DRAMMA: a multifaceted machine learning approach for novel antimicrobial resistance gene detection in metagenomic data

BACKGROUND

Antibiotics are essential for medical procedures, food security, and public health. However, ill-advised usage leads to increased pathogen resistance to antimicrobial substances, posing a threat of fatal infections and limiting the benefits of antibiotics. Therefore, early detection of antimicrobial resistance genes (ARGs), especially in pathogens, is crucial for human health. Most computational methods for ARG detection rely on homology to a predefined gene database and therefore are limited in their ability to discover novel genes.

RESULTS

We introduce DRAMMA, a machine learning method for predicting new ARGs with no sequence similarity to known ARGs or any annotated gene. DRAMMA utilizes various features, including protein properties, genomic context, and evolutionary patterns. The model demonstrated robust predictive performance both in cross-validation and an external validation set annotated by an empirical ARG database. Analyses of the high-ranking model-generated candidates revealed a significant enrichment of candidates within the Bacteroidetes/Chlorobi and Betaproteobacteria taxonomic groups.

CONCLUSIONS

DRAMMA enables rapid ARG identification for global-scale genomic and metagenomic samples, thus holding promise for the discovery of novel ARGs that lack sequence similarity to any known resistance genes. Further, our model has the potential to facilitate early detection of specific ARGs, potentially influencing the selection of antibiotics administered to patients. Video Abstract.

Distinct Patterns of Antibiotic Sensitivities in Ammonia-Oxidising Archaea

Ammonia-oxidising archaea (AOA) are important microorganisms contributing towards the nitrogen flux in the environment. Unlike archaea from other major phyla, genetic tools are yet to be developed for the AOA, and identification of antibiotic resistance markers for selecting mutants is required for a genetic system. The aim of this study was to test the effects of selected antibiotics (hygromycin B, neomycin, apramycin, puromycin, novobiocin) on pure cultures of three well studied AOA strains, 'Candidatus Nitrosocosmicus franklandianus C13', Nitrososphaera viennensis EN76 and Nitrosopumilus maritimus SCM1. Puromycin, hygromycin B and neomycin inhibited some but not all tested archaeal strains. All strains were resistant to apramycin and inhibited by novobiocin to various degrees. As N. viennensis EN76 was relatively more resistant to the tested antibiotics, a wider range of concentrations and compounds (chloramphenicol, trimethoprim, statins) was tested against this strain. N. viennensis EN76 was inhibited by trimethoprim, but not by chloramphenicol, and growth recovered within days in the presence of simvastatin, suggesting either degradation of, or spontaneous resistance against, this compound. This study highlights the physiological differences between different genera of AOA and has identified new candidate antibiotics for selective enrichment and the development of selectable markers for genetic systems in AOA.

Methanobrevibacter oralis: a comprehensive review

Methanobrevibacter oralis (M. oralis) has predominated human oral microbiota methanogenic archaea as far back as the Palaeolithic era in Neanderthal populations and gained dominance from the 18th century onwards. M. oralis was initially isolated from dental plaque samples collected from two apparently healthy individuals allowing its first characterization. The culture of M. oralis is fastidious and has been the subject of several studies to improve its laboratory growth. Various PCR methods are used to identify M. oralis, targeting either the 16S rRNA gene or the mcrA gene. However, only one RTQ-PCR system, based on a chaperonin gene, offers specificity, and allows for microbial load quantification. Next-generation sequencing contributed five draft genomes, each approximately 2.08 Mb (±0.052 Mb) with a 27.82 (±0.104) average GC%, and two ancient metagenomic assembled genomes. M. oralis was then detected in various oral cavity sites in healthy individuals and those diagnosed with oral pathologies, notably periodontal diseases, and endodontic infections. Transmission pathways, possibly involving maternal milk and breastfeeding, remain to be clarified. M. oralis was further detected in brain abscesses and respiratory tract samples, bringing its clinical significance into question. This review summarizes the current knowledge about M. oralis, emphasizing its prevalence, associations with dysbiosis and pathologies in oral and extra-oral situations, and symbiotic relationships, with the aim of paving the way for further investigations.

Methanobrevibacter smithii cell variants in human physiology and pathology: A review

Methanobrevibacter smithii (M. smithii), initially isolated from human feces, has been recognised as a distinct taxon within the Archaea domain following comprehensive phenotypic, genetic, and genomic analyses confirming its uniqueness among methanogens. Its diversity, encompassing 15 genotypes, mirrors that of biotic and host-associated ecosystems in which M. smithii plays a crucial role in detoxifying hydrogen from bacterial fermentations, converting it into mechanically expelled gaseous methane. In microbiota in contact with host epithelial mucosae, M. smithii centres metabolism-driven microbial networks with Bacteroides, Prevotella, Ruminococcus, Veillonella, Enterococcus, Escherichia, Enterobacter, Klebsiella, whereas symbiotic association with the nanoarchaea Candidatus Nanopusillus phoceensis determines small and large cell variants of M. smithii. The former translocate with bacteria to induce detectable inflammatory and serological responses and are co-cultured from blood, urine, and tissular abscesses with bacteria, prototyping M. smithii as a model organism for pathogenicity by association. The sources, mechanisms and dynamics of in utero and lifespan M. smithii acquisition, its diversity, and its susceptibility to molecules of environmental, veterinary, and medical interest still have to be deeply investigated, as only four strains of M. smithii are available in microbial collections, despite the pivotal role this neglected microorganism plays in microbiota physiology and pathologies.

Identification and characterisation of two functional antibiotic MATE efflux pumps in the archaeon Halorubrum amylolyticum

Multidrug efflux pumps have been found to play a crucial role in drug resistance in bacteria and eukaryotes. In this study, we investigated the presence of functional multidrug and toxic compound extrusion (MATE) efflux pumps, inferred from whole genome sequencing, in the halophilic archaeon Halorubrum amylolyticum CSM52 using Hoechst 33342 dye accumulation and antimicrobial sensitivity tests in the presence and absence of efflux pump inhibitors (EPIs). The whole genome sequence of H. amylolyticum CSM52 contained two putative MATE-type efflux pump genes, which may contribute to the inherent resistance to conventional antimicrobial agents reported in archaea. Antimicrobial susceptibility of the wild-type H. amylolyticum CSM52 testing revealed a lack of sensitivity to a wide range of antimicrobials, including glycopeptides, aminoglycosides, macrolides, fluoroquinolones, tetracycline, and chloramphenicol. However, the presence of EPIs, such as thioridazine, fluoxetine, and chlorpromazine, significantly increased the susceptibility of H. amylolyticum CSM52 to a number of these antimicrobials, indicating the potential involvement of efflux pumps in the observed resistance. A molecular modelling study with EPIs and substrate antimicrobials provided important insights into the molecular interactions with the putative transporter. It suggests that the occupancy of the transporter channel by EPIs has the potential to impact the efflux of antimicrobials. Phylogenetic analysis of the amino acid sequences of both MATE pumps showed low similarity with bacterial representatives, suggesting the presence of novel and distinct MATE efflux pumps in archaea. Our findings provide the first experimental evidence of active antibiotic efflux mechanisms in archaea and their potential roles in antimicrobial resistance, broadening our understanding of mechanisms of archaeal antimicrobial resistance, an overlooked aspect of AMR research.

