Butyricimonas phoceensis sp. nov., a new anaerobic species isolated from the human gut microbiota of a French morbidly obese patient

Unraveling the mystery: a Mendelian randomized exploration of gut microbiota and different types of obesity

Background

Numerous studies have demonstrated the influence of gut microbiota on the development of obesity. In this study, we utilized Mendelian randomization (MR) analysis to investigate the gut microbiota characteristics among different types of obese patients, aiming to elucidate the underlying mechanisms and provide novel insights for obesity treatment.

Methods

Two-sample multivariable Mendelian randomization (MR) analysis was employed to assess causal relationships between gut microbiota and various obesity subtypes. Gut microbiota data were obtained from the international consortium MiBioGen, and data on obese individuals were sourced from the Finnish National Biobank FinnGen. Eligible single-nucleotide polymorphisms (SNPs) were selected as instrumental variables. Various analytical methods, including inverse variance weighted (IVW), MR-Egger regression, weighted median, MR-RAPS, and Lasso regression, were applied. Sensitivity analyses for quality control included MR-Egger intercept tests, Cochran's Q tests, and leave-one-out analyses and others.

Results

Mendelian randomization studies revealed distinct gut microbiota profiles among European populations with different obesity subtypes. Following multivariable MR analysis, we found that Ruminococcaceae UCG010 [Odds Ratio (OR): 0.842, 95% confidence interval (CI): 0.766-0.926, Adjusted P value: 0.028] independently reduced the risk of obesity induced by excessive calorie intake, while Butyricimonas [OR: 4.252, 95% CI: 2.177-8.307, Adjusted P value: 0.002] independently increased the risk of medication-induced obesity. For localized adiposity, Pasteurellaceae [OR: 0.213, 95% CI: 0.115-0.395, Adjusted P value: <0.001] acted as a protective factor. In the case of extreme obesity with alveolar hypoventilation, lactobacillus [OR: 0.724, 95% CI: 0.609-0.860, Adjusted P value: 0.035] reduced the risk of its occurrence. Additionally, six gut microbiota may have potential roles in the onset of different types of obesity. Specifically, the Ruminococcus torques group may increase the risk of its occurrence. Desulfovibrio and Catenabacterium may serve as protective factors in the onset of Drug-induced obesity. Oxalobacteraceae, Actinomycetaceae, and Ruminiclostridium 9, on the other hand, could potentially increase the risk of Drug-induced obesity. No evidence of heterogeneity or horizontal pleiotropy among SNPs was found in the above studies (all P values for Q test and MR-Egger intercept > 0.05).

Conclusion

Gut microbiota abundance is causally related to obesity, with distinct gut microbiota profiles observed among different obesity subtypes. Four bacterial species, including Ruminococcaceae UCG010, Butyricimonas, Pasteurellaceae and lactobacillus independently influence the development of various types of obesity. Probiotic and prebiotic supplementation may represent a novel approach in future obesity management.

Butyricimonas virosa Peritonitis in Peritoneal Dialysis Patient: A Case Report and Review

Butyricimonas virosa is a Gram-negative bacillus, which was first discovered in rat faeces in 2009. To date, only seven human infections have been reported in literature. To our knowledge, this is the first reported case of peritoneal dialysis (PD)-related peritonitis due to B. virosa. A 65-year-old Chinese man presented to the hospital with complaints of dizziness and vomiting. On admission, the drained peritoneal dialysate was cloudy. He was empirically treated as a case of PD-related peritonitis with intraperitoneal (IP) cefazolin, ceftazidime, and gentamicin. B. virosa was isolated from peritoneal fluid sample and the antibiotics were changed to IP imipenem and amikacin. Three weeks after completion of the antibiotics, the patient presented again with cloudy peritoneal dialysate and blood stained diarrhoea. IP imipenem and amikacin were recommenced. Multiple peritoneal dialysate samples were sent to the microbiology laboratory, but this time no microorganism was isolated. Colonoscopy examination revealed the presence of extensive rectosigmoidal ulcerations. IP imipenem was replaced with IP piperacillin-tazobactam when the patient developed imipenem-associated neurotoxicity at Day 9 of treatment. The patient recovered fully after completing 3 weeks of IP piperacillin-tazobactam and 2 weeks of IP amikacin. This is the first reported case of PD-related peritonitis due to B. virosa. Susceptibility data for B. virosa are scarce, but a 3-week course of IP piperacillin-tazobactam, imipenem, or meropenem could be potentially useful in treating PD-related peritonitis caused by this organism.

