Taxonogenomics description of Bacillus marasmi sp. nov., a new species isolated from the stool sample

Using the culturomics method, two strains were isolated, identified, and characterised following the taxonogenomics concept. Bacillus marasmi sp. nov. strain Marseille-P3556 (= CSURP3556) is isolated from a 13-month-old girl living in Niger. The phylogenetic tree, phenotypic criteria, and genomic analysis described here clearly show that this bacterium is different from previously known bacterial species withstanding in nomenclature and new members of Bacillus genus.

Virgibacillus doumboii sp. nov., a halophilic bacterium isolated from the stool of a healthy child in Mali

A moderately halophilic and strictly aerobic bacterium was isolated from a human stool as part of a study on the diagnosis of childhood malnutrition in Mali. Strain Marseille-Q1616T is a Gram-stain-positive, rod-shaped, catalase-positive and oxidase-negative bacterium. It has a genome size of 3.91 Mbp with 39.79% G+C content, which contains 3954 protein-coding genes including genes encoding phosphomycin resistance and Listeria monocytogenes, 16 rRNA genes and 64 tRNA genes. Strain Marseille-Q1616T exhibited a 96.3% 16S rRNA gene sequence similarity and shared an OrthoANI value of 70.64% (the highest observed) with Virgibacillus kekensis, the phylogenetically closest validly published species. Based on phenotypic and phylogenetic evidence and genomic average nucleotide identity values, we suggest the creation of a new species within the Virgibacillus genus, named Virgibacillus doumboii sp. nov., type strain Marseille-Q1616T (= CSURQ1616).

Neobacillus massiliamazoniensis sp. nov., a new bacterial species isolated from stool sample of an inhabitant of the Amazon region

Using a culturomics approach, a strain was isolated, identified and characterised following the taxonogenomics concept. Neobacillus massiliamazoniensis sp. nov., strain LF1^T (=CSURP1359) was isolated from human stool. The 16S rRNA gene sequence analysis of strain LF1^T (accession number: LK021124) exhibits 98.32% similarity levels with Neobacillus bataviensis strain IDA1115 (accession number: NR_036766.1), the phylogenetically closest related species with standing in nomenclature. The draft genome size of strain LF1^T (accession number: CVRB00000000) is 4.6 Mbp with a G+C content of 34.1 mol%. Analysis of phylogenic tree, genomic analysis and phenotypic criteria described here sufficiently prove that this bacterium is different from previously known bacterial species with standing in nomenclature and represents a new Neobacillus species belonging to Firmicutes phylum.

Evaluating the serological status of COVID-19 patients using an indirect immunofluorescent assay, France

An indirect in-house immunofluorescent assay was developed in order to assess the serological status of COVID-19 patients in Marseille, France. Performance of IFA was compared to a commercial ELISA IgG kit. We tested 888 RT-qPCR-confirmed COVID-19 patients (1302 serum samples) and 350 controls including 200 sera collected before the pandemic, 64 sera known to be associated with nonspecific serological interference, 36 sera from non-coronavirus pneumonia and 50 sera from patient with other common coronavirus to elicit false-positive serology. Incorporating an inactivated clinical SARS-CoV-2 isolate as the antigen, the specificity of the assay was measured as 100% for IgA titre ≥ 1:200, 98.6% for IgM titre ≥ 1:200 and 96.3% for IgG titre ≥ 1:100 after testing a series of negative controls. IFA presented substantial agreement (86%) with ELISA EUROIMMUN SARS-CoV-2 IgG kit (Cohen's Kappa = 0.61). The presence of antibodies was then measured at 3% before a 5-day evolution up to 47% after more than 15 days of evolution. We observed that the rates of seropositivity as well as the titre of specific antibodies were both significantly higher in patients with a poor clinical outcome than in patients with a favourable evolution. These data, which have to be integrated into the ongoing understanding of the immunological phase of the infection, suggest that detection anti-SARS-CoV-2 antibodies is useful as a marker associated with COVID-19 severity. The IFA assay reported here is useful for monitoring SARS-CoV-2 exposure at the individual and population levels.

18F-FDG brain PET hypometabolism in patients with long COVID

PURPOSE

In the context of the worldwide outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), some patients report functional complaints after apparent recovery from COVID-19. This clinical presentation has been referred as "long COVID." We here present a retrospective analysis of ¹⁸F-FDG brain PET of long COVID patients from the same center with a biologically confirmed diagnosis of SARS-CoV-2 infection and persistent functional complaints at least 3 weeks after the initial infection.