Application of single-cell Raman-deuterium isotope probing to reveal the resistance of marine ammonia-oxidizing archaea SCM1 against common antibiotics

Antimicrobial resistance (AMR) in oceans poses a significant threat to human health through the seafood supply chain. Ammonia-oxidizing archaea (AOA) are important marine microorganisms and play a key role in the biogeochemical nitrogen cycle around the world. However, the AMR of marine AOA to aquicultural antibiotics is poorly explored. Here, Raman-deuterium isotope probing (Raman-DIP), a single-cell tool, was developed to reveal the AMR of a typical marine species of AOA, Nitrosopumilus maritimus (designated SCM1), against six antibiotics, including erythromycin, tetracycline, novobiocin, neomycin, bacitracin, and vancomycin. The D2O concentration (30% v/v) and culture period (9 days) were optimized for the precise detection of metabolic activity in SCM1 cells through Raman-DIP. The relative metabolic activity of SCM1 upon exposure to antibiotics was semi-quantitatively calculated based on single-cell Raman spectra. SCM1 exhibited high resistance to erythromycin, tetracycline, novobiocin, neomycin, and vancomycin, with minimum inhibitory concentration (MIC) values between 100 and 400 mg/L, while SCM1 is very sensitive to bacitracin (MIC: 0.8 mg/L). Notably, SCM1 cells were completely inactive under the metabolic activity minimum inhibitory concentration conditions (MA-MIC: 1.6-800 mg/L) for the six antibiotics. Further genomic analysis revealed the antibiotic resistance genes (ARGs) of SCM1, including 14 types categorized into 33 subtypes. This work increases our knowledge of the AMR of marine AOA by linking the resistant phenome to the genome, contributing to the risk assessment of AMR in the underexplored ocean environment. As antibiotic resistance in marine microorganisms is significantly affected by the concentration of antibiotics in coastal environments, we encourage more studies concentrating on both the phenotypic and genotypic antibiotic resistance of marine archaea. This may facilitate a comprehensive evaluation of the capacity of marine microorganisms to spread AMR and the implementation of suitable control measures to protect environmental safety and human health.

The Archaea domain: Exploring historical and contemporary perspectives with in silico primer coverage analysis for future research in Dentistry

OBJECTIVE

The complete picture of how the human microbiome interacts with its host is still largely unknown, particularly concerning microorganisms beyond bacteria. Although existing in very low abundance and not directly linked to causing diseases, archaea have been detected in various sites of the human body, including the gastrointestinal tract, oral cavity, skin, eyes, respiratory and urinary systems. But what exactly are these microorganisms? In the early 1990 s, archaea were classified as a distinct domain of life, sharing a more recent common ancestor with eukaryotes than with bacteria. While archaea's presence and potential significance in Dentistry remain under-recognized, there are concerns that they may contribute to oral dysbiosis. However, detecting archaea in oral samples presents challenges, including difficulties in culturing, the selection of DNA extraction methods, primer design, bioinformatic analysis, and databases.

DESIGN

This is a comprehensive review on the oral archaeome, presenting an in-depth in silico analysis of various primers commonly used for detecting archaea in human body sites.

RESULTS

Among several primer pairs used for detecting archaea in human samples across the literature, only one specifically designed for detecting methanogenic archaea in stool samples, exhibited exceptional coverage levels for the domain and various archaea phyla.

CONCLUSIONS

Our in silico analysis underscores the need for designing new primers targeting not only methanogenic archaea but also nanoarchaeal and thaumarchaeota groups to gain a comprehensive understanding of the archaeal oral community. By doing so, researchers can pave the way for further advancements in the field of oral archaeome research.

Probing Denitrifying Anaerobic Methane Oxidation via Antimicrobial Intervention: Implications for Innovative Wastewater Management

Methane emissions present a significant environmental challenge in both natural and engineered aquatic environments. Denitrifying anaerobic methane oxidation (N-DAMO) has the potential for application in wastewater treatment plants. However, our understanding of the N-DAMO process is primarily based on studies conducted on environmental samples or enrichment cultures using metagenomic approaches. To gain deeper insights into N-DAMO, we used antimicrobial compounds to study the function and physiology of 'Candidatus Methanoperedens nitroreducens' and 'Candidatus Methylomirabilis oxyfera' in N-DAMO enrichment cultures. We explored the effects of inhibitors and antibiotics and investigated the potential application of N-DAMO in wastewater contaminated with ammonium and heavy metals. Our results showed that 'Ca. M. nitroreducens' was susceptible to puromycin and 2-bromoethanesulfonate, while the novel methanogen inhibitor 3-nitrooxypropanol had no effect on N-DAMO. Furthermore, 'Ca. M. oxyfera' was shown to be susceptible to the particulate methane monooxygenase inhibitor 1,7-octadiyne and a bacteria-suppressing antibiotic cocktail. The N-DAMO activity was not affected by ammonium concentrations below 10 mM. Finally, the N-DAMO community appeared to be remarkably resistant to lead (Pb) but susceptible to nickel (Ni) and cadmium (Cd). This study provides insights into microbial functions in N-DAMO communities, facilitating further investigation of their application in methanogenic, nitrogen-polluted water systems.

CPR bacteria and DPANN archaea play pivotal roles in response of microbial community to antibiotic stress in groundwater

The accumulation of antibiotics in the natural environment can disrupt microbial population dynamics. However, our understanding of how microbial communities adapt to the antibiotic stress in groundwater ecosystems remains limited. By recovering 2675 metagenome-assembled genomes (MAGs) from 66 groundwater samples, we explored the effect of antibiotics on bacterial, archaeal, and fungal communities, and revealed the pivotal microbes and their mechanisms in coping with antibiotic stress. The results indicated that antibiotics had the most significant influence on bacterial and archaeal communities, while the impact on the fungal community was minimal. Analysis of co-occurrence networks between antibiotics and microbes revealed the critical roles of Candidate Phyla Radiation (CPR) bacteria and DPANN archaea, two representative microbial groups in groundwater ecosystem, in coping with antibiotic resistance and enhancing network connectivity and complexity. Further genomic analysis demonstrated that CPR bacteria carried approximately 6 % of the identified antibiotic resistance genes (ARGs), indicating their potential to withstand antibiotics on their own. Meanwhile, the genomes of CPR bacteria and DPANN archaea were found to encode diverse biosynthetic gene clusters (BGCs) responsible for producing antimicrobial metabolites, which could not only assist CPR and DPANN organisms but also benefit the surrounding microbes in combating antibiotic stress. These findings underscore the significant impact of antibiotics on prokaryotic microbial communities in groundwater, and highlight the importance of CPR bacteria and DPANN archaea in enhancing the overall resilience and functionality of the microbial community in the face of antibiotic stress.

The bacterial and archaeal communities of flies, manure, lagoons, and troughs at a working dairy

Background

Fundamental investigations into the location, load, and persistence of microbes, whether beneficial or detrimental, are scarce. Many questions about the retention and survival of microbes on various surfaces, as well as the load necessary for spread, exist. To answer these questions, we must know more about where to find various microbes and in what concentrations, the composition of the microbial communities, and the extent of dissemination between various elements. This study investigated the diversity, composition, and relative abundance of the communities associated with manure, lagoons, troughs, house flies, and stable flies present at a dairy, implementing two different free-stall management systems: flow-through and cross-vent. Shotgun metagenomics at the community level was used to compare the microbiomes within the dairy, allowing confident interpretation at the species level.

Results

The results showed that there were significant difference in microbial composition between not only each of the dairy elements but also management styles. The primary exceptions were the microbiomes of the house fly and the stable fly. Their compositions heavily overlapped with one another, but interestingly, not with the other components sampled. Additionally, both species of flies carried more pathogens than the other elements of the dairy, indicating that they may not share these organisms with the other components, or that the environments offered by the other components are unsatisfactory for the survival of some pathogens..

Conclusion

The lack of overlapping pathogen profiles suggests a lack of transfer from flies to other dairy elements. Dairy health data, showing a low incidence of disease, suggests minimal sharing of bacteria by the flies at a level required for infection, given the health program of this dairy. While flies did carry a multitude of pathogenic bacteria, the mere presence of the bacteria associated with the flies did not necessarily translate into high risk leading to morbidity and mortality at this dairy. Thus, using flies as the sole sentinel of dairy health may not be appropriate for all bacterial pathogens or dairies.

