The gut microbiota of a patient with resistant tuberculosis is more comprehensively studied by culturomics than by metagenomics

The oral microbiome of newly diagnosed tuberculosis patients; a pilot study

BACKGROUND

Changes in oral microbiota composition (dysbiosis) have long been known to play a key role in the pathogenesis of oral and systemic diseases including respiratory diseases. However, till now, no study has assessed changes in oral microbiota following tuberculosis (TB) infection in humans.

AIMS

This is the first study of its kind that aimed to investigate oral microbial dysbiosis in newly diagnosed, treatment naïve, TB patients.

METHODS

Oral swab samples were collected from newly diagnosed TB patients (n = 20) and age, gender and ethnicity matched healthy controls (n = 10). DNA was extracted and microbiota analyzed by sequencing the hypervariable (V3-V4) region of the bacterial 16S rRNA gene using Illumina MiSeq platform. Bioinformatics and statistical analyses were performed using QIIME and R.

RESULTS

Bacterial richness, diversity and community composition were significantly different between TB patients and healthy controls. The two groups also exhibit differential abundance at phylum, class, genus and species levels. LEfSe analysis revealed enrichment (LDA scores (log10) >2, P < 0.05) of Firmicutes (especially Streptococcus) and Actinobacteriota (especially Rothia) in TB patients relative to healthy controls. Gene function prediction analysis showed upregulation of metabolic pathways related to carbohydrates (butanoate, galactose) and fatty acids metabolism, antibiotics biosynthesis, proteosome and immune system signaling.

CONCLUSION

These observations suggest significant variations in diversity, relative abundance and functional potential of oral microbiota of TB patients compared to healthy controls thereby suggesting potential role of oral bacterial dysbiosis in TB pathogenesis. However, longitudinal studies using powerful metagenomic and transcriptomic approaches are crucial to more fully understand and confrim these findings.

Ethanol-Producing Enterocloster bolteae Is Enriched in Chronic Hepatitis B-Associated Gut Dysbiosis: A Case-Control Culturomics Study

BACKGROUND

Hepatitis B virus (HBV) infection is a global health epidemic that causes fatal complications, leading to liver cirrhosis and hepatocellular carcinoma. The link between HBV-related dysbiosis and specific bacterial taxa is still under investigation. Enterocloster is emerging as a new genus (formerly Clostridium), including Enterocloster bolteae, a gut pathogen previously associated with dysbiosis and human diseases such as autism, multiple sclerosis, and inflammatory bowel diseases. Its role in liver diseases, especially HBV infection, is not reported.

METHODS

The fecal samples of eight patients with chronic HBV infection and ten healthy individuals were analyzed using the high-throughput culturomics approach and compared to 16S rRNA sequencing. Quantification of ethanol, known for its damaging effect on the liver, produced from bacterial strains enriched in chronic HBV was carried out by gas chromatography-mass spectrometry.

RESULTS

Using culturomics, 29,120 isolated colonies were analyzed by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry (MALDI-TOF); 340 species were identified (240 species in chronic HBV samples, 254 species in control samples) belonging to 169 genera and 6 phyla. In the chronic HBV group, 65 species were already known in the literature; 48 were associated with humans but had not been previously found in the gut, and 17 had never been associated with humans previously. Six species were newly isolated in our study. By comparing bacterial species frequency, three bacterial genera were serendipitously found with significantly enriched bacterial diversity in patients with chronic HBV: Enterocloster, Clostridium, and Streptococcus (p = 0.0016, p = 0.041, p = 0.053, respectively). However, metagenomics could not identify this enrichment, possibly concerning its insufficient taxonomical resolution (equivocal assignment of operational taxonomic units). At the species level, the significantly enriched species in the chronic HBV group almost all belonged to class Clostridia, such as Clostridium perfringens, Clostridium sporogenes, Enterocloster aldenensis, Enterocloster bolteae, Enterocloster clostridioformis, and Clostridium innocuum. Two E. bolteae strains, isolated from two patients with chronic HBV infection, showed high ethanol production (27 and 200 mM).

CONCLUSIONS

Culturomics allowed us to identify Enterocloster species, specifically, E. bolteae, enriched in the gut microbiota of patients with chronic HBV. These species had never been isolated in chronic HBV infection before. Moreover, ethanol production by E. bolteae strains isolated from the chronic HBV group could contribute to liver disease progression. Additionally, culturomics might be critical for better elucidating the relationship between dysbiosis and chronic HBV infection in the future.

Therapeutically targeting the consequences of HIV-1-associated gastrointestinal dysbiosis: Implications for neurocognitive and affective alterations

Approximately 50 % of the individuals living with human immunodeficiency virus type 1 (HIV-1) are plagued by debilitating neurocognitive impairments (NCI) and/or affective alterations. Sizeable alterations in the composition of the gut microbiome, or gastrointestinal dysbiosis, may underlie, at least in part, the NCI, apathy, and/or depression observed in this population. Herein, two interrelated aims will be critically addressed, including: 1) the evidence for, and functional implications of, gastrointestinal microbiome dysbiosis in HIV-1 seropositive individuals; and 2) the potential for therapeutically targeting the consequences of this dysbiosis for the treatment of HIV-1-associated NCI and affective alterations. First, gastrointestinal microbiome dysbiosis in HIV-1 seropositive individuals is characterized by decreased alpha (α) diversity, a decreased relative abundance of bacterial species belonging to the Bacteroidetes phylum, and geographic-specific alterations in Bacillota (formerly Firmicutes) spp. Fundamentally, changes in the relative abundance of Bacteroidetes and Bacillota spp. may underlie, at least in part, the deficits in γ-aminobutyric acid and serotonin neurotransmission, as well as prominent synaptodendritic dysfunction, observed in this population. Second, there is compelling evidence for the therapeutic utility of targeting synaptodendritic dysfunction as a method to enhance neurocognitive function and improve motivational dysregulation in HIV-1. Further research is needed to determine whether the therapeutics enhancing synaptic efficacy exert their effects by altering the gut microbiome. Taken together, understanding gastrointestinal microbiome dysbiosis resulting from chronic HIV-1 viral protein exposure may afford insight into the mechanisms underlying HIV-1-associated neurocognitive and/or affective alterations; mechanisms which can be subsequently targeted via novel therapeutics.

Maliibacterium massiliense gen. nov. sp. nov., Isolated from Human Feces and Proposal of Maliibacteriaceae fam. nov

Bacterial strain Marseille-P3954 was isolated from a stool sample of a 35-year-old male patient living in France. It was a gram-positive, rod-shaped anaerobic, non-motile, and non-spore-forming bacterium. C_16:0 and C_18:1n9 were the major fatty acid, while its genome measured 2,422,126 bp with 60.8 mol% of G+C content. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain Marseille-P3954 had 85.51% of similarity with Christensenella minuta, its closest related species with standing in nomenclature. As this value is very low compared to the recommended threshold, it suggested that the Marseille-P3954 strain belongs to a new bacterial genus, classified in a new family. On the basis of these genomic, phenotypic, and phylogenetic evidences, we propose that strain Marseille-P3954 should be classified as a new genus and species, Maliibacterium massiliense gen. nov., sp. nov. The type strain of M. massiliense sp. nov. is Marseille-P3954 (CSUR P3954 = CECT 9568).