METHODS

PET scans of 35 patients with long COVID were compared using whole-brain voxel-based analysis to a local database of 44 healthy subjects controlled for age and sex to characterize cerebral hypometabolism. The individual relevance of this metabolic profile was evaluated to classify patients and healthy subjects. Finally, the PET abnormalities were exploratory compared with the patients' characteristics and functional complaints.

RESULTS

In comparison to healthy subjects, patients with long COVID exhibited bilateral hypometabolism in the bilateral rectal/orbital gyrus, including the olfactory gyrus; the right temporal lobe, including the amygdala and the hippocampus, extending to the right thalamus; the bilateral pons/medulla brainstem; the bilateral cerebellum (p-voxel < 0.001 uncorrected, p-cluster < 0.05 FWE-corrected). These metabolic clusters were highly discriminant to distinguish patients and healthy subjects (100% correct classification). These clusters of hypometabolism were significantly associated with more numerous functional complaints (brainstem and cerebellar clusters), and all associated with the occurrence of certain symptoms (hyposmia/anosmia, memory/cognitive impairment, pain and insomnia) (p < 0.05). In a more preliminary analysis, the metabolism of the frontal cluster which included the olfactory gyrus was worse in the 7 patients treated by ACE drugs for high blood pressure (p = 0.032), and better in the 3 patients that had used nasal decongestant spray at the infectious stage (p < 0.001).

CONCLUSION

This study demonstrates a profile of brain PET hypometabolism in long COVID patients with biologically confirmed SARS-CoV-2 and persistent functional complaints more than 3 weeks after the initial infection symptoms, involving the olfactory gyrus and connected limbic/paralimbic regions, extended to the brainstem and the cerebellum. These hypometabolisms are associated with patients' symptoms, with a biomarker value to identify and potentially follow these patients. The hypometabolism of the frontal cluster, which included the olfactory gyrus, seems to be linked to ACE drugs in patients with high blood pressure, with also a better metabolism of this olfactory region in patients using nasal decongestant spray, suggesting a possible role of ACE receptors as an olfactory gateway for this neurotropism.

Virgibacillus ihumii sp. nov., a new bacterium isolated from the stool of healthy African children

During a case–control study on severe acute malnutrition, strain Marseille-Q1233 was isolated. It is a Gram-positive, rod-shaped and halophilic bacillus isolated from a stool sample of Malian child under the age of 5. The fatty acid profile of the strain consisted of C15:0-anteiso and C14:0-iso as major components. Digital DNA-DNA hybridization and average nucleotide identity calculation showed 23.10% and 80.81% similarity respectively between strain Marseille-Q1233 and Virgibacillus siamensis strain Marseille-P2607, the phylogenetically closely related species with standing in nomenclature. On the basis of these results, we report the description of Virgibacillus ihumii sp. nov. strain Marseille-Q1233 as a new bacterial species.

Clinical efficacy of chloroquine derivatives in COVID-19 infection: comparative meta-analysis between the big data and the real world

In the context of the current coronavirus disease 2019 (COVID-19) pandemic, we conducted a meta-analysis on the effects of chloroquine derivatives in patients, based on unpublished and published reports available publicly on the internet as of 27 May 2020. The keywords 'hydroxychloroquine', 'chloroquine', 'coronavirus', 'COVID-19' and 'SARS-Cov-2' were used in the PubMed, Google Scholar and Google search engines without any restrictions as to date or language. Twenty studies were identified involving 105 040 patients (19 270 treated patients) from nine countries (Brazil, China, France, Iran, Saudi Arabia, South Korea, Spain and the USA). Big data observational studies were associated with conflict of interest, lack of treatment dosage and duration, and absence of favourable outcome. Clinical studies were associated with favourable outcomes and details on therapy. Among clinical studies, three of four randomized controlled trials reported a significant favourable effect. Among clinical studies, a significant favourable summary effect was observed for duration of cough (OR 0.19, p 0.00003), duration of fever (OR 0.11, p 0.039), clinical cure (OR 0.21, p 0.0495), death (OR 0.32, p 4.1 × 10-6) and viral shedding (OR 0.43, p 0.031). A trend for a favourable effect was noted for the outcome 'death and/or intensive care unit transfer' (OR 0.29, p 0.069) with a point estimate remarkably similar to that observed for death (∼0.3). In conclusion, a meta-analysis of publicly available clinical reports demonstrates that chloroquine derivatives are effective to improve clinical and virological outcomes, but, more importantly, they reduce mortality by a factor of 3 in patients with COVID-19. Big data are lacking basic treatment definitions and are linked to conflict of interest. The retraction of the only big data study associated with a significantly deleterious effect the day after (June 5, 2020) the acceptance of the present work (June 4, 2020) confirms the relevance of this work.