Candidatus Methanosphaera massiliense sp. nov., a methanogenic archaeal species found in a human fecal sample and prevalent in pigs and red kangaroos

Methanosphaera stadtmanae was the sole Methanosphaera representative to be cultured and detected by molecular methods in the human gut microbiota, further associated with digestive and respiratory diseases, leaving unknown the actual diversity of human-associated Methanosphaera species. Here, a novel Methanosphaera species, Candidatus Methanosphaera massiliense (Ca. M. massiliense) sp. nov. was isolated by culture using a hydrogen- and carbon dioxide-free medium from one human feces sample. Ca. M. massiliense is a non-motile, 850 nm Gram-positive coccus autofluorescent at 420 nm. Whole-genome sequencing yielded a 29.7% GC content, gapless 1,785,773 bp genome sequence with an 84.5% coding ratio, encoding for alcohol and aldehyde dehydrogenases promoting the growth of Ca. M. massiliense without hydrogen. Screening additional mammal and human feces using a specific genome sequence-derived DNA-polymerase RT-PCR system yielded a prevalence of 22% in pigs, 12% in red kangaroos, and no detection in 149 other human samples. This study, extending the diversity of Methanosphaera in human microbiota, questions the zoonotic sources of Ca. M. massiliense and possible transfer between hosts.IMPORTANCEMethanogens are constant inhabitants in the human gut microbiota in which Methanosphaera stadtmanae was the only cultivated Methanosphaera representative. We grew Candidatus Methanosphaera massiliense sp. nov. from one human feces sample in a novel culture medium under a nitrogen atmosphere. Systematic research for methanogens in human and animal fecal samples detected Ca. M. massiliense in pig and red kangaroo feces, raising the possibility of its zoonotic acquisition. Host specificity, source of acquisition, and adaptation of methanogens should be further investigated.

Exploring the effects of antimicrobial treatment on the gut and oral microbiomes and resistomes from elderly long-term care facility residents via shotgun DNA sequencing

Monitoring antibiotic-resistant bacteria (ARB) and understanding the effects of antimicrobial drugs on the human microbiome and resistome are crucial for public health. However, no study has investigated the association between antimicrobial treatment and the microbiome-resistome relationship in long-term care facilities, where residents act as reservoirs of ARB but are not included in the national surveillance for ARB. We conducted shotgun metagenome sequencing of oral and stool samples from long-term care facility residents and explored the effects of antimicrobial treatment on the human microbiome and resistome using two types of comparisons: cross-sectional comparisons based on antimicrobial treatment history in the past 6 months and within-subject comparisons between stool samples before, during and 2-4 weeks after treatment using a single antimicrobial drug. Cross-sectional analysis revealed two characteristics in the group with a history of antimicrobial treatment: the archaeon Methanobrevibacter was the only taxon that significantly increased in abundance, and the total abundance of antimicrobial resistance genes (ARGs) was also significantly higher. Within-subject comparisons showed that taxonomic diversity did not decrease during treatment, suggesting that the effect of the prescription of a single antimicrobial drug in usual clinical treatment on the gut microbiota is likely to be smaller than previously thought, even among very elderly people. Additional analysis of the detection limit of ARGs revealed that they could not be detected when contig coverage was <2.0. This study is the first to report the effects of usual antimicrobial treatments on the microbiome and resistome of long-term care facility residents.

Methanobrevibacter massiliense and Pyramidobacter piscolens Co-Culture Illustrates Transkingdom Symbiosis

Among oral microbiota methanogens, Methanobrevibacter massiliense (M. massiliense) has remained less studied than the well-characterised and cultivated methanogens Methanobrevibacter oralis and Methanobrevibacter smithii. M. massiliense has been associated with different oral pathologies and was co-isolated with the Synergistetes bacterium Pyramidobacter piscolens (P. piscolens) in one case of severe periodontitis. Here, reporting on two additional necrotic pulp cases yielded the opportunity to characterise two co-cultivated M. massiliense isolates, both with P. piscolens, as non-motile, 1-2-µm-long and 0.6-0.8-µm-wide Gram-positive coccobacilli which were autofluorescent at 420 nm. The two whole genome sequences featured a 31.3% GC content, gapless 1,834,388-base-pair chromosome exhibiting an 85.9% coding ratio, encoding a formate dehydrogenase promoting M. massiliense growth without hydrogen in GG medium. These data pave the way to understanding a symbiotic, transkingdom association with P. piscolens and its role in oral pathologies.

Sweet Orange Juice Processing By-Product Extracts: A Caries Management Alternative to Chlorhexidine

Dental caries is one of the most prevalent chronic diseases globally in both children and adults. This study investigated the potential of industrial sweet orange waste extracts (ISOWE) as a substitute for chlorhexidine (CHX) in managing dental caries. First, the cytotoxicity of ISOWE (40, 80, 120 mg/mL) and CHX (0.1 and 0.2%) on buccal epithelial cells was determined. ISOWE exhibited no overall toxicity, whereas CHX strongly affected cell viability. The combination of ISOWE and CHX significantly enhanced cell proliferation compared to CHX alone. Next, the antimicrobial efficacy of ISOWE, CHX, and their combination was assessed against a 7-day complex biofilm model inoculated with oral samples from human volunteers. CHX exhibited indiscriminate antimicrobial action, affecting both pathogenic and health-associated oral microorganisms. ISOWE demonstrated lower antimicrobial efficacy than CHX but showed enhanced efficacy against pathogenic species while preserving the oral microbiome's balance. When applied to a cariogenic biofilm, the combined treatment of ISOWE with 0.1% CHX showed similar efficacy to 0.2% CHX treatment alone. Overall, the findings suggest that ISOWE is a promising natural anti-cariogenic agent with lower toxicity and enhanced selectivity for pathogenic species compared to CHX.

Unraveling the Endodontic Archaeome: A Systematic Review with Meta-Analysis

INTRODUCTION

The controversial issue of whether the Archaea domain plays a role in endodontic infections is the focus of this systematic review with meta-analysis. The aim is to emphasize the significance of minority microbial domains in oral dysbiosis by evaluating the prevalence of archaea in root canals and its association with clinical parameters such as symptomatology and type of endodontic infection.

METHODS

The search strategy involved researching 6 databases and the gray literature. Publications were accepted in any year or language that identified archaea in samples from endodontic canals. A 2-step selection process narrowed the final choice to 16 articles. The methodological quality of the studies was evaluated using tools from the Joanna Briggs Institute, and the certainty of evidence was assessed using the Grading of Recommendations, Assessment, Development, and Evaluation (GRADE) approach.

RESULTS

The results showed that archaea were present in 20% (95% [confidence interval] CI = 8%-32%) of individuals with endodontic samples analyzed. The samples were about twice as likely to be archaeal-positive if collected from individuals with primary vs. persistent/secondary infection (odds ratio = 2.33; 95% CI = 1.31-4.14; I2 = 0%), or individuals with self-reported vs. symptom-free infections (odds ratio = 2.67; 95% CI = 1.47-4.85; I2 = 0%). Methanogenic archaea were reported in 66% of the included studies. Representative members of phyla Thaumarchaeota and Crenarchaeota were also identified.

CONCLUSIONS

Archaea are present in about one-fifth of the infected root canals. Recognized biases in experimental approaches for researching archaea must be addressed to understand the prevalence and roles of archaea in endodontic infections, and to determine whether the decontamination process should include the elimination or neutralization of archaea from root canals (International Prospective Register of Systematic Reviews protocol = CRD42021264308).

Irritable Bowel Syndrome-Like Symptoms in Quiescent Inflammatory Bowel Disease: A Practical Approach to Diagnosis and Treatment of Organic Causes

BACKGROUND

Despite achieving remission in inflammatory bowel disease (IBD), persistent gastrointestinal symptoms are common in quiescent IBD. While irritable bowel syndrome (IBS) is commonly diagnosed in IBD, IBS-like symptoms of recurrent abdominal pain and altered bowel habits can also be attributed to a wide range of overlapping gastrointestinal (GI) etiologies and systemic disorders with GI manifestations that often do not respond to conventional IBS therapies. Delay in diagnosis of these conditions can lead to ongoing patient suffering, reduced quality of life, repetition of invasive testing, increased healthcare utilization, and potentially unnecessary empirical escalation of IBD-related treatments.