Impact of tuberculosis disease on human gut microbiota: a systematic review

INTRODUCTION

This systematic review evaluates the gut microbiota (GM) status in tuberculosis (TB) patients compared to healthy volunteers due to the disease or its treatment.

AREAS COVERED

We conducted a systematic review of all articles published in PubMed, Web of Science, and Embase that assessed the impact of TB disease and anti-tubercular therapy (ATT) on GM from inception till January 2022 (Protocol registration number in PROSPERO: CRD42021261884). Regarding the microbial diversity indices and taxonomy, we found a significant difference in GM status between the TB and healthy control (HC) groups. We found an overabundance of Phylum Proteobacteria and depletion of some short-chain fatty acid-producing bacteria genera like Bifidobacteria, Roseburia, and Ruminococcus in the TB group. We found that ATT exacerbates the degree of dysbiosis caused by Mycobacteria tuberculosis disease.

EXPERT OPINION

The modulation of GM in TB patients in clinical practice may serve as a promising target to reverse the dysbiosis caused. Moreover, this can optimistically change the TB treatment outcome. We expect that appropriate probiotic supplementation with antimycobacterial treatment during tuberculosis disease will help stabilize the GM throughout the treatment phase and protect the GM from dysbiosis.

Marine Bioprospecting, Biocatalysis and Process Development

Oceans possess tremendous diversity in microbial life. The enzymatic machinery that marine bacteria present is the result of extensive evolution to assist cell survival under the harsh and continuously changing conditions found in the marine environment. Several bacterial cells and enzymes are already used at an industrial scale, but novel biocatalysts are still needed for sustainable industrial applications, with benefits for both public health and the environment. Metagenomic techniques have enabled the discovery of novel biocatalysts, biosynthetic pathways, and microbial identification without their cultivation. However, a key stage for application of novel biocatalysts is the need for rapid evaluation of the feasibility of the bioprocess. Cultivation of not-yet-cultured bacteria is challenging and requires new methodologies to enable growth of the bacteria present in collected environmental samples, but, once a bacterium is isolated, its enzyme activities are easily measured. High-throughput screening techniques have also been used successfully, and innovative in vitro screening platforms to rapidly identify relevant enzymatic activities continue to improve. Small-scale approaches and process integration could improve the study and development of new bioprocesses to produce commercially interesting products. In this work, the latest studies related to (i) the growth of marine bacteria under laboratorial conditions, (ii) screening techniques for bioprospecting, and (iii) bioprocess development using microreactors and miniaturized systems are reviewed and discussed.

Culturomics, a potential approach paving the way toward bacteriotherapy

The human microbiota has been extensively studied over the past decade to describe its role in health and diseases. Numerous studies showed the presence of bacterial imbalance in a variety of human health conditions, suggesting great potential for the development of bacteriotherapies. Identifying mechanisms involving the human microbiota has been very challenging due to the complex data generated by molecular approaches and the limited number of organisms isolated by culture and described. This review summarizes the efforts done to describe the human microbiota through culturomics and the advancements in culturing the organisms residing at different body sites.

Cultivating marine bacteria under laboratory conditions: Overcoming the “unculturable” dogma

Underexplored seawater environments may contain biological resources with potential for new biotechnological applications. Metagenomic techniques revolutionized the study of bacterial communities but culture dependent methods will still be important to help the biodiscovery of new products and enzymes from marine bacteria. In this context, we promoted the growth of bacteria from a marine rock pond by culture dependent techniques and compared the results with culture independent methods. The total number of bacteria and diversity were studied in different agar plate media during 6 weeks. Agar plate counting was of the same order of magnitude of direct microscopy counts. The highest efficiency of cultivation was 45% attained in marine agar medium. Molecular analysis revealed 10 different phyla of which only four were isolated by the culture dependent method. On the other hand, four taxonomic orders were detected by cultivation but not by the molecular technique. These include bacteria from the phyla Bacillota and Actinomycetota. Our study shows that it is possible to grow more than the traditionally considered 1% of bacteria from a seawater sample using standard agar plate techniques and laboratorial conditions. The results also demonstrate the importance of culture methods to grow bacteria not detected by molecular approaches for future biotechnological applications.

Exploring the role of Microbiome in Susceptibility, Treatment Response and Outcome among Tuberculosis Patients from Pakistan: study protocol for a prospective cohort study (Micro-STOP)

INTRODUCTION

Tuberculosis (TB) caused by Mycobacterium tuberculosis is a common infectious disease associated with significant morbidity and mortality, especially in low-income and middle-income countries. Successful treatment of the disease requires prolonged intake (6-8 months) of multiple antibiotics with potentially detrimental consequences on the composition and functional potential of the human microbiome. The protocol described in the current study aims to identify microbiome (oral and gut) signatures associated with TB pathogenesis, treatment response and outcome in humans.

METHODS AND ANALYSIS

Four hundred and fifty, newly diagnosed patients with TB from three district levels (Peshawar, Mardan and Swat) TB diagnosis and treatment centres, will be recruited in this non-interventional, prospective cohort study and will be followed and monitored until treatment completion. Demographic and dietary intake data, anthropometric measurement and blood, stool and salivary rinse samples will be collected at baseline, day 15, month-2 and end of the treatment. Additionally, we will recruit age (±3 years) and sex-matched healthy controls (n=30). Blood sampling will allow monitoring of the immune response during the treatment, while salivary rinse and faecal samples will allow monitoring of dynamic changes in oral and gut microbiome diversity. Within this prospective cohort study, a nested case-control study design will be conducted to assess perturbations in oral and gut microbiome diversity (microbial dysbiosis) and immune response and compare between the patients groups (treatment success vs failure).

ETHICS AND DISSEMINATION

The study has received ethics approval from the Ethic Board of Khyber Medical University Peshawar, and administrative approval from Provincial TB Control Programme of Khyber Pakhtunkhwa, Pakistan. The study results will be presented in national and international conferences and published in peer-reviewed journals.

TRIAL REGISTRATION NUMBER

NCT04985994.