Characterization of Bacterial Microbiota Composition in Healthy and Diarrheal Early-Weaned Tibetan Piglets

The occurrence of diarrhea in Tibetan piglets is highly notable, but the microorganisms responsible are yet unclear. Its high incidence results in serious economic losses for the Tibetan pig industry. Moreover, the dynamic balance of intestinal microflora plays a crucial role in maintaining host health, as it is a prime cause of diarrhea. Therefore, the present study was performed to analyze the characteristics of bacterial microbiota structure in healthy, diarrheal and treated weaned piglets in Tibet autonomous region for providing a theoretical basis to prevent and control diarrhea. The study was based on the V3–V4 region of the 16S rRNA gene and gut microbiota functions following the metagenome analysis of fresh fecal samples (n = 5) from different groups. The Shannon and Simpson indices differed substantially between diarrheal and treated groups (p < 0.05). According to our findings, the beta diversities, especially between healthy and diarrheal groups, were found different. Firmicutes, Bacteroidetes and Proteobacteria were the dominant phyla in three groups. Furthermore, the abundance of Fusobacteria in the diarrheal group was higher than the other groups. The dominant genera in the diarrheal group were Fusobacterium, Butyricimonas, Sutterella, Peptostreptococcus, and Pasteurella. Moreover, Lactobacillus, Megasphaera and Clavibacter were distinctly less abundant in this group. It is noteworthy that the specific decrease in the abundance of pathogenic bacteria after antibiotic treatment in piglets was noticed, while the level of Lactobacillus was evidently increased. In conclusion, fecal microbial composition and structure variations were discovered across the three groups. Also, the ecological balance of the intestinal microflora was disrupted in diarrheal piglets. It might be caused by a reduction in the relative number of beneficial bacteria and an increase in the abundance of pathogenic bacteria. In the context of advocating for non-resistant feeding, we suspect that the addition of probiotics to feed may prevent early-weaning diarrhea in piglets. Moreover, our findings might help for preventing diarrhea in weaned Tibetan piglets with a better understanding of microbial population dynamics.

A subcutaneous infection mimicking necrotizing fasciitis due to Butyricimonas virosa

INTRODUCTION

Butyricimonas virosa is a Gram-negative rod who was first identified in rat faces in 2009. Since then only six human infections have been described in literature of which five bacteremia and one bone abscess. We report a clinical case of a subcutaneous infection mimicking necrotizing fasciitis due to B. virosa.

PATIENT AND METHODS

A 78-year-old man was referred to our hospital because of a wound infection at the surgical site with suspicion of necrotizing fasciitis. Treatment consisted of immediate surgical exploration with obtainment of intra-operative specimens for microbiologic examination, 15 d of negative pressure wound therapy (NPWT) and antibiotic treatment with piperacillin-tazobactam (12 d) plus vancomycin (9 d).

RESULTS

Surgical exploration did not show necrotising fasciitis but a subcutaneous infection mimicking necrotising fasciitis. The results of the intra-operative specimens revealed the presence of B.virosa and Finegoldia magna. Cultures taken during the NPWT replacements became negative and the patient was able to leave the hospital after 18 d.

CONCLUSIONS

Considering there was no necrotizing infection present it may have been possible to safely close the wound sooner. However, it is difficult to differentiate between an actual necrotizing fasciitis and a subcutaneous infection mimicking necrotizing fasciitis. Therefore further studies on effective assessment tools to diagnose necrotizing fasciitis, such as the (modified) laboratory risk indicator for necrotizing fasciitis (LRINEC) score and enhanced computed tomography (CT), could be helpful.

Draft genome and description of Negativicoccus massiliensis strain Marseille-P2082, a new species isolated from the gut microbiota of an obese patient

Strain Marseille-P2082, an anaerobic, non-motile, asporogenous, Gram-negative, coccoid bacterium was isolated from the faeces of a 33 year-old obese French woman before bariatric surgery. The isolate exhibits 98.65% 16S rRNA gene nucleotide sequence similarity with Negativicoccus succinicivorans strain ADV 07/08/06-B-1388^T, its current closest phylogenetic neighbour with standing in nomenclature. However, the dDDH relatedness between