AIMS

This review provides a practical approach for the evaluation and diagnosis of IBS mimickers in IBD. We summarize the definition, pathophysiology, diagnosis and treatment of the potential etiologies causing unexplained GI symptoms.

CONCLUSION

Overlapping conditions can co-exist with IBD and explain IBS-like symptoms. The diagnostic work-up in this population should be individualized and tailored to the predominant symptom pattern, associated clinical signs and symptoms and predisposing conditions that can be obtained from a detailed history and physical examination.

The evolving role of methanogenic archaea in mammalian microbiomes

Methanogenic archaea (methanogens) represent a diverse group of microorganisms that inhabit various environmental and host-associated microbiomes. These organisms play an essential role in global carbon cycling given their ability to produce methane, a potent greenhouse gas, as a by-product of their energy production. Recent advances in culture-independent and -dependent studies have highlighted an increased prevalence of methanogens in the host-associated microbiome of diverse animal species. Moreover, there is increasing evidence that methanogens, and/or the methane they produce, may play a substantial role in human health and disease. This review addresses the expanding host-range and the emerging view of host-specific adaptations in methanogen biology and ecology, and the implications for host health and disease.

Enhanced anaerobic oxidation of methane with the coexistence of iron oxides and sulfate fertilizer in paddy soil

Iron oxides and sulfate are usually abundant in paddy soil, but their role in reducing methane emissions is little known. In this work, paddy soil was anaerobically cultivated with ferrihydrite and sulfate for 380 days. An activity assay, inhibition experiment, and microbial analysis were conducted to evaluate the microbial activity, possible pathways, and community structure, respectively. The results showed that anaerobic oxidation of methane (AOM) was active in the paddy soil. The AOM activity was much higher with ferrihydrite than sulfate, and an extra 10% of AOM activity was stimulated when ferrihydrite and sulfate coexisted. The microbial community was highly similar to the duplicates but totally different with different electron acceptors. The microbial abundance and diversity decreased due to the oligotrophic condition, but mcrA-carrying archaea increased 2-3 times after 380 days. Both the microbial community and the inhibition experiment implied that there was an intersection between iron and sulfur cycles. A "cryptic sulfur cycle" might link the two cycles, in which sulfate was quickly regenerated by iron oxides, and it might contribute 33% of AOM in the tested paddy soil. Complex links between methane, iron, and sulfur geochemical cycles occur in paddy soil, which may be significant in reducing methane emissions from rice fields.

Origin, Diversity, and Multiple Roles of Enzymes with Metallo-β-Lactamase Fold from Different Organisms

β-lactamase enzymes have generated significant interest due to their ability to confer resistance to the most commonly used family of antibiotics in human medicine. Among these enzymes, the class B β-lactamases are members of a superfamily of metallo-β-lactamase (MβL) fold proteins which are characterised by conserved motifs (i.e., HxHxDH) and are not only limited to bacteria. Indeed, as the result of several barriers, including low sequence similarity, default protein annotation, or untested enzymatic activity, MβL fold proteins have long been unexplored in other organisms. However, thanks to search approaches which are more sensitive compared to classical Blast analysis, such as the use of common ancestors to identify distant homologous sequences, we are now able to highlight their presence in different organisms including Bacteria, Archaea, Nanoarchaeota, Asgard, Humans, Giant viruses, and Candidate Phyla Radiation (CPR). These MβL fold proteins are multifunctional enzymes with diverse enzymatic or non-enzymatic activities of which, at least thirteen activities have been reported such as β-lactamase, ribonuclease, nuclease, glyoxalase, lactonase, phytase, ascorbic acid degradation, anti-cancer drug degradation, or membrane transport. In this review, we (i) discuss the existence of MβL fold enzymes in the different domains of life, (ii) present more suitable approaches to better investigating their homologous sequences in unsuspected sources, and (iii) report described MβL fold enzymes with demonstrated enzymatic or non-enzymatic activities.

Characterizing sediment functional traits and ecological consequences respond to increasing antibiotic pollution

Current studies have shown that the taxonomic structures of ecologically important microbial communities are altered by antibiotic exposure, but the resulting effects on functional potentials and subsequent biogeochemical processes are poorly understood. However, this knowledge is indispensable for developing an accurate projection of nutrient dynamics in the future. Using metagenomic analyses, here we explored the responses of taxonomical and functional structures of a sediment microbial community, and their links with key biogeochemical processes to increasing antibiotic pollution from the pristine inlet to the outfall sites along an aquaculture discharge channel. We identified sharply contrasting sedimentary microbial communities and functional traits along increasing antibiotic pollution. Functional structures exhibited steeper distance-decay relationships than taxonomical structures along both the antibiotic distance and physicochemical distance, revealing higher functional sensitivity. Sediment enzyme activities were significantly and positively coupled with the relative abundances of their coding genes, thus the abundances of genes were indicative of functional potentials. The nitrogen cycling pathways were commonly inhibited by antibiotics, but not for the first step of nitrification, which could synergistically mitigate nitrous oxide emission. However, antibiotic pollution stimulated methanogens and inhibited methanotrophs, thereby promoting methane efflux. Furthermore, microbes could adapt to antibiotic pollution through enriched potential of sulfate uptake. Antibiotics indirectly affected taxonomic structures through alterations in network topological features, which in turn affected sediment functional structures and biogeochemical processes. Notably, only 13 antibiotics concentration-discriminatory genes contributed an overall 95.9% accuracy in diagnosing in situ antibiotic concentrations, in which just two indicators were antibiotic resistance genes. Our study comprehensively integrates sediment compositional and functional traits, biotic interactions, and enzymatic activities, thus generating a better understanding about ecological consequences of increasing antibiotics pollution. KEY POINTS: • Contrasting functional traits respond to increasing antibiotic pollution. • Antibiotics pollution stimulates CH₄ efflux, while mitigating N₂O emission and may drive an adaptive response of enriched sulfate uptake. • Indicator genes contribute 95.9% accuracy in diagnosing antibiotic concentrations.

Estimation of silent phenotypes of calf antibiotic dysbiosis

Reducing antibiotic usage among livestock animals to prevent antimicrobial resistance has become an urgent issue worldwide. This study evaluated the effects of administering chlortetracycline (CTC), a versatile antibacterial agent, on the performance, blood components, fecal microbiota, and organic acid concentrations of calves. Japanese Black calves were fed with milk replacers containing CTC at 10 g/kg (CON group) or 0 g/kg (EXP group). Growth performance was not affected by CTC administration. However, CTC administration altered the correlation between fecal organic acids and bacterial genera. Machine learning (ML) methods such as association analysis, linear discriminant analysis, and energy landscape analysis revealed that CTC administration affected populations of various types of fecal bacteria. Interestingly, the abundance of several methane-producing bacteria at 60 days of age was high in the CON group, and the abundance of Lachnospiraceae, a butyrate-producing bacterium, was high in the EXP group. Furthermore, statistical causal inference based on ML data estimated that CTC treatment affected the entire intestinal environment, potentially suppressing butyrate production, which may be attributed to methanogens in feces. Thus, these observations highlight the multiple harmful impacts of antibiotics on the intestinal health of calves and the potential production of greenhouse gases by calves.