Integrating 16S rRNA amplicon metagenomics and selective culture for developing thermophilic bacterial inoculants to enhance manure composting

Composting is an important method for treating and recycling organic waste, and the use of microbial inoculants can increase the efficiency of composting. Herein, we illustrate an approach that integrate 16S rRNA amplicon metagenomics and selective culture of thermophilic bacteria for the development of inoculants to improve manure composting. The 16S rRNA amplicon sequencing analysis revealed that Firmicutes and Actinobacteria were dominant in the composting mixture, and that different microbial hubs succeeded during the thermophilic stage. All isolated thermophilic bacteria were affiliated with the order Bacillales, such as Geobacillus, Bacillus, and Aeribacillus. These isolated thermophilic bacteria were grouped into 11 phylotypes, which shared ＞99% sequence identity to 0.15% to 5.32% of 16S rRNA reads by the amplicon sequencing. Three of these phylotypes transiently enriched during the thermophilic stage. Six thermophilic bacteria were selected from the three phylotypes to obtain seven microbial inoculants. Five out of seven of the microbial inoculants enhanced the thermophilic stage of composting by 16.9% to 52.2%. Three-dimensional excitation emission matrix analysis further revealed that two inoculants (Thermoactinomyces intermedius and Ureibacillus thermophilus) stimulated humification. Additionally, the 16S rRNA amplicon sequencing analysis revealed that inoculation with thermophilic bacteria enhanced the succession of the microbial community during composting. In conclusion, 16S rRNA amplicon metagenomics is a useful tool for the development of microbial inoculants to enhance manure composting.

Effect of red osier dogwood extract on growth performance, blood biochemical parameters, and gut functionality of broiler chickens challenged or unchallenged intraperitoneally with Salmonella Enteritidis lipopolysaccharide

As we advance in the search for antibiotic-alternatives, harnessing plant materials with high total polyphenol concentration (TPC) would be quintessential. Given the high TPC in red osier dogwood (ROD) extract, the current study aimed to determine its efficacy on the growth performance, intestinal health, blood biochemistry, and antioxidant capacity of broiler chickens. A 21-day 4x2 factorial feeding trial was conducted based on two main factors namely, dietary treatments and Salmonella Enteritidis Lipopolysaccharides SE-LPS) challenge. A total of 384 one-day-old mixed-sex Cobb-500 broiler chicks were randomly allotted to four dietary treatments - Negative control (NC), NC + 0.05% bacitracin methylene disalicylate (BMD), NC + 0.3%ROD, and NC+0.5% ROD. Each treatment was assigned to eight replicates with six birds/replicate. On d 13 and 20, half of the birds were intraperitoneally injected with 1mL phosphate-buffered-saline /kg BW of birds (Unchallenged-group) and the remaining half with 1mg SE-LPS /kg BW of birds (Challenged-group). Average weight gain (AWG), average feed intake (AFI), feed conversion ratio (FCR), and mortality were determined weekly. On d 21, ten chickens/treatment were euthanized for measuring blood biochemical parameters, immune organ weights, caecal SCFA, and caeca microbiota. The SE-LPS decreased (P < 0.05) AWG and FCR on d 14 and 21, respectively. On d 14, 21, and overall basis, both ROD extract levels marginally improved (P < 0.05) the AWG of unchallenged birds compared to other treatments in the unchallenged-group. Challenged and unchallenged birds fed ROD extract had deeper (P < 0.05) crypt depth (CD) and higher villus height:CD, respectively, in the ileum. Globulin (GLB) and albumin:GLB were increased and reduced (P < 0.05), respectively, among birds fed 0.3%ROD compared to other treatments. There was no treatment effect on caeca SCFA, relative weight of immune organs, and serum antioxidants. Birds fed ROD extract had a higher (P < 0.05) relative abundance of caecal Lactobacillus and Streptococcus genera compared to the antibiotic treatment. Conclusively, incorporating 0.3% and 0.5%ROD extract into broiler chickens' nutrition improved growth performance and ileal morphology, and modified caecal microbiota of broiler chickens, regardless of the intraperitoneal SE-LPS challenge.

Alterations of gut microbiota in patients with active pulmonary tuberculosis in China: a pilot study

BACKGROUND

The aim of this study was to identify the differences in diversity, composition, and function of the gut microbiota between tuberculosis (TB) patients and healthy controls (HCs).

METHODS

A cross-sectional study was conducted in three cities of China. Stool samples from 94 treatment-naive TB patients and 62 HCs were analyzed by 16S rRNA gene sequencing. TB patients were further divided into antibiotic-free and antibiotic-exposure according to their use of non-specific antibiotics before the TB diagnosis.

RESULTS

Compared with HCs, antibiotic-free TB patients presented a different gut microbial community (P < 0.005) and decreased Shannon diversity (P < 0.005). Among TB patients, the relative abundances of short-chain fatty acid (SCFA)-producing genera such as Lachnospiraceae ND3007 group (log2(FC) = -2.74) were lower, while several conditional pathogen-related genera such as Enterococcus (log2(FC) = 12.05) and Rothia (log2(FC) = 6.322) were at higher levels. In addition, 41% of patients received antibiotics before TB diagnosis. Antibiotic exposure was correlated with an additional reduction in α diversity and depletion of SCFA-producing bacteria. Microbial functional analysis revealed that the biosynthesis capacity of amino acids and fatty acids was lower among TB patients compared to HCs.

CONCLUSIONS

Significant alterations in gut microbiota composition and metabolic pathways of TB patients were observed. Antibiotic exposure could alter the gut microbiota of TB patients, which should be considered in anti-TB treatment.

Clostridium culturomicium sp. nov. and Clostridium jeddahitimonense sp. nov., novel members of the Clostridium genus isolated from the stool of an obese Saudi Arabian

Taxono-genomics is an innovative concept coined for the description of new bacterial species. Phenotypic characteristics were combined with a genomic approach to describe two new species within the Clostridium senso stricto genus: Clostridium culturomicium strain CL-6^T and Clostridium jeddahitimonense strain CL-2^T, both isolated from the gut microbiota of an obese man from Saudi Arabia. Strains CL-6^T and CL-2^T shared a similarity of 98.4% with the 16S rRNA gene of Clostridium subterminale strain JCM 1417^T (accession number NR113027) and 98% with that of Clostridium disporicum strain DS1^T (accession number NR026491), respectively. The highest OrthoANI values were shared with Clostridium punense for strain CL-6^T (70.8%) and with Clostridium disporicum for strain CL-2^T (87.1%). Additionally, strain CL-6^T and strain CL-2^T shared a 16S rRNA similarity of 91.4%. Both strains were anaerobic, spore-forming and Gram-stain-positive non-motile bacilli. The genome of Clostridium culturomicium strain CL-6^T is 4,325,182 bp long with 32.2% GC content. As for Clostridium jeddahitimonense strain CL-2^T, the genome is 4,074,758 bp long with 29.2% GC content.

Defined gut microbial communities: promising tools to understand and combat disease

Defined gut microbial communities are emerging tools that allow detailed studies of microbial ecosystems and their interactions with the host. In this article, we review strategies underlying the design of defined consortia and summarize the efforts to introduce simplified communities into in vitro and in vivo models. We conclude by highlighting the potential of defined microbial ecosystems as effective modulation strategies for health benefits.

