId":8050,"journal":{"name":"Anaerobe","volume":"97 ","pages":"Article 103031"},"PeriodicalIF":2.6,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146193927","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}