Proposed minimal standards for description of methanogenic archaea

Methanogenic archaea are a diverse, polyphyletic group of strictly anaerobic prokaryotes capable of producing methane as their primary metabolic product. It has been over three decades since minimal standards for their taxonomic description have been proposed. In light of advancements in technology and amendments in systematic microbiology, revision of the older criteria for taxonomic description is essential. Most of the previously recommended minimum standards regarding phenotypic characterization of pure cultures are maintained. Electron microscopy and chemotaxonomic methods like whole-cell protein and lipid analysis are desirable but not required. Because of advancements in DNA sequencing technologies, obtaining a complete or draft whole genome sequence for type strains and its deposition in a public database are now mandatory. Genomic data should be used for rigorous comparison to close relatives using overall genome related indices such as average nucleotide identity and digital DNA-DNA hybridization. Phylogenetic analysis of the 16S rRNA gene is also required and can be supplemented by phylogenies of the mcrA gene and phylogenomic analysis using multiple conserved, single-copy marker genes. Additionally, it is now established that culture purity is not essential for studying prokaryotes, and description of Candidatus methanogenic taxa using single-cell or metagenomics along with other appropriate criteria is a viable alternative. The revisions to the minimal criteria proposed here by the members of the Subcommittee on the Taxonomy of Methanogenic Archaea of the International Committee on Systematics of Prokaryotes should allow for rigorous yet practical taxonomic description of these important and diverse microbes.

Culturing the Human Oral Microbiota, Updating Methodologies and Cultivation Techniques

Recent years have been marked by a paradigm shift in the study of the human microbiota, with a re-emergence of culture-dependent approaches. Numerous studies have been devoted to the human microbiota, while studies on the oral microbiota still remain limited. Indeed, various techniques described in the literature may enable an exhaustive study of the microbial composition of a complex ecosystem. In this article, we report different methodologies and culture media described in the literature that can be applied to study the oral microbiota by culture. We report on specific methodologies for targeted culture and specific culture techniques and selection methodologies for cultivating members of the three kingdoms of life commonly found in the human oral cavity, namely, eukaryota, bacteria and archaea. This bibliographic review aims to bring together the various techniques described in the literature, enabling a comprehensive study of the oral microbiota in order to demonstrate its involvement in oral health and diseases.

Residual enrofloxacin in cattle manure increased persistence and dissemination risk of antibiotic resistance genes during anaerobic digestion

Anaerobic digestion is a common approach to dispose and recycle livestock manures, and the agricultural application of anaerobic digestives represents an important pathway of spreading antibiotic resistance genes (ARGs) from livestock manures to soils. Enrofloxacin is a clinically important fluoroquinolone antibiotic with high residual concentrations in livestock manure, and propagation of fluoroquinolone resistance genes poses a huge risk to public health. Compared with other antibiotics, enrofloxacin is relatively durable in anaerobic digestion system. However, its effect on the persistence of ARGs during anaerobic digestion and its mechanism are not clear. In this study, we investigated effects of 0, 4, and 8 mg/L enrofloxacin on the abundance, persistence, and transferring risk of five plasmid-mediated fluroquinolone ARGs and five typic clinically important non-fluoroquinolone ARGs during cattle manure digestion. The responses of integrons and microbial communities to enrofloxacin were assessed to uncover the underlying mechanisms. All the ten detected ARGs were highly persistent in anaerobic digestion, among them seven ARGs increased over 8.2 times after digestion. Network analysis revealed that the potential hosts of ARGs were critical functional taxa during anaerobic digestion, which can explain the high persistence of ARGs. Residual enrofloxacin significantly increased the abundance of aac(6')-ib-cr, sul1, intI1, and intI2 throughout the digestion, but had no impact on the other ARGs, demonstrating its role in facilitating horizontal gene transfer of the plasmid-mediated aac(6')-ib-cr. The influence of enrofloxacin on microbial communities disappeared at the end of digestion, but the ARG profiles remained distinctive between the enrofloxacin treatments and the control, suggesting the high persistence of enrofloxacin induced ARGs. Our results suggested the high persistence of ARGs in anaerobic digestion system, and highlighted the role of residual enrofloxacin in livestock manure in increasing dissemination risk of fluroquinolone resistance genes.

Methanogenic archaea in the human gastrointestinal tract

The human microbiome is strongly interwoven with human health and disease. Besides bacteria, viruses and eukaryotes, numerous archaea are located in the human gastrointestinal tract and are responsible for methane production, which can be measured in clinical methane breath analyses. Methane is an important readout for various diseases, including intestinal methanogen overgrowth. Notably, the archaea responsible for methane production are largely overlooked in human microbiome studies due to their non-bacterial biology and resulting detection issues. As such, their importance for health and disease remains largely unclear to date, in particular as not a single archaeal representative has been deemed to be pathogenic. In this Perspective, we discuss the current knowledge on the clinical relevance of methanogenic archaea. We explain the archaeal unique response to antibiotics and their negative and positive effects on human physiology, and present the current understanding of the use of methane as a diagnostic marker.

"Universal" Antimicrobial Combination of Bacitracin and His6-OPH with Lactonase Activity, Acting against Various Bacterial and Yeast Cells

The effect of Bacitracin as an antibiotic acting against Gram-positive bacterial cells was evaluated in combination with hexahistidine-containing organophosphate hydrolase (His6-OPH), possessing lactonase activity against various N-acylhomoserine lactones produced by most Gram-negative bacteria as quorum-sensing molecules. The molecular docking technique was used to obtain in silico confirmation of possible interactions between molecules of His6-OPH and Bacitracin as well as the absence of a significant influence of such interactions on the enzymatic catalysis. The in vitro experiments showed a sufficient catalytic efficiency of action of the His6-OPH/Bacitracin combination as compared to the native enzyme. The notable improvement (up to 3.3 times) of antibacterial efficiency of Bacitracin was revealed in relation to Gram-negative bacteria when it was used in combination with His6-OPH. For the first time, the action of the Bacitracin with and without His6-OPH was shown to be effective against various yeast strains, and the presence of the enzyme increased the antibiotic effect up to 8.5 times. To estimate the role of the enzyme in the success of His6-OPH/Bacitracin with yeast, in silico experiments (molecular docking) with various fungous lactone-containing molecules were undertaken, and the opportunity of their enzymatic hydrolysis by His6-OPH was revealed in the presence and absence of Bacitracin.

Distinctive Clinical Correlates of Small Intestinal Bacterial Overgrowth with Methanogens

BACKGROUND AND AIMS

Most patients with small intestinal bacterial overgrowth (SIBO) produce hydrogen by fermentation of dietary carbohydrates; however, ∼30% of patients with SIBO are colonized with Archaea, anaerobic organisms that produce methane. SIBO is associated with a plethora of symptoms and conditions, but their diagnostic significance is unclear. We aimed to determine if specific symptoms and conditions are associated with methanogenic SIBO.

METHODS

This study received institutional review board approval (IRB00059873). In this retrospective cross-sectional study, we queried a database of glucose breath tests conducted for suspected SIBO at our tertiary care medical center, which included data on the presence or absence of gastrointestinal symptoms and conditions often associated with SIBO. All patients had undergone a standardized breath testing protocol.

RESULTS

In a cohort of 1461 patients, 33.1% were SIBO positive; of these, 49.8% produced only hydrogen, 38.8% produced only methane, and 11.4% produced both gases. The following factors distinguished patients with hydrogen-producing SIBO, but not methanogenic SIBO, from SIBO-negative patients: vitamin B₁₂ deficiency (odds ratio, 1.44; confidence interval [CI], 1.01-2.06; P = .046), Roux-en-Y gastric bypass (odds ratio, 2.14; CI, 1.09-4.18; P = .027), cholecystectomy (odds ratio, 1.42; CI, 1.06-1.91; P = .020), and diabetes (odds ratio, 1.59; CI, 1.13-2.24; P = .008). The absence of vitamin B₁₂ deficiency was the sole discriminating factor between methanogenic and hydrogenic SIBO (odds ratio, 0.57; CI, 0.34-0.97; P = .038).

CONCLUSIONS

Patients with SIBO caused by methane-producing Archaea display a different spectrum of associated symptoms and clinical conditions compared with patients with SIBO caused by hydrogen-producing bacteria, particularly a lower incidence of vitamin B₁₂ deficiency.