Gut Microbiota: the Emerging Link to Lung Homeostasis and Disease

The gut microbiota plays a crucial role in the development of the immune system and confers benefits or disease susceptibility to the host. Emerging studies have indicated the gut microbiota could affect pulmonary health and disease through cross talk between the gut microbiota and the lungs. Gut microbiota dysbiosis could lead to acute or chronic lung disease, such as asthma, tuberculosis, and lung cancer. In addition, the composition of the gut microbiota may be associated with different lung diseases, the prevalence of which also varies by age. Modulation of the gut microbiota through short-chain fatty acids, probiotics, and micronutrients may present potential therapeutic strategies to protect against lung diseases. In this review, we will provide an overview of the cross-talk between the gut microbiota and the lungs, as well as elucidate the underlying pathogenesis and/or potential therapeutic strategies of some lung diseases from the point of view of the gut microbiota.

Multicenter analysis of sputum microbiota in tuberculosis patients

The impact of tuberculosis and of anti-tuberculosis therapy on composition and modification of human lung microbiota has been the object of several investigations. However, no clear outcome has been presented so far and the relationship between M. tuberculosis pulmonary infection and the resident lung microbiota remains vague. In this work we describe the results obtained from a multicenter study of the microbiota of sputum samples from patients with tuberculosis or unrelated lung diseases and healthy donors recruited in Switzerland, Italy and Bangladesh, with the ultimate goal of discovering a microbiota-based biomarker associated with tuberculosis. Bacterial 16S rDNA amplification, high-throughput sequencing and extensive bioinformatic analyses revealed patient-specific flora and high variability in taxon abundance. No common signature could be identified among the individuals enrolled except for minor differences which were not consistent among the different geographical settings. Moreover, anti-tuberculosis therapy did not cause any important variation in microbiota diversity, thus precluding its exploitation as a biomarker for the follow up of tuberculosis patients undergoing treatment.

Multi-Omics Approaches: The Key to Improving Respiratory Health in People With Cystic Fibrosis?

The advent of high-throughput multi-omics technologies has underpinned the expansion in lung microbiome research, increasing our understanding of the nature, complexity and significance of the polymicrobial communities harbored by people with CF (PWCF). Having established that structurally complex microbial communities exist within the airways, the focus of recent research has now widened to investigating the function and dynamics of the resident microbiota during disease as well as in health. With further refinement, multi-omics approaches present the opportunity to untangle the complex interplay between microbe-microbe and microbe-host interactions in the lung and the relationship with respiratory disease progression, offering invaluable opportunities to discover new therapeutic approaches for our management of airway infection in CF.

Intestinal microbiota disruption limits the isoniazid mediated clearance of Mycobacterium tuberculosis in mice

Tuberculosis (TB) continues to remain a global threat due to the emergence of drug-resistant Mycobacterium tuberculosis (Mtb) strains and toxicity associated with TB drugs. Intestinal microbiota has been reported to affect the host response to immunotherapy and drugs. However, how it affects the potency of first-line TB drug isoniazid (INH) is largely unknown. Here, we examined the impact of gut microbial dysbiosis on INH efficiency to kill Mtb. In this study, we employed in vivo mouse model, pretreated with broad-spectrum antibiotics (Abx) cocktail to disrupt their intestinal microbial population prior to Mtb infection and subsequent INH therapy. We demonstrated that microbiota disruption results in the impairment of INH-mediated Mtb clearance, and aggravated TB-associated tissue pathology. Further, it suppressed the innate immunity and reduced CD4 T-cell response against Mtb. Interestingly, a distinct shift of gut microbial profile was noted with abundance of Enterococcus and reduction of Lactobacillus and Bifidobacterium population. Our results show that the intestinal microbiota is crucial determinant in efficacy of INH to kill Mtb and impacts the host immune response against infection. This work provides an intriguing insight into the potential links between host gut microbiota and potency of INH.

Alternative primers to identify a range of apicomplexan parasites

Here we present an alternative polymerase chain reaction (PCR) approach using 18S rDNA to identify apicomplexan parasites. A new primer set was designed and evaluated in silico and in vitro. This new PCR could detect some apicomplexan genera based on amplicon size and identify at least 45 species after sequencing.

Characterization of native knee microorganisms using next-generation sequencing in patients undergoing primary total knee arthroplasty

BACKGROUND

Next-generation sequencing (NGS) offers improved sensitivity compared to culture-based methods for identifying organisms from synovial joints. It remains unclear whether native microorganisms exist in a joint, and positive NGS results may be interpreted as pathologic when in fact they may represent this native microbiome. The purpose of this study was to characterize the native knee microorganism profile in patients undergoing primary total knee arthroplasty (TKA).

METHODS

Forty consecutive patients with osteoarthritis undergoing primary total knee arthroplasty were enrolled prospectively. During TKA surgery but prior to arthrotomy, the native knee was aspirated and the fluid was sent for NGS analysis. Immediately after arthrotomy, four separate tissue samples were also sent for NGS analysis. All microbes identified by NGS were recorded.

RESULTS

Twelve out of forty patients (30%) had at least one positive organism identified by NGS from their native knee. Of those with positive NGS results, 9/12 (75%) had more than one organism identified (range two to 11). There were no significant differences in demographics, comorbidities, or incidence of prior knee injections between the two groups. There were 48 unique organisms identified from all patients, and the average number of organisms identified by NGS was 4.6 per patient. Four sterile water controls were all negative for organisms.

CONCLUSION

A proportion of patients with osteoarthritis undergoing primary total knee arthroplasty have organisms identified in their joint by NGS at the time of surgery. Organisms identified after TKA by NGS when concern for periprosthetic joint infection exists may represent the native microbiome rather than pathogenic microbes.

Shen-ling-bai-zhu-san ameliorates inflammation and lung injury by increasing the gut microbiota in the murine model of Streptococcus pneumonia-induced pneumonia

Background

Shen-ling-bai-zhu-san (SLBZS) regulates inflammation and gut microbiota which are associated with Streptococcus pneumoniae (Spn)-induced pneumonia. So, we studied the therapeutic effect of SLBZS and evaluated whether gut microbiota is associated with the effects of SLBZS in improving Spn-induced pneumonia.

Methods

Spn-induced pneumonia NIH mice were treated by SLBZS and cefixime. A CT scan was performed and Myeloperoxidase (MPO) activity in lung homogenates was determined using the MPO Colorimetric Assay Kit. Inflammation levels in lung homogenates were measured using ELISA. Bacterial load was coated on a TSAII sheep blood agar. Intestinal gut microbiota information was analyzed according to sequencing libraries.

Results

SLBZS decreased bacterial load, reduced wet/dry weight ratio, inhibited myeloperoxidase activity, reduced the neutrophils count, and ameliorated lung injury. Furthermore, SLBZS inhibited interleukin (IL)-1β, IL-6, tumor necrosis factor-α, IL-2, IL-8, IL-12, and interferon-γ secretion and enhanced IL-10 secretion. These results suggest that SLBZS ameliorates lung injury in mice with Spn-induced pneumonia. Moreover, SLBZS reduced inflammatory cytokine levels in a concentration-dependent manner and increased gut microbiota abundance and diversity. After SLBZS treatment, bacteria such as Epsilonbacteraeota, Bacteroidetes, Actinobacteria, Proteobacteria, and Patescibacteria were significantly reduced, while Tenericutes and Firmicutes were significantly increased.