Halobacillus ihumii sp. nov., a new bacterium isolated from stool of healthy children living in Mali

Strain Marseille-Q1234^T is a new species from the genus Halobacillus that was isolated in 2019 from a stool sample in a healthy Malian child <5 years old. Cells are Gram-positive and strictly halophilic bacilli. Strain Marseille-Q1234^T exhibits 98.46% 16S rRNA gene sequence similarity to Halobacillus naozhouensis strain JSM 071068^T (NR_116505.1), the phylogenetically closely related species with standing in nomenclature. Based on the phenotypic and phylogenetic evidence, OrthoANI values and results of the biochemical tests, the new species is named Halobacillus ihumii sp. nov., for which strain Marseille-Q1234^T (= CSURQ1234) is proposed as the type strain.

Taxonogenomics description of Bacillus dakarensis sp. nov., Bacillus sinesaloumensis sp. nov. and Bacillus massiliogabonensis sp. nov., three new species isolated from human stools

Using microbial culturomics, three Bacillus strains were isolated, identified and characterized following the taxonogenomics strategy. Bacillus dakarensis strain Marseille-P3515^T (=CSURP3515), Bacillus sinesaloumensis strain Marseille-P3516^T (=CSURP3516), and Bacillus massiliogabonensis strain Marseille-P2639^T (=CSURP2639) were isolated from human stool samples. The phylogenetic analysis, phenotypic characteristics and genotypic data presented here prove that these three bacteria are different from previously known bacterial species with standing in nomenclature and represent new Bacillus species.

18F-FDG brain PET hypometabolism in post-SARS-CoV-2 infection: substrate for persistent/delayed disorders?

PURPOSE

Several brain complications of SARS-CoV-2 infection have been reported. It has been moreover speculated that this neurotropism could potentially cause a delayed outbreak of neuropsychiatric and neurodegenerative diseases of neuroinflammatory origin. A propagation mechanism has been proposed across the cribriform plate of the ethmoid bone, from the nose to the olfactory epithelium, and possibly afterward to other limbic structures, and deeper parts of the brain including the brainstem.

METHODS

Review of clinical examination, and whole-brain voxel-based analysis of ¹⁸F-FDG PET metabolism in comparison with healthy subjects (p voxel < 0.001, p-cluster < 0.05, uncorrected), of two patients with confirmed diagnosis of SARS-CoV-2 explored at the post-viral stage of the disease.

RESULTS

Hypometabolism of the olfactory/rectus gyrus was found on the two patients, especially one with 4-week prolonged anosmia. Additional hypometabolisms were found within amygdala, hippocampus, parahippocampus, cingulate cortex, pre-/post-central gyrus, thalamus/hypothalamus, cerebellum, pons, and medulla in the other patient who complained of delayed onset of a painful syndrome.

CONCLUSION

These preliminary findings reinforce the hypotheses of SARS-CoV-2 neurotropism through the olfactory bulb and the possible extension of this impairment to other brain structures. ¹⁸F-FDG PET hypometabolism could constitute a cerebral quantitative biomarker of this involvement. Post-viral cohort studies are required to specify the exact relationship between such hypometabolisms and the possible persistent disorders, especially involving cognitive or emotion disturbances, residual respiratory symptoms, or painful complaints.

Lactimicrobium massiliense gen. nov., sp. nov.; Anaerolactibacter massiliensis gen. nov., sp. nov.; Galactobacillus timonensis gen. nov., sp. nov. and Acidipropionibacterium timonense sp. nov. isolated from breast milk from healthy breastfeeding African women

Four strains isolated by microbial culturomics from breast milk of healthy mothers from Mali were not identified and characterized by taxono-genomics. This led us to propose the new genera and species Lactimicrobium massiliense, Anaerolactibacter massiliensis and Galactobacillus timonensis containing type strain Marseille-P4301^T (CSUR P4301^T), Marseille-P4302^T (CSUR P4302^T) and Marseille-P4641^T (CSUR P4641^T), respectively. The strain Marseille-P4482 represents a novel species, Acidipropionibacterium timonense, in a previously known genus with type strain being Marseille-P4482^T (CSUR P4482^T).