Beyond the approved: target sites and inhibitors of bacterial RNA polymerase from bacteria and fungi

Covering: 2016 to 2022RNA polymerase (RNAP) is the central enzyme in bacterial gene expression representing an attractive and validated target for antibiotics. Two well-known and clinically approved classes of natural product RNAP inhibitors are the rifamycins and the fidaxomycins. Rifampicin (Rif), a semi-synthetic derivative of rifamycin, plays a crucial role as a first line antibiotic in the treatment of tuberculosis and a broad range of bacterial infections. However, more and more pathogens such as Mycobacterium tuberculosis develop resistance, not only against Rif and other RNAP inhibitors. To overcome this problem, novel RNAP inhibitors exhibiting different target sites are urgently needed. This review includes recent developments published between 2016 and today. Particular focus is placed on novel findings concerning already known bacterial RNAP inhibitors, the characterization and development of new compounds isolated from bacteria and fungi, and providing brief insights into promising new synthetic compounds.

The Historical Development of Cultivation Techniques for Methanogens and Other Strict Anaerobes and Their Application in Modern Microbiology

The cultivation and investigation of strictly anaerobic microorganisms belong to the fields of anaerobic microbial physiology, microbiology, and biotechnology. Anaerobic cultivation methods differ from classic microbiological techniques in several aspects. The requirement for special instruments, which are designed to prevent the contact of the specimen with air/molecular oxygen by different means of manipulation, makes this field more challenging for general research compared to working with aerobic microorganisms. Anaerobic microbiological methods are required for many purposes, such as for the isolation and characterization of new species and their physiological examination, as well as for anaerobic biotechnological applications or medical indications. This review presents the historical development of methods for the cultivation of strictly anaerobic microorganisms focusing on methanogenic archaea, anaerobic cultivation methods that are still widely used today, novel methods for anaerobic cultivation, and almost forgotten, but still relevant, techniques.

Going Beyond Bacteria: Uncovering the Role of Archaeome and Mycobiome in Inflammatory Bowel Disease

Inflammatory Bowel Disease (IBD) is a multifaceted class of relapsing-remitting chronic inflammatory conditions where microbiota dysbiosis plays a key role during its onset and progression. The human microbiota is a rich community of bacteria, viruses, fungi, protists, and archaea, and is an integral part of the body influencing its overall homeostasis. Emerging evidence highlights dysbiosis of the archaeome and mycobiome to influence the overall intestinal microbiota composition in health and disease, including IBD, although they remain some of the least understood components of the gut microbiota. Nonetheless, their ability to directly impact the other commensals, or the host, reasonably makes them important contributors to either the maintenance of the mucosal tissue physiology or to chronic intestinal inflammation development. Therefore, the full understanding of the archaeome and mycobiome dysbiosis during IBD pathogenesis may pave the way to the discovery of novel mechanisms, finally providing innovative therapeutic targets that can soon implement the currently available treatments for IBD patients.

Detection of methanogens in peri-appendicular abscesses: Report of four cases

The aetiology of appendicular abscess is predominantly microbial with aerobic and anaerobic bacteria from gut flora. In this study, by using specific laboratory tools, we co-detected Methanobrevibacter oralis and Methanobrevibacter smithii among a mixture of enterobacteria including Escherichia coli, Enterococcus faecium and Enterococcus avium in four unrelated cases of postoperative appendiceal abscesses. These unprecedented observations raise a question on the role of methanogens in peri-appendicular abscesses, supporting antibiotics as an alternative therapeutic option for appendicitis, including antibiotics active against methanogens such as metronidazole or fusidic acid.

Synthesis and Biological Activities of Naturally Functionalized Polyamines: An Overview

Recently, extensive researches have emphasized the fact that polyamine conjugates are becoming important in all biological and medicinal fields. In this review, we will focus our attention on natural polyamines and highlight recent progress in both fundamental mechanism studies and interests in the development and application for the therapeutic use of polyamine derivatives.

Interkingdom Gut Microbiome and Resistome of the Cockroach Blattella germanica

Cockroaches are intriguing animals with two coexisting symbiotic systems, an endosymbiont in the fat body, involved in nitrogen metabolism, and a gut microbiome whose diversity, complexity, role, and developmental dynamics have not been fully elucidated. In this work, we present a metagenomic approach to study Blattella germanica populations not treated, treated with kanamycin, and recovered after treatment, both naturally and by adding feces to the diet, with the aim of better understanding the structure and function of its gut microbiome along the development as well as the characterization of its resistome.IMPORTANCE For the first time, we analyze the interkingdom hindgut microbiome of this species, including bacteria, fungi, archaea, and viruses. Network analysis reveals putative cooperation between core bacteria that could be key for ecosystem equilibrium. We also show how antibiotic treatments alter microbiota diversity and function, while both features are restored after one untreated generation. Combining data from B. germanica treated with three antibiotics, we have characterized this species' resistome. It includes genes involved in resistance to several broad-spectrum antibiotics frequently used in the clinic. The presence of genetic elements involved in DNA mobilization indicates that they can be transferred among microbiota partners. Therefore, cockroaches can be considered reservoirs of antibiotic resistance genes (ARGs) and potential transmission vectors.

Small Intestinal Bacterial Overgrowth: How to Diagnose and Treat (and Then Treat Again)

Small intestinal bacterial overgrowth (SIBO) is a condition with presentation that can vary from asymptomatic to steatorrhea and malnutrition. Small bowel aspiration and culture is the current gold standard of diagnosis; however, this is invasive and is not without risk to the patient. Breath testing is a noninvasive and less expensive alternative method; however, it lacks diagnostic sensitivity and specificity. Novel diagnostic methods being studied include gas-sensing capsules. The mainstay of treatment is antibiotics; alternative therapies include herbal medications, dietary modifications, and prokinetic agents. Further investigation into less invasive and less harmful diagnostic methods and treatment options is warranted.

Digestive tract methanodrome: Physiological roles of human microbiota-associated methanogens

Methanogens are the archaea most commonly found in humans, in particular in the digestive tract and are an integral part of the digestive microbiota. They are present in humans from the earliest moments of life and represent the only known source of methane production to date. They are notably detected in humans by microscopy, fluorescent in situ hybridization, molecular biology including PCR-sequencing, metagenomics, matrix-assisted laser desorption ionization time-of-flight mass spectrometry and culture. Methanogens present in the human digestive tract play major roles, in particular the use of hydrogen from the fermentation products of bacteria, thus promoting digestion. They are also involved in the transformation of heavy metals and in the use of trimethylamine produced by intestinal bacteria, thus preventing major health problems, in particular cardiovascular diseases. Several pieces of evidence suggest their close physical contacts with bacteria support symbiotic metabolism. Their imbalance during dysbiosis is associated with many pathologies in humans, particularly digestive tract diseases such as Crohn's disease, ulcerative colitis, diverticulosis, inflammatory bowel disease, irritable bowel syndrome, colonic polyposis, and colorectal cancer. There is a huge deficit of knowledge and partially contradictory information concerning human methanogens, so much remains to be done to fully understand their physiological role in humans. It is necessary to develop new methods for the identification and culture of methanogens from clinical samples. This will permit to isolate new methanogens species as well as their phenotypic characterization, to explore their genome by sequencing and to study the population dynamics of methanogens by specifying in particular their exact role within the complex flora associated with the mucous microbiota of human.

Methanobrevibacter smithii archaemia in febrile patients with bacteremia, including those with endocarditis

BACKGROUND

The spectrum of infections caused by the emerging opportunistic pathogens methanogens which escape routine detection remains to be described. To determine the prevalence of archaemia, we searched for methanogens in the blood of febrile patients using specific tools.