Conclusion

SLBZS ameliorates inflammation, lung injury, and gut microbiota in mice with S. pneumoniae-induced pneumonia.

Alcohol pretreatment of stools effect on culturomics

Recent studies have used ethanol stool disinfection as a mean of promoting valuable species’ cultivation in bacteriotherapy trials for Clostridium difficile infections (CDI) treatment with a particular focus on sporulating bacteria. Moreover, the culturomic approach has considerably enriched the repertoire of cultivable organisms in the human gut in recent years. This study aimed to apply this culturomic approach on fecal donor samples treated with ethanol disinfection to evidence potential beneficial microbes that could be used in bacteriotherapy trials for the treatment of CDI. Thereby, a total of 254 bacterial species were identified, 9 of which were novel. Of these, 242 have never been included in clinical trials for the treatment of CDIs, representing potential new candidates for bacteriotherapy trials. While non-sporulating species were nevertheless more affected by the ethanol pretreatment than sporulating species, the ethanol disinfection technique did not specifically select bacteria able to sporulate, as suggested by previous studies. Furthermore, some bacteria previously considered as potential candidates for bacteriotherapy have been lost after ethanol treatment. This study, while enriching the bacterial repertoire of the human intestine, would nevertheless require determining the exact contribution of each of species composing the bacterial consortia intended to be administered for CDI treatment.

Consolidation of Clinical Microbiology Laboratories and Introduction of Transformative Technologies

Clinical microbiology is experiencing revolutionary advances in the deployment of molecular, genome sequencing-based, and mass spectrometry-driven detection, identification, and characterization assays. Laboratory automation and the linkage of information systems for big(ger) data management, including artificial intelligence (AI) approaches, also are being introduced. The initial optimism associated with these developments has now entered a more reality-driven phase of reflection on the significant challenges, complexities, and health care benefits posed by these innovations. With this in mind, the ongoing process of clinical laboratory consolidation, covering large geographical regions, represents an opportunity for the efficient and cost-effective introduction of new laboratory technologies and improvements in translational research and development. This will further define and generate the mandatory infrastructure used in validation and implementation of newer high-throughput diagnostic approaches. Effective, structured access to large numbers of well-documented biobanked biological materials from networked laboratories will release countless opportunities for clinical and scientific infectious disease research and will generate positive health care impacts. We describe why consolidation of clinical microbiology laboratories will generate quality benefits for many, if not most, aspects of the services separate institutions already provided individually. We also define the important role of innovative and large-scale diagnostic platforms. Such platforms lend themselves particularly well to computational (AI)-driven genomics and bioinformatics applications. These and other diagnostic innovations will allow for better infectious disease detection, surveillance, and prevention with novel translational research and optimized (diagnostic) product and service development opportunities as key results.

Single-Anastomosis Duodenal Jejunal Bypass Improve Glucose Metabolism by Regulating Gut Microbiota and Short-Chain Fatty Acids in Goto-Kakisaki Rats

In recent years, bariatric surgery has emerged as a promising treatment for type 2 diabetes. Bariatric surgery is known to cause alterations in the relative abundance and composition of gut microbiota, which may lead to alterations in the levels of Short-Chain Fatty Acids (SCFAs) that are produced during fermentation by gut microbes. However, little is known about the mechanism of improved glucose metabolism mediated by gut microbiota following bariatric surgery. The aim of our study was to explore whether changes in gut microbiota and in fecal SCFA could be detected following single-anastomosis duodenal jejunal bypass (DJB-sa) surgery, a type of bariatric surgery, and whether these alterations might be related to the improvement of glucose metabolism. To this end, we performed DJB-sa or SHAM surgery on Goto-Kakisaki (GK) rats. We then compared the glucose metabolism as well as changes in gut microbiota and SCFAs levels between both groups. Our results showed that DJB-sa surgery was associated with a significant decrease in fasting blood glucose (FBG), intraperitoneal glucose tolerance test (IPGTT), and fasting serum insulin (FSI). And, DJB-sa led to a change in the composition of gut microbiota including an increase in the relative abundance of SCFA-producing bacteria (Bifidobacterium and Subdoligranulum). Moreover, the levels of six SCFAs in feces, as well as the intestinal expression of SCFA receptors including G-protein-coupled receptor 41 (GPR41), G-protein-coupled receptor 43 (GPR43), and G-protein-coupled receptor 109A (GPR109A), and the expression of Glucagon-like peptide-1 (GLP-1) displayed a significant increase following DJB-sa compared with the Sham group. Thus, the gut microbiota may contribute to the improvement of glucose metabolism in type 2 diabetes following DJB-sa. In conclusion, our study shows that DJB-sa improves glucose metabolism by modulating gut microbiota and by increasing short-chain fatty acid production.

The microbiome and tuberculosis: state of the art, potential applications, and defining the clinical research agenda

The diverse microbial communities within our bodies produce metabolites that modulate host immune responses. Even the microbiome at distal sites has an important function in respiratory health. However, the clinical importance of the microbiome in tuberculosis, the biggest infectious cause of death worldwide, is only starting to be understood. Here, we critically review research on the microbiome's association with pulmonary tuberculosis. The research indicates five main points: (1) susceptibility to infection and progression to active tuberculosis is altered by gut Helicobacter co-infection, (2) aerosol Mycobacterium tuberculosis infection changes the gut microbiota, (3) oral anaerobes in the lung make metabolites that decrease pulmonary immunity and predict progression, (4) the increased susceptibility to reinfection of patients who have previously been treated for tuberculosis is likely due to the depletion of T-cell epitopes on commensal gut non-tuberculosis mycobacteria, and (5) the prolonged antibiotic treatment required for cure of tuberculosis has long-term detrimental effects on the microbiome. We highlight knowledge gaps, considerations for addressing these knowledge gaps, and describe potential targets for modifying the microbiome to control tuberculosis.

How MALDI-TOF mass spectrometry can aid the diagnosis of hard-to-identify pathogenic bacteria - the rare and the unknown

Introduction: Ten years after its introduction into clinical microbiology, MALDI-TOF mass spectrometry has become the standard routine identification tool for bacteria in most laboratories. The technology has accelerated analyses and improved the quality of results. The greatest significance has been observed for bacteria that were challenging to be identified by traditional methods. Areas covered: We searched in existing literature (Pubmed) for reports how MALDI-TOF MS has contributed to identification of rare and unknown bacteria from different groups. We describe how this has improved the diagnostics in different groups of bacteria. Reference patterns for strains which yet cannot be assigned to a known species even enable the search for related bacteria in studies as well as in routine diagnostics. MALDI-TOF MS can help to discover and investigate new species and their clinical relevance. It is a powerful tool in the elucidation of the bacterial composition of complex microbiota in culturomics studies. Expert opinion: MALDI-TOF MS has improved the diagnosis of bacterial infections. It also enables knowledge generation for prospective diagnostics. The term 'hard-to-identify' might only be rarely attributed to bacteria in the future. Novel applications are being developed, e.g. subspecies differentiation, typing, and antibiotic resistance testing which may further contribute to improved microbial diagnostics.