Brain corticotropin-releasing factor signaling: Involvement in acute stress-induced visceral analgesia in male rats

BACKGROUND

Water avoidance stress (WAS) induces a naloxone-independent visceral analgesia in male rats under non-invasive conditions of monitoring. The objective of the study was to examine the role of brain CRF signaling in acute stress-induced visceral analgesia (SIVA).

METHODS

Adult male Sprague-Dawley rats were chronically implanted with an intracerebroventricular (ICV) cannula. The visceromotor response (VMR) to graded phasic colorectal distension (CRD: 10, 20, 40, 60 mm Hg, 20 seconds, 4 minutes intervals) was monitored using manometry. The VMR to a first CRD (baseline) was recorded 5 minutes after an ICV saline injection, followed 1 hour later by ICV injection of either CRF (30, 100, or 300 ng and 1, 3, or 5 μg/rat) or saline and a second CRD, 5 minutes later. Receptor antagonists against CRF₁ /CRF₂ (astressin-B, 30 μg/rat), CRF₂ (astressin₂ -B, 10 μg/rat), oxytocin (tocinoic acid, 20 μg/rat), or vehicle were injected ICV 5 minutes before CRF (300 ng/rat, ICV) or 15 minutes before WAS (1 hour).

KEY RESULTS

ICV CRF (100 and 300 ng) reduced the VMR to CRD at 60 mm Hg by -36.6% ± 6.8% and -48.7% ± 11.7%, respectively, vs baseline (P < 0.001), while other doses had no effect and IP CRF (10 µg/kg) induced visceral hyperalgesia. Astressin-B and tocinoic acid injected ICV induced hyperalgesia and prevented the analgesic effect of ICV CRF (300 ng/rat) and WAS, while astressin₂ -B only blocked WAS-induced SIVA.

CONCLUSIONS & INFERENCES

These data support a role for brain CRF signaling via CRF₂ in SIVA in a model of WAS and CRD likely mediated by the activation of brain oxytocin pathway.

Anaerotruncus massiliensis sp. nov., a succinate-producing bacterium isolated from human stool from an obese patient after bariatric surgery

A new bacterium, strain AT3^T, was isolated by microbial culturomics from a faecal sample from a Frenchman after bariatric surgery. The isolate exhibited 96.6% 16S ribosomal RNA gene nucleotide sequence similarity with Anaerotruncus colihominis strain WAL 14565^T = CCUG 45055^T = CIP 107754^T. Phenotypic and genomic characteristics showed that the new strain represents a novel species, for which the name Anaerotruncus massiliensis sp. nov. is proposed. The type strain is strain AT3^T = CSUR P2007^T = DSM 100567^T.

CHARACTERIZATION OF FLUORESCENT NUCLEAR TRACK DETECTORS AS CRITICALITY DOSIMETERS II

Fluorescent nuclear track detectors (FNTDs) as criticality dosimeters for both neutrons and gamma are further characterized in terms of angular dependence and quick dose assessment. The power spectrum integral depth profiles obtained from stacks of fluorescent images acquired within FNTDs exposed to a broad spectrum neutron field at various angles are analyzed to determine a calibration curve for angular dependence. MCNPX simulations were shown to be in good agreement with experimental results. A prototype triage reader was also designed and tested for quick assessment of dose. An unfolding technique incorporating both energy dependence and angular dependence is discussed. The advantages and shortcomings of using FNTDs in the event of a criticality excursion accident are analyzed.

COMPARISON BETWEEN PADC AND FNTD NEUTRON DETECTOR SYSTEMS IN BLIND TESTS

The objective of this study was to compare a neutron dosimetry system based on polyallyl diglycol carbonate (PADC) detectors with a new system based on Al2O3:C,Mg fluorescence nuclear track detectors (FNTD). The irradiations, performed as part of an intercomparison organized by the Physikalisch-Technische Bundesanstalt (PTB), Germany, were on a PMMA phantom with 252Cf or 241Am-Be source, usually with the phantom surface perpendicular to the radiation beam (0° angle), and with Hp(10) values between 0.3 and 7 mSv. One 252Cf irradiation was performed at 30° angle, and one with an additional 1 mSv gamma irradiation. The results showed an agreement between the two techniques with an average and maximum difference between PADCs and FNTDs of 1.5 and 22%, respectively, if one compares only cases of doses >1 mSv. For one of the irradiation conditions with dose of 0.9 mSv, use of the incorrect calibration factor for the FNTD (252Cf instead of 241Am-Be) led to reported values ~×2 larger than the given doses, due to low statistics in the determination of the ratio between 6Li-doped glass and polyethylene neutron converters. Although the FNTD track analysis algorithm may need further development, the results presented here demonstrate the feasibility of the FNTD technology and indicate areas requiring improvements.