METHODS

We conducted a prospective study at Institut Hospitalier Universitaire Méditerranée Infection, Marseille, France, September 2018 - April 2020, enrolling 7,716 blood culture samples routinely collected in patients with fever. Blood samples were screened by specific PCR assays for the presence of methanogens. Positive samples were observed by autofluorescence and electron microscopy, analyzed by metagenomics and cultured using previously developed methods. Blood culture bottles experimentally inoculated were used as controls. The presence of methanogens in vascular and cardiac tissues was assessed by indirect immunofluorescence, fluorescent in situ hybridization and PCR-based investigations.

RESULTS

PCR detection attempted in 7,716 blood samples, was negative in all 1,312 aerobic bottles and 810 bacterial culture-negative anaerobic bottles. PCRs were positive in 27/5,594 (0.5%) bacterial culture-positive anaerobic bottles that contained cultures collected from 26 patients. Sequencing confirmed Methanobrevibacter smithii associated with staphylococci in 14 patients, fermentative Enterobacteriaceae in nine patients and streptococci in three patients. Metagenomics confirmed M. smithii in five blood samples, and M. smithii was isolated via culture in broth from two samples; the genomes of these two isolates were sequenced. Blood cultures experimentally inoculated with Enterobacteriaceae, Staphylococcus epidermidis or Staphylococcus hominis yielded hydrogen, but no methane, authentifying observational data.Three patients, all diagnosed with infectious mitral endocarditis, were diagnosed by microscopy, PCR-based detections and culture: we showed M. smithii microscopically and by a specific PCR followed by sequencing method in two of three cardiovascular tissues.

CONCLUSIONS

Using appropriate methods of detection, M. smithii is demonstrated as causing archaemia and endocarditis in febrile patients who are coinfected by bacteria.

Antibiotic resistance genes are increased by combined exposure to sulfamethoxazole and naproxen but relieved by low-salinity

Combined pollution of antibiotic and non-antibiotic pharmaceutical residues is ubiquitous in realistic polluted environments, which is regarded as a complicated emerging pollution. Herein, high-throughput sequencing and high-throughput quantitative PCR were applied to profile the overall changes in microbial communities and antibiotic resistance genes (ARGs) of biofilms in response to a combination of naproxen and sulfamethoxazole pollution. After continuous operation for 120 days, naproxen or/and sulfamethoxazole were efficiently removed, and the salinity of 1.00% enhanced the removal rate of sulfamethoxazole. The high-throughput sequencing revealed that Eubacterium spp. with abundances of over 40.00% dominated in all samples, and combined pollution of naproxen and sulfamethoxazole more readily promoted the occurrence of multidrug-resistant microbes, including Pseudomonas and Methylophilus. The high-throughput quantitative PCR results showed that the combined pollution of naproxen and sulfamethoxazole increased the total abundance of ARGs to approximately 9 copies per cell. In contrast, increasing the salinity to 1.00% greatly reduced the overall abundance of ARGs to below 2 copies per bacterial cell. Mantel test and Procrustes analysis indicated that microbiomes from different treatments had tight links to their respective antibiotic resistomes. Furthermore, network analysis revealed that multidrug-resistant microbes were potential hosts for greatly enriched numbers of ARGs in the combined treatment. As increased salinity eliminated those multidrug-resistant but salt-sensitive microbes, the abundance of ARGs was significantly decreased. These results showed the high probability of the transmission of ARGs in biofilms exposed to combined pollution of naproxen and sulfamethoxazole, which could be relieved by increased salinity.

Nutrient Level Determines Biofilm Characteristics and Subsequent Impact on Microbial Corrosion and Biocide Effectiveness

The impact that nutrient level has on biofilm characteristics, biocide effectiveness, and the associated risk of microbiologically influenced corrosion (MIC) was assessed using multispecies biofilms from two different oilfield consortia. A range of microbiological, microscopy, and corrosion methods demonstrated that the continuous flow of nutrients for the microbial growth resulted in higher activity, thickness, and robustness of the biofilms formed on carbon steel, which induced greater localized corrosion compared to biofilms formed under batch, nutrient-depleted conditions. Despite of the differences in biofilm characteristics, biofilms displayed comparable susceptibilities to glutaraldehyde biocide, with similar log10 reductions and percent reductions of microorganisms under both nutrient conditions. Nevertheless, nutrient replenishment impacted the effectiveness of the biocide in controlling microbial populations; a higher concentration of cells survived the biocide treatment in biofilms formed under a continuous flow of nutrients. Complementary DNA-/RNA-based amplicon sequencing and bioinformatics analysis were used to discriminate the active within the total populations in biofilms established at the different nutrient conditions and allowed the identification of the microbial species that remained active despite nutrient depletion and biocide treatment. Detection of persistent active microorganisms after exposure to glutaraldehyde, regardless of biofilm structure, suggested the presence of microorganisms less susceptible to this biocide and highlighted the importance of monitoring active microbial species for the early detection of biocide resistance in oil production facilities.IMPORTANCE Microbiologically influenced corrosion (MIC) is a complex process that generates economic losses to the industry every year. Corrosion must be managed to prevent a loss of containment of produced fluids to the external environment. MIC management includes the identification of assets with higher MIC risk, which could be influenced by nutrient levels in the system. Assessing biofilms under different nutrient conditions is essential for understanding the impact of flow regime on microbial communities and the subsequent impact on microbial corrosion and on the effectiveness of biocide treatment. This investigation simulates closely oil production systems, which contain piping sections exposed to continuous flow and sections that remain stagnant for long periods. Therefore, the results reported here are useful for MIC management and prevention. Moreover, the complementary methodological approach applied in this investigation highlighted the importance of implementing RNA-based methods for better identification of active microorganisms that survive stress conditions in oil systems.

Effective removal of antibiotic resistance genes and potential links with archaeal communities during vacuum-type composting and positive-pressure composting

As a major reservoir of antibiotics, animal manure contributes a lot to the augmented environmental pressure of antibiotic resistance genes (ARGs). This might be the first study to explore the effects of different ventilation types on the control of ARGs and to identify the relationships between archaeal communities and ARGs during the composting of dairy manure. Several ARGs were quantified via Real-time qPCR and microbial communities including bacteria and archaea were analyzed by High-throughput sequencing during vacuum-type composting (VTC) and positive-pressure composting (PPC). The total detected ARGs and class I integrase gene (intI1) under VTC were significantly lower than that under PPC during each stage of the composting (p<0.001). The relative abundance of potential human pathogenic bacteria (HPB) which were identified based on sequencing information and correlation analysis decreased by 74.6% and 91.4% at the end of PPC and VTC, respectively. The composition of archaeal communities indicated that methane-producing archaea including Methanobrevibacter, Methanocorpusculum and Methanosphaera were dominant throughout the composting. Redundancy analysis suggested that Methanobrevibacter and Methanocorpusculum were positively correlated with all of the detected ARGs. Network analysis determined that the possible hosts of ARGs were different under VTC and PPC, and provided new sights about potential links between archaea and ARGs. Our results showed better performance of VTC in reducing ARGs and potential HPB and demonstrated that some archaea could also be influential hosts of ARGs, and caution the risks of archaea carrying ARGs.

Uneven host cell growth causes lysogenic virus induction in the Baltic Sea

In the Baltic Sea redoxcline, lysogenic viruses infecting prokaryotes have rarely been detected using the commonly used inducing agent mitomycin C. However, it is well known that not all viruses are induceable by mitomycin C and growing evidence suggests that changes in trophic conditions may trigger the induction of lysogenic viruses. We hypothesized that using antibiotics to simulate a strong change in trophic conditions for antibiotica-resistant cells due to reduced competition for resources might lead to the induction of lysogenic viruses into the lytic cycle within these cells. This hypothesis was tested by incubating prokaryotes obtained throughout the Baltic Sea redoxcline in seawater with substantially reduced numbers of viruses. We used a mixture of the protein synthesis-inhibiting antibiotics streptomycin and erythromycin to induce the desired changes in trophic conditions for resistant cells and at the same time ensuring that no progeny viruses were formed in sensitive cells. No inducible lysogenic viruses could be detected in incubations amended with mitomycin C. Yet, the presence of streptomycin and erythromycin increased virus-induced mortality of prokaryotes by 56-930% compared to controls, resulting in the induction of lysogenic viruses equivalent to 2-14% of in situ prokaryotic abundance. The results indicate the existence of a previously unrecognized induction mechanism for lysogenic viruses in the Baltic Sea redoxcline, as the mode of action distinctly differs between the used antibiotics (no virus production within affected cells) and mitomycin C (lysogenic viruses are produced within affected cells). Obtaining accurate experimental data on levels of lysogeny in prokaryotic host cells remains challenging, as relying on mitomycin C alone may severely underestimate lysogeny.