Using fecal microbiota as biomarkers for predictions of performance in the selective breeding process of pedigree broiler breeders

Much work has been dedicated to identifying members of the microbial gut community that have potential to augment the growth rate of agricultural animals including chickens. Here, we assessed any correlations between the fecal microbiome, a proxy for the gut microbiome, and feed efficiency or weight gain at the pedigree chicken level, the highest tier of the production process. Because selective breeding is conducted at the pedigree level, our aim was to determine if microbiome profiles could be used to predict feed conversion or weight gain in order to improve selective breeding. Using 16s rRNA amplicon sequencing, we profiled the microbiomes of high and low weight gain (WG) birds and good and poor feed efficient (FE) birds in two pedigree lineages of broiler chickens. We also aimed to understand the dynamics of the microbiome with respect to maturation. A time series experiment was conducted, where fecal samples of chickens were collected at 6 points of the rearing process and the microbiome of these samples profiled. We identified OTUs differences at different taxonomic levels in the fecal community between high and low performing birds within each genetic line, indicating a specificity of the microbial community profiles correlated to performance factors. Using machine-learning methods, we built a classification model that could predict feed conversion performance from the fecal microbial community. With respect to maturation, we found that the fecal microbiome is dynamic in early life but stabilizes after 3 weeks of age independent of lineage. Our results indicate that the fecal microbiome profile can be used to predict feed conversion, but not weight gain in these pedigree lines. From the time series experiments, it appears that these predictions can be evaluated as early as 20 days of age. Our data also indicates that there is a genetic factor for the microbiome profile.

The Gut Microbiome Signatures Discriminate Healthy From Pulmonary Tuberculosis Patients

Cross talk occurs between the human gut and the lung through a gut-lung axis involving the gut microbiota. However, the signatures of the human gut microbiota after active Mycobacterium tuberculosis infection have not been fully understood. Here, we investigated changes in the gut microbiota in tuberculosis (TB) patients by shotgun sequencing the gut microbiomes of 31 healthy controls and 46 patients. We observed a dramatic changes in gut microbiota in tuberculosis patients as reflected by significant decreases in species number and microbial diversity. The gut microbiota of TB patients were mostly featured by the striking decrease of short-chain fatty acids (SCFAs)-producingbacteria as well as associated metabolic pathways. A classification model based on the abundance of three species, Haemophilus parainfluenzae, Roseburia inulinivorans, and Roseburia hominis, performed well for discriminating between healthy and diseased patients. Additionally, the healthy and diseased states can be distinguished by SNPs in the species of B. vulgatus. We present a comprehensive profile of changes in the microbiota in clinical TB patients. Our findings will shed light on the design of future diagnoses and treatments for M. tuberculosis infections.

Gut microbiota in children and altered profiles in juvenile idiopathic arthritis

Microbial diversity plays a key role in the maintenance of intestinal homeostasis and in the development of the immune system in the gut mucosa. Maybe one of the most important function of our gut microbiota is the immune system education, in particular the discrimination of friends from foes that occurs during childhood. In addition to bacterial antigens, several metabolites of microbial origin have a crucial role in training of the immune system, such as Short Chain Fatty Acids (SCFAs). There are many evidences on the role of the gut microbiota in rheumatic diseases, in particular modifications of microbiota composition causing dysbiosis that, in turn, can induce gut permeability, and thus immunological imbalance and trigger inflammation. In particular, immune cells can reach extra-intestinal sites, such as joints and trigger local inflammation. Childhood is a crucial period of life for development and evolution of the gut microbiota, especially for the acquisition of fundamental functions such as immunotolerance of commensal microorganisms. For this reason, gut dysbiosis is gaining interest as a potential pathogenetic factor for Juvenile Idiopathic Arthritis (JIA). Here we summarized the studies conducted on JIA patients in which a pro-arthritogenic microbial profiles has been observed; this, together with a depletion of microbial biodiversity, clearly distinguish patients' from healthy subjects' microbiota. Further studies are however needed to better clarify the role of microbiota in JIA pathogenesis.

Repertoire of bacterial species cultured from the human oral cavity and respiratory tract

While the gut microbiota is currently in the spotlight, the airway microbiome has been recently associated with several pulmonary diseases and carcinogenesis. As there are several biases associated with high-throughput sequencing methods, cultivation techniques are crucial for the investigation of the human microbiome. We thus aimed to build an exhaustive database, including a list of microbes isolated by culture from respiratory specimens, by performing a review of the literature. Herein, we have listed a total of 756 species cultured from the human respiratory tract. This represents 27.23% of the overall bacterial richness captured from human being by culture methods. This repertoire could be valuable for the elucidation of the interactions between the respiratory microbiome and human health.

The human microbiota in pulmonary tuberculosis: Not so innocent bystanders

Mycobacterium tuberculosis (Mtb) infection is a worldwide health concern, which needs robust and efficient control strategies, and the evaluation of human microbiota can be very important in this regard. Dysbiosis of normal microbiota is an important issue in the pathogenesis of Mtb. However, only few studies demonstrated the interaction between Mtb infection and microbiota. The current study aimed at reviewing literature on gut and lung microbiota in Mtb infection. Eleven articles regarding gut and lung microbiota composition in individuals with Mtb infection were selected, and then the importance of gut-lung axis in Mtb infection was evaluated. Also the relationship between microbiota composition and Mtb infection were discussed in terms of treatment, epigenetic field, and biomarkers.

Noncontiguous finished genome sequences and descriptions of Actinomyces ihuae, Actinomyces bouchesdurhonensis, Actinomyces urinae, Actinomyces marseillensis, Actinomyces mediterranea and Actinomyces oralis sp. nov. identified by culturomics

The taxonogenomic approach, including the culturomics techniques, is now currently used to isolate and characterize new bacteria. These approaches notably allowed us to discover six new species of the Actinomyces genus: Actinomyces ihuae strain SD1, Actinomyces bouchesdurhonensis strain Marseille-P2825, Actinomyces urinae strain Marseille-P2225, Actinomyces marseillensis strain Marseille-P2818, Actinomyces mediterranea strain Marseille-P3257 and Actinomyces oralis strain Marseille-P3109. Each is the type strain of the corresponding bacterial species. 16S ribosomal RNA gene sequence comparison was used to classify these strains among the Actinomyces genus. These strains are all Gram positive, rod shaped and facultative aerobic. We describe the main characteristics of each bacterium and present their complete genome sequence and annotation.