ENERGY RESPONSE OF FLUORESCENT NUCLEAR TRACK DETECTORS OF VARIOUS COLORATIONS TO MONOENERGETIC NEUTRONS

The neutron-energy dependence of the track-counting sensitivity of fluorescent nuclear track detectors (FNTDs) at two ranges of Mg doping, resulting in different crystal colorations, was investigated. The performance of FNTDs was studied with the following converters: Li-glass for thermal to intermediate-energy neutrons, polyethylene for fast neutrons, and polytetrafluoroethylene (Teflon™) for photon- and radon-background subtraction. The irradiations with monoenergetic neutrons were performed at the National Physics Laboratory (NPL), UK. The energy range was varied from 144 keV to 16.5 MeV in the personal dose equivalent range from 1 to 3 mSv. Monte Carlo simulations were performed to model the response of FNTDs to monoenergetic neutrons. A good agreement with the experimental data was observed suggesting the development of a basic model for future MC studies. Further work will focus on increasing FNTD sensitivity to low-energy neutrons and developing a faster imaging technique for scanning larger areas to improve counting statistics.

'Lactomassilus timonensis,' a new anaerobic bacterial species isolated from the milk of a healthy African mother

We here report the main characteristics of a new anaerobic bacterial genus and species ‘Lactomassilus timonensis,’ strain Marseille-P4641^T (CSUR = P4641), isolated by microbial culturomics from the milk of a 35-year-old healthy lactating mother from Mali.

Noncontiguous finished genome sequence and description of Mediterranea massiliensis gen. nov., sp. nov., a new member of the Bacteroidaceae family isolated from human colon

Strain Marseille-P2645^T was isolated in a colon sample from a Frenchwoman who underwent a colonoscopy. Bacterial cells were Gram negative, non–spore forming, mobile and strictly anaerobic. The genome of strain Marseille-P2645^T is 3 950 441 bp long and contains 3374 protein-coding genes. The DNA G+C content is of 51.66 mol%. Strain Marseille-P2645^T exhibited a 92.9% sequence similarity with Bacteroides helcogenes strain P36-108^T (GenBank accession no. CP002352), the phylogenetically closest species with standing in nomenclature. Strain Marseille-P2645^T (= CSUR P2645 = DSM 103034) is therefore a candidate as a type species of a new genus belonging to the Bacteroidaceae family, for which the name of Mediterranea massiliensis gen. nov., sp. nov., is proposed.

'Marasmitruncus massiliensis' gen. nov., sp. nov., 'Clostridium culturomicum' sp. nov., 'Blautia provencensis' sp. nov., 'Bacillus caccae' sp. nov. and 'Ornithinibacillus massiliensis' sp. nov., isolated from stool samples of undernourished African children

We report here the main characteristics of five new species, ‘Marasmitruncus massiliensis’ strain Marseille-P3646^T (CSUR P3646), ‘Clostridium culturomicum’ strain Marseille-P3545^T (CSUR P3545), ‘Blautia provencensis’ strain Marseille-P3502^T (CSUR P3502), ‘Bacillus caccae’ strain Marseille-P3604^T (CSUR P3604) and ‘Ornithinibacillus massiliensis’ strain Marseille-P3601^T (CSUR P3601), which were isolated recently from undernourished children's stool samples from Niger using microbial culturomics.

'Urmitella timonensis' gen. nov., sp. nov., 'Blautia marasmi' sp. nov., 'Lachnoclostridium pacaense' sp. nov., 'Bacillus marasmi' sp. nov. and 'Anaerotruncus rubiinfantis' sp. nov., isolated from stool samples of undernourished African children

We report here the main characteristics of five new species ‘Urmitella timonensis’ strain Marseille-P2918^T (CSUR P2918), ‘Blautia marasmi’ strain Marseille-P2377^T (CSUR P2377), ‘Lachnoclostridium pacaense’ strain Marseille-P3100^T (CSUR P3100), ‘Bacillus marasmi’ strain Marseille-P3556^T (CSUR P3556) and ‘Anaerotruncus rubiinfantis’ strain MT15^T (CSUR P2276), which were isolated recently from stool samples taken from undernourished children in Niger and Senegal using microbial culturomics.

Noncontiguous finished genome sequence and description of Prevotella phocaeensis sp. nov., a new anaerobic species isolated from human gut infected by Clostridium difficile

Prevotella phocaeensis sp. nov. strain SN19^T (= DSM 103364) is a new species isolated from the gut microbiota of patient with colitis due to Clostridium difficile. Strain SN19^T is Gram-negative rod-shaped bacteria, strictly anaerobic, nonmotile and non-endospore forming. The predominance fatty acid is hexadecanoic acid. Its 16S rRNA showed a 97.70% sequence identity with its phylogenetically closest species, Prevotella oralis. The genome is 2 922 117 bp long and contains 2486 predicted genes including 56 RNA genes.

Noncontiguous finished genome sequence and description of Fusobacterium massiliense sp. nov. isolated from human duodenum

The strain Marseille-P2749^T (= CSUR P2749 = DSM 103085) was isolated as part of culturomics study from a liquid duodenum sample from a French man. Bacterial cells were Gram-negative bacilli, fusiform shaped and non–spore forming, and they grew in microaerophilic and anaerobic atmosphere. Its genome is 1 809 169 bp long and contains 1646 protein-coding genes. The DNA G+C content was 27.33 mol%. This strain exhibited a 95.9% sequence similarity with Fusobacterium periodonticum, the phylogenetically closest species with standing in nomenclature. Strain Marseille-P2749^T is suggested to be a novel species belonging to the genus Fusobacterium, for which the name Fusobacterium massiliense sp. nov. is proposed.

Noncontiguous finished genome sequence and description of Streptococcus timonensis sp. nov. isolated from the human stomach

Strain Marseille-P2915^T, a Gram-positive, facultative anaerobic and nonmotile coccus, was isolated from the gastric lavage of a patient with severe anaemia. The 16S rRNA and rpoB gene comparison exhibited a sequence identity of 98.7 and 92.6% with Streptococcus infantis strain JCM 10157^T, respectively, collocating it within the ‘Streptococcus mitis’ group. On the basis of phenotypic and genomic analysis, we propose the validation of the type strain Streptococcus timonensis sp. nov. Marseille-P2915T (= DSM 103349 = CSUR P2915).

"Ruminococcus phoceensis," a new species identified from human stool from an obese patient before bariatric surgery

We report here the main characteristics of a new bacterium species, "Ruminococcus phoceensis" strain AT10 (CSUR = P2086, DSM = 100837). This bacterium was isolated from the faeces of a 37-year-old woman from Marseille, France, with morbid obesity before bariatric surgery.

"Anaerotruncus massiliensis," a new species identified from human stool from an obese patient after bariatric surgery

We report the main characteristics of a new bacterial species strain AT3^T (CSUR = P2007, DSM = 100567) that was isolated from the stool sample collected from a 47-year-old obese French man after he underwent bariatric surgery.

'Negativicoccus massiliensis', a new species identified from human stool from an obese patient after bariatric surgery

We report here the main characteristics of ‘Negativicoccus massiliensis’ strain AT7 (CSURP = P2082, DSM = 100853) isolated from a stool sample collected from a 47-year-old obese French man before bariatric surgery.

'Eisenbergiella massiliensis', a new species isolated from human stool collected after bariatric surgery

We report the principal characteristics of ‘Eisenbergiella massiliensis’ sp. nov. strain AT11 (CSURP = P2120, DSM = 101499) that was isolated from a stool sample collected after bariatric surgery of a 56-year-old obese French woman.

Noncontiguous finished genome sequence and description of Enterococcus massiliensis sp. nov

Enterococcus massiliensis strain sp. nov. (= CSUR P1927 = DSM 100308) is a new species within the genus Enterococcus. This strain was first isolated from a fresh stool sample of a man during culturomics study of intestinal microflora. Enterococcus massiliensis is a Gram-positive cocci, facultative anaerobic and motile. E. massiliensis is negative for mannitol and positive for β-galactosidase, contrary to E. gallinarum. The complete genome sequence is 2 712 841 bp in length with a GC content of 39.6% and contains 2617 protein-coding genes and 70 RNA genes, including nine rRNA genes.

Romboutsia timonensis, a new species isolated from human gut

The exploration of the human microbiome was recently revolutionized by microbial culturomics and taxonogenomics. Thanks to this approach, we report here the main characteristics of Romboutsia timonensis strain Marseille-P326, a new bacterium isolated from the right human colon by colonoscopy in a 63-year-old French man with severe anaemia with melaena.

Isolation of new species "Peptoniphilus phoceensis" from human gut

Taxonogenomics coupled with culturomics leads to descriptions of new bacteria. Thanks to this strategy, we report the main characteristics of "Peptoniphilus phoceensis" strain SIT15, a new bacterium isolated from a stool sample of a 1-year-old healthy Senegalese boy.

Dramatic reduction in Clostridium difficile ribotype 027-associated mortality with early fecal transplantation by the nasogastric route: a preliminary report

Clostridium difficile ribotype 027 (CD027)-associated diarrhea preferentially affects elderly patients and causes a high mortality rate. Fecal microbiota transplantation has become an alternative treatment for recurrent C. difficile infections. An outbreak of CD027 infections has occurred in Marseille since March 2013. From March to November 2013, we treated patients using only antibiotics or fecal microbiota transplantation after at least three relapses. Beginning in November 2013, we performed early transplantation using a nasogastric tube during the first week of infection, in combination with antibiotic treatment. Sixty-one patients with a mean age of 84 years were hospitalized, including 42 patients treated only with antibiotics, three with tardive transplantation, and 16 with early transplantation. The patients were comparable in clinical involvement. The global mortality rate was 3/16 (18.75 %) among the patients treated by early transplantation and 29/45 (64.4 %) among the patients only treated by antibiotics or by tardive transplantation (p < 0.01). Among these 45 patients, 23 (51 %) died at day 31, including 17 who died at day 7. Early fecal transplantation was associated with a significantly reduced mortality rate, with only one patient dead at day 31 (6.25 %). In a Cox model, early transplantation was the only independent predictor of survival (hazard ratio 0.18, 95 % confidence interval 0.05-0.61, p = 0.006). Six of the 16 patients (37.5 %) needed a second transplantation before symptom resolution. Early fecal microbiota transplantation in combination with antibiotics should be the first-line treatment for CD027 infections.

Draft genome sequence of Coxiella burnetii Dog Utad, a strain isolated from a dog-related outbreak of Q fever

Coxiella burnetii Dog Utad, with a 2 008 938 bp genome is a strain isolated from a parturient dog responsible for a human familial outbreak of acute Q fever in Nova Scotia, Canada. Its genotype, determined by multispacer typing, is 21; the only one found in Canada that includes Q212, which causes endocarditis. Only 107 single nucleotide polymorphisms and 16 INDELs differed from Q212, suggesting a recent clonal radiation.

Genome of a chronic osteitis-causing Clostridium tetani

We sequenced the genome of a Clostridium tetani strain that caused chronic tibial osteitis without any clinical sign of tetanus in a 26-year-old man previously vaccinated against this disease. The genome contained a plasmid that harboured the tetX-tetR tetanospasmin operon, and was highly similar to that of a tetanus-causing strain.

Correlation between body mass index and gut concentrations of Lactobacillus reuteri, Bifidobacterium animalis, Methanobrevibacter smithii and Escherichia coli

BACKGROUND

Genus and species level analysis is the best way to characterize alterations in the human gut microbiota that are associated with obesity, because the clustering of obese and lean microbiotas increases with the taxonomic depth of the analysis. Bifidobacterium genus members have been associated with a lean status, whereas different Lactobacillus species are associated both with a lean and an obese status.

OBJECTIVES AND METHODS

We analyzed the fecal concentrations of Bacteroidetes, Firmicutes, Methanobrevibacter smithii, the genus Lactobacillus, five other Lactobacillus species previously linked with lean or obese populations, Escherichia coli and Bifidobacterium animalis in 263 individuals, including 134 obese, 38 overweight, 76 lean and 15 anorexic subjects to test for the correlation between bacterial concentration and body mass index (BMI). Of these subjects, 137 were used in our previous study.

FINDINGS

Firmicutes were found in >98.5%, Bacteroidetes in 67%, M. smithii in 64%, E. coli in 51%, Lactobacillus species between 17 and 25% and B. animalis in 11% of individuals. The fecal concentration of Lactobacillus reuteri was positively correlated with BMI (coefficient=0.85; 95% confidence interval (CI) 0.12-0.58; P=0.02) in agreement with what was reported for Lactobacillus sakei. As reported, B. animalis (coefficient=-0.84; 95% CI -1.61 to -0.07; P=0.03) and M. smithii (coefficient=-0.43, 95% CI -0.90 to 0.05; P=0.08) were negatively associated with the BMI. Unexpectedly, E. coli was found here for the first time to negatively correlate with the BMI (coefficient=-1.05; 95% CI -1.60 to -0.50; P<0.001).

CONCLUSION

Our findings confirm the specificity of the obese microbiota and emphasize the correlation between the concentration of certain Lactobacillus species and obesity.

Gut bacterial microbiota and obesity

Although probiotics and antibiotics have been used for decades as growth promoters in animals, attention has only recently been drawn to the association between the gut microbiota composition, its manipulation, and obesity. Studies in mice have associated the phylum Firmicutes with obesity and the phylum Bacteroidetes with weight loss. Proposed mechanisms linking the microbiota to fat content and weight include differential effects of bacteria on the efficiency of energy extraction from the diet, and changes in host metabolism of absorbed calories. The independent effect of the microbiota on fat accumulation has been demonstrated in mice, where transplantation of microbiota from obese mice or mice fed western diets to lean or germ-free mice produced fat accumulation among recipients. The microbiota can be manipulated by prebiotics, probiotics, and antibiotics. Probiotics affect the microbiota directly by modulating its bacterial content, and indirectly through bacteriocins produced by the probiotic bacteria. Interestingly, certain probiotics are associated with weight gain both in animals and in humans. The effects are dependent on the probiotic strain, the host, and specific host characteristics, such as age and baseline nutritional status. Attention has recently been drawn to the association between antibiotic use and weight gain in children and adults. We herein review the studies describing the associations between the microbiota composition, its manipulation, and obesity.

Microbial culturomics: paradigm shift in the human gut microbiome study

Comprehensive determination of the microbial composition of the gut microbiota and the relationships with health and disease are major challenges in the 21st century. Metagenomic analysis of the human gut microbiota detects mostly uncultured bacteria. We studied stools from two lean Africans and one obese European, using 212 different culture conditions (microbial culturomics), and tested the colonies by using mass spectrometry and 16S rRNA amplification and sequencing. In parallel, we analysed the same three samples by pyrosequencing 16S rRNA amplicons targeting the V6 region. The 32 500 colonies obtained by culturomics have yielded 340 species of bacteria from seven phyla and 117 genera, including two species from rare phyla (Deinococcus-Thermus and Synergistetes, five fungi, and a giant virus (Senegalvirus). The microbiome identified by culturomics included 174 species never described previously in the human gut, including 31 new species and genera for which the genomes were sequenced, generating c. 10 000 new unknown genes (ORFans), which will help in future molecular studies. Among these, the new species Microvirga massiliensis has the largest bacterial genome so far obtained from a human, and Senegalvirus is the largest virus reported in the human gut. Concurrent metagenomic analysis of the same samples produced 698 phylotypes, including 282 known species, 51 of which overlapped with the microbiome identified by culturomics. Thus, culturomics complements metagenomics by overcoming the depth bias inherent in metagenomic approaches.

Q fever and pregnancy: disease, prevention, and strain specificity

The link between fetal morbidity and Q fever and the necessity of long-term antibiotics for Coxiella burnetii infection during pregnancy have been recently questioned in the Netherlands, where the clone responsible for the Q fever outbreak harbors the QpH1 plasmid. In this context, we assessed pregnancy outcomes according to antibiotic administration in a new series and compared the plasmid type between isolates associated with abortion and other clinical isolates to determine if there is a link between genotype and abortion in humans. All French patients who received a diagnosis of Q fever during pregnancy at the French National Referral Centre for Q Fever from 2006 through July 2011 were included. On the other hand, the plasmid types of 160 clinical isolates, including seven isolates from patients who experienced an abortion, were compared. The differences between the QpDV and QpH1 plasmid sequences were analyzed. Acute Q fever was a cause of fetal morbidity, and the absence of long-term cotrimoxazole therapy was associated with fetal death (p < 0.0001). Genotypic analysis showed that the QpDV plasmid was more frequent in isolates associated with abortion (p = 0.03). A comparison of the plasmid sequences revealed that four QpDV proteins had no direct counterparts in QpH1, with two whose functions were not present in QpH1. The different obstetrical morbidity of C. burnetii relative to different geographical areas could be related to strain specificity, possibly based on differences in plasmid sequences, or to a failure of public health authorities to detect early miscarriages.