Detection of Methanobrevibacter smithii in vaginal samples collected from women diagnosed with bacterial vaginosis

Vaginosis is a dysbiotic condition of the vaginal cavity that has deleterious effects during pregnancy. The role of methanogens in this disease is unknown since current methods of investigation are not appropriate for the search of methanogens. We prospectively investigated the presence of methanogens in vaginal specimens collected from 33 women thereafter diagnosed with bacterial vaginosis and 92 women thereafter diagnosed without bacterial vaginosis (control group) by direct microscopic examination and fluorescent in situ hybridization, PCR-sequencing, and real-time PCR and isolation and culture. These investigations found only one methanogen, Methanobrevibacter smithii, exclusively in 97% bacterial vaginosis specimens and in two intermediate microbiota specimens. M. smithii was detected microscopically in 2/20 specimens analyzed, by PCR-based observations in 34/125 specimens with 99% sequence similarity with the reference 16S rRNA and mcrA gene sequences and was cultured in 9/40 specimens. These data suggest that the detection of M. smithii could be used as a biomarker for the laboratory diagnosis of bacterial vaginosis.

Co-culture of Methanobrevibacter smithii with enterobacteria during urinary infection

BACKGROUND

Urinary tract infections are known to be caused by bacteria, but the potential implications of archaea have never been studied in this context.

METHODS

In two different university hospital centres we used specific laboratory methods for the detection and culture of archaeal methanogens in 383 urine specimens prospectively collected for diagnosing urinary tract infection (UTI).

FINDINGS

Methanobrevibacter smithii was detected by quantitative PCR and sequencing in 34 (9%) of the specimens collected from 34 patients. Escherichia coli, Klebsiella pneumoniae, Enterobacter sp., Enterococcus faecium and mixed cultures were detected along with M. smithii in eighteen, six, three, one and six urine samples, respectively. Interestingly, using our specific culture method for methanogens, we also isolated M. smithii in 31 (91%) of the 34 PCR positive urine samples. Genotyping the 31 isolates using multispacer sequence typing revealed three different genotypes which have been previously reported in intestinal microbiota. Antibiotic susceptibility testing found the 31 isolates to be in vitro susceptible to metronidazole (MIC: 1 mg/L) but resistant to fosfomycin, sulfamethoxazole-trimethoprim, amoxicillin-clavulanate and ofloxacin, commonly used to treat bacterial UTI. Finally, 19 (54%) of the 34 patients in whose urine samples M. smithii was detected were diagnosed with UTIs, including cystitis, pyelonephritis and prostatitis.

INTERPRETATION

Our results show that M. smithii is part of the urinary microbiota of some individuals and could play a role in community-acquired UTI in association with enteric bacteria. FUND: This study was supported by IHU Méditerranée Infection, Marseille, France.

Nine Cases of Methanogenic Archaea in Refractory Sinusitis, an Emerging Clinical Entity

The authors report the cases of 9 patients eventually diagnosed with methanogenic archaea refractory or recalcitrant chronic rhinosinusitis, a condition known to involve various anaerobic bacteria but in which the role of methanogenic archaea is unknown. The authors retrospectively searched these microorganisms by PCR in surgically-collected sinusal pus specimens from patients diagnosed with refractory sinusitis, defined by the persistance of sinus inflammation and related-symptoms for more than 12 weeks despite appropriate treatment. Of the 116 tested sinus surgical specimens, 12 (10.3%) from 9 patients (six females, three males; aged 20-71 years) were PCR-positive. These specimens were further investigated by fluorescence in-situ hybridization, PCR amplicon-sequencing and culture. Methanobrevibacter smithii was documented in four patients and Methanobrevibacter oralis in another four, one of whom was also culture-positive. They were associated with a mixed flora including Gram-positive and Gram-negative bacteria. In the latter patient, "Methanobrevibacter massiliense" was the sole microorganism detected. These results highlight methanogenic archaea as being part of a mixed anaerobic flora involved in refractory sinusitis, and suggest that the treatment of this condition should include an antibiotic active against methanogens, notably a nitroimidazole derivative.

Metronidazole: an update on metabolism, structure-cytotoxicity and resistance mechanisms

Metronidazole, a nitroimidazole, remains a front-line choice for treatment of infections related to inflammatory disorders of the gastrointestinal tract including colitis linked to Clostridium difficile. Despite >60 years of research, the metabolism of metronidazole and associated cytotoxicity is not definitively characterized. Nitroimidazoles are prodrugs that are reductively activated (the nitro group is reduced) under low oxygen tension, leading to imidazole fragmentation and cytotoxicity. It remains unclear if nitroimidazole reduction (activation) contributes to the cytotoxicity profile, or whether subsequent fragmentation of the imidazole ring and formed metabolites alone mediate cytotoxicity. A molecular mechanism underpinning high level (>256 mg/L) bacterial resistance to metronidazole also remains elusive. Considering the widespread use of metronidazole and other nitroimidazoles, this review was undertaken to emphasize the structure-cytotoxicity profile of the numerous metabolites of metronidazole in human and murine models and to examine conflicting reports regarding metabolite-DNA interactions. An alternative hypothesis, that DNA synthesis and repair of existing DNA is indirectly inhibited by metronidazole is proposed. Prokaryotic metabolism of metronidazole is detailed to discuss new resistance mechanisms. Additionally, the review contextualizes the history and current use of metronidazole, rates of metronidazole resistance including metronidazole MDR as well as the biosynthesis of azomycin, the natural precursor of metronidazole. Changes in the gastrointestinal microbiome and the host after metronidazole administration are also reviewed. Finally, novel nitroimidazoles and new antibiotic strategies are discussed.

Identification and biosynthesis of 2-(1H-imidazol-5-yl) ethan-1-ol (histaminol) in methanogenic archaea

Histaminol is a relatively rare metabolite most commonly resulting from histidine metabolism. Here we describe histaminol production and secretion into the culture broth by the methanogen Methanococcus maripaludis S2 as well as a number of other methanogens. This work is the first identification of this compound as a natural product in methanogens. Its biosynthesis from histidine was confirmed by the incorporation of ²H3-histidine into histaminol by growing cells of M. maripaludis S2. Possible functions of this molecule could be cell signaling as observed with histamine in eukaryotes or uptake of metal ions.

Exploring tRNA gene cluster in archaea

BACKGROUND

Shared traits between prokaryotes and eukaryotes are helpful in the understanding of the tree of life evolution. In bacteria and eukaryotes, it has been shown a particular organisation of tRNA genes as clusters, but this trait has not been explored in the archaea domain.

OBJECTIVE

Explore the occurrence of tRNA gene clusters in archaea.

METHODS

In-silico analyses of complete and draft archaeal genomes based on tRNA gene isotype and synteny, tRNA gene cluster content and mobilome elements.

FINDINGS

We demonstrated the prevalence of tRNA gene clusters in archaea. tRNA gene clusters, composed of archaeal-type tRNAs, were identified in two Archaea class, Halobacteria and Methanobacteria from Euryarchaeota supergroup. Genomic analyses also revealed evidence of the association between tRNA gene clusters to mobile genetic elements and intra-domain horizontal gene transfer.

MAIN CONCLUSIONS

tRNA gene cluster occurs in the three domains of life, suggesting a role of this type of tRNA gene organisation in the biology of the living organisms.