The pulmonary microbiome: challenges of a new paradigm

The study of the human microbiome-and, more recently, that of the respiratory system-by means of sophisticated molecular biology techniques, has revealed the immense diversity of microbial colonization in humans, in human health, and in various diseases. Apparently, contrary to what has been believed, there can be nonpathogenic colonization of the lungs by microorganisms such as bacteria, fungi, and viruses. Although this physiological lung microbiome presents low colony density, it presents high diversity. However, some pathological conditions lead to a loss of that diversity, with increasing concentrations of some bacterial genera, to the detriment of others. Although we possess qualitative knowledge of the bacteria present in the lungs in different states of health or disease, that knowledge has advanced to an understanding of the interaction of this microbiota with the local and systemic immune systems, through which it modulates the immune response. Given this intrinsic relationship between the microbiota and the lungs, studies have put forth new concepts about the pathophysiological mechanisms of homeostasis in the respiratory system and the potential dysbiosis in some diseases, such as cystic fibrosis, COPD, asthma, and interstitial lung disease. This departure from the paradigm regarding knowledge of the lung microbiota has made it imperative to improve understanding of the role of the microbiome, in order to identify possible therapeutic targets and to develop innovative clinical approaches. Through this new leap of knowledge, the results of preliminary studies could translate to benefits for our patients.

Complex ecological interactions of Staphylococcus aureus in tampons during menstruation

Menstrual toxic shock syndrome (mTSS) is a severe disease that occurs in healthy women vaginally colonized by Staphylococcus aureus producing toxic shock toxin 1 and who use tampons. The aim of the present study was to determine the impact of the composition of vaginal microbial communities on tampon colonisation by S. aureus during menses. We analysed the microbiota in menstrual fluids extracted from tampons from 108 healthy women and 7 mTSS cases. Using culture, S. aureus was detected in menstrual fluids of 40% of healthy volunteers and 100% of mTSS patients. Between class analysis of culturomic and 16S rRNA gene metabarcoding data indicated that the composition of the tampons' microbiota differs according to the presence or absence of S. aureus and identify discriminating genera. However, the bacterial communities of tampon fluid positive for S. aureus did not cluster together. No difference in tampon microbiome richness, diversity, and ecological distance was observed between tampon vaginal fluids with or without S. aureus, and between healthy donors carrying S. aureus and mTSS patients. Our results show that the vagina is a major niche of. S. aureus in tampon users and the composition of the tampon microbiota control its virulence though more complex interactions than simple inhibition by lactic acid-producing bacterial species.

Perspectives for personalized therapy for patients with multidrug-resistant tuberculosis

According to the World Health Organization (WHO), tuberculosis is the leading cause of death attributed to a single microbial pathogen worldwide. In addition to the large number of patients affected by tuberculosis, the emergence of Mycobacterium tuberculosis drug-resistance is complicating tuberculosis control in many high-burden countries. During the past 5 years, the global number of patients identified with multidrug-resistant tuberculosis (MDR-TB), defined as bacillary resistance at least against rifampicin and isoniazid, the two most active drugs in a treatment regimen, has increased by more than 20% annually. Today we experience a historical peak in the number of patients affected by MDR-TB. The management of MDR-TB is characterized by delayed diagnosis, uncertainty of the extent of bacillary drug-resistance, imprecise standardized drug regimens and dosages, very long duration of therapy and high frequency of adverse events which all translate into a poor prognosis for many of the affected patients. Major scientific and technological advances in recent years provide new perspectives through treatment regimens tailor-made to individual needs. Where available, such personalized treatment has major implications on the treatment outcomes of patients with MDR-TB. The challenge now is to bring these adances to those patients that need them most.

The contribution of culturomics to the repertoire of isolated human bacterial and archaeal species

After a decade of research and metagenomic analyses, our knowledge of the human microbiota appears to have reached a plateau despite promising results. In many studies, culture has proven to be essential in describing new prokaryotic species and filling metagenomic gaps. In 2015, only 2172 different prokaryotic species were reported to have been isolated at least once from the human body as pathogens or commensals. In this review, we update the previous repertoire by reporting the different species isolated from the human body to date, increasing it by 28% to reach a total of 2776 species associated with human beings. They have been classified into 11 different phyla, mostly the Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria. Finally, culturomics contributed up to 66.2% towards updating this repertoire by reporting 400 species, of which 288 were novel. This demonstrates the need to continue the culturing work, which seems essential in order to decipher the hidden human microbial content.

Noncontiguous finished genome sequence and description of Intestinimonas massiliensis sp. nov strain GD2T , the second Intestinimonas species cultured from the human gut

Intestinimonas massiliensis sp. nov strain GD2^T is a new species of the genus Intestinimonas (the second, following Intestinimonas butyriciproducens gen. nov., sp. nov). First isolated from the gut microbiota of a healthy subject of French origin using a culturomics approach combined with taxono-genomics, it is strictly anaerobic, nonspore-forming, rod-shaped, with catalase- and oxidase-negative reactions. Its growth was observed after preincubation in an anaerobic blood culture enriched with sheep blood (5%) and rumen fluid (5%), incubated at 37°C. Its phenotypic and genotypic descriptions are presented in this paper with a full annotation of its genome sequence. This genome consists of 3,104,261 bp in length and contains 3,074 predicted genes, including 3,012 protein-coding genes and 62 RNA-coding genes. Strain GD2^T significantly produces butyrate and is frequently found among available 16S rRNA gene amplicon datasets, which leads consideration of Intestinimonas massiliensis as an important human gut commensal.

Corynebacterium fournierii sp. nov., isolated from the female genital tract of a patient with bacterial vaginosis

Strain Marseille-P2948^T, a novel Gram-positive, catalase-positive bacterium was isolated from a vaginal sample of a patient with bacterial vaginosis. It was characterised using the taxonogenomic approach. Phylogenetic analysis revealed that the 16S rRNA and the rpoB genes exhibit 98.7 and 93.4% similarity, respectively, with those of Corynebacterium ureicelerivorans strain IMMIB RIV-301^T. Biochemical tests of strain Marseille-P2948^T gave results that were similar to those of other validly named Corynebacterium species, whereas chemotaxonomic tests showed the presence of C_16:0, C_18:1n9, C_18:0, and C_18:2n6 in the fatty acid profile. The draft genome of strain Marseille-P2948^T is 2,383,644 bp long in size with a G+C content of 65.03%. Of the 2210 predicted genes, 2147 are protein-coding genes and 63 are RNAs. Based on phenotypic, phylogenic and genomic results, it was concluded that the isolate represents a new species within the genus Corynebacterium. The name Corynebacterium fournierii sp. nov. is proposed and the type strain is Marseille-P2948^T (= CSUR P2948 = DSM 103271).

How mass spectrometric approaches applied to bacterial identification have revolutionized the study of human gut microbiota

INTRODUCTION

Describing the human hut gut microbiota is one the most exciting challenges of the 21^st century. Currently, high-throughput sequencing methods are considered as the gold standard for this purpose, however, they suffer from several drawbacks, including their inability to detect minority populations. The advent of mass-spectrometric (MS) approaches to identify cultured bacteria in clinical microbiology enabled the creation of the culturomics approach, which aims to establish a comprehensive repertoire of cultured prokaryotes from human specimens using extensive culture conditions. Areas covered: This review first underlines how mass spectrometric approaches have revolutionized clinical microbiology. It then highlights the contribution of MS-based methods to culturomics studies, paying particular attention to the extension of the human gut microbiota repertoire through the discovery of new bacterial species. Expert commentary: MS-based approaches have enabled cultivation methods to be resuscitated to study the human gut microbiota and thus to fill in the blanks left by high-throughput sequencing methods in terms of culturing minority populations. Continued efforts to recover new taxa using culture methods, combined with their rapid implementation in genomic databases, would allow for an exhaustive analysis of the gut microbiota through the use of a comprehensive approach.

Gut microbiome contributes to impairment of immunity in pulmonary tuberculosis patients by alteration of butyrate and propionate producers

Tuberculosis (TB) is primarily associated with decline in immune health status. As gut microbiome (GM) is implicated in the regulation of host immunity and metabolism, here we investigate GM alteration in TB patients by 16S rRNA gene and whole-genome shotgun sequencing. The study group constituted of patients with pulmonary TB and their healthy household contacts as controls (HCs). Significant alteration of microbial taxonomic and functional capacity was observed in patients with active TB as compared to the HCs. We observed that Prevotella and Bifidobacterium abundance were associated with HCs, whereas butyrate and propionate-producing bacteria like Faecalibacterium, Roseburia, Eubacterium and Phascolarctobacterium were significantly enriched in TB patients. Functional analysis showed reduced biosynthesis of vitamins and amino acids in favour of enriched metabolism of butyrate and propionate in TB subjects. The TB subjects were also investigated during the course of treatment, to analyse the variation of GM. Although perturbation in microbial composition was still evident after a month's administration of anti-TB drugs, significant changes were observed in metagenome gene pool that pointed towards recovery in functional capacity. Therefore, the findings from this pilot study suggest that microbial dysbiosis may contribute to pathophysiology of TB by enhancing the anti-inflammatory milieu in the host.

Noncontiguous finished genome sequences and descriptions of 'Paenibacillus bouchesdurhonensis,' 'Paenibacillus rubinfantis,' 'Paenibacillus senegalimassiliensis' and 'Paenibacillus tuaregi' identified by culturomics

Microbial culturomics represents a completely new approach to investigate microbial diversity by using different optimized culture conditions, mass spectrometry, genome sequencing and annotation and phenotypic description that allow for an extensive characterization of new species and the study of the human microbiome. Here we present four new species within the genus Paenibacillus: 'Paenibacillus bouchesdurhonensis' strain Marseille-P3071T, 'Paenibacillus rubinfantis' strain MT18T, 'Paenibacillus senegalimassiliensis' strain SIT18T and 'Paenibacillus tuaregi' strain Marseille-P2472T, which are all facultatively aerobic and Gram-positive bacilli.

Noncontiguous finished genome sequences and description of Bacillus massiliglaciei, Bacillus mediterraneensis, Bacillus massilinigeriensis, Bacillus phocaeensis and Bacillus tuaregi, five new species identified by culturomics

Microbial culturomics, which investigates microbial diversity by combining diversified culture conditions, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and 16S rDNA identification, allowed to identify five new species within the Bacillus genus. Bacillus massiliglaciei strain Marseille-P2600T, Bacillus mediterraneensis strain Marseille-P2384T, Bacillus massilinigeriensis strain Marseille-P2366T, Bacillus tuaregi strain Marseille-P2489T and Bacillus phocaeensis strain SIT16T are each the type strain of the corresponding bacterial species. These strains, the genomes of which are described here, are facultative anaerobic Gram-positive bacilli. Here, we describe the main characteristics of each bacterium and present their complete genome sequence and annotation.

The Human Microbiome in the Fight Against Tuberculosis

AbstractThe human microbiome is an intriguing potentially modifiable risk factor in our arsenal against Mycobacterium tuberculosis, the leading infectious disease killer globally. Previous studies have shown associations between the human microbiome and pulmonary disease states; however, etiological links between the microbiome and tuberculosis (TB) infection or disease remain unclear. Immunomodulatory roles of the microbiome may prove to be a critical asset in the host response against TB, including in preventing TB infection, reducing progression from latency, mitigating disease severity, and lowering the incidence of drug resistance and coinfections. This review examined the associations between TB and the gut and lung microbiome. Eight studies were identified through a PubMed database search, including one animal study (N = 1), case report (N = 1), and case-control studies (N = 6). TB infection and disease were associated with reduced gastrointestinal microbial diversity in a murine model and human case report. Sputum microbial diversity differed by TB status in case-control studies, although some reported heterogeneous findings. Current evidence suggests that the gut and lung microbiome are associated with TB infection and disease. However, as studies are limited, etiological and longitudinal research is needed to determine clinical relevance.

Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy

BACKGROUND

Effective treatment of Mycobacterium tuberculosis (Mtb) infection requires at least 6 months of daily therapy with multiple orally administered antibiotics. Although this drug regimen is administered annually to millions worldwide, the impact of such intensive antimicrobial treatment on the host microbiome has never been formally investigated. Here, we characterized the longitudinal outcome of conventional isoniazid-rifampin-pyrazinamide (HRZ) TB drug administration on the diversity and composition of the intestinal microbiota in Mtb-infected mice by means of 16S rRNA sequencing. We also investigated the effects of each of the individual antibiotics alone and in different combinations.

RESULTS

While inducing only a transient decrease in microbial diversity, HRZ treatment triggered a marked, immediate and reproducible alteration in community structure that persisted for the entire course of therapy and for at least 3 months following its cessation. Members of order Clostridiales were among the taxa that decreased in relative frequencies during treatment and family Porphyromonadaceae significantly increased post treatment. Experiments comparing monotherapy and different combination therapies identified rifampin as the major driver of the observed alterations induced by the HRZ cocktail but also revealed unexpected effects of isoniazid and pyrazinamide in certain drug pairings.

CONCLUSIONS

This report provides the first detailed analysis of the longitudinal changes in the intestinal microbiota due to anti-tuberculosis therapy. Importantly, many of the affected taxa have been previously shown in other systems to be associated with modifications in immunologic function. Together, our findings reveal that the antibiotics used in conventional TB treatment induce a distinct and long lasting dysbiosis. In addition, they establish a murine model for studying the potential impact of this dysbiosis on host resistance and physiology.

Old antibiotics for emerging multidrug-resistant/extensively drug-resistant tuberculosis (MDR/XDR-TB)

Recently, multidrug-resistant tuberculosis (MDR-TB) has become a therapeutic challenge. In addition to drug resistance, drug adverse events, intravenous delivery, cost and availability of some antibiotics in low-income countries have led to a look back to old drugs, especially those efficient against closely related organisms such as Mycobacterium leprae. Here we review the available drugs that respect the conditions above and could be upgraded to first-line therapy for treating MDR-TB and extensively drug-resistant tuberculosis (XDR-TB).

'Bacillus massiliglaciei', a new bacterial species isolated from Siberian permafrost

We describe here the main characteristics of a new species isolated from Siberian permafrost dated around 10 million years. This species was named 'Bacillus massiliglaciei' strain Marseille-P2600^T (= CSUR P2600 = DSM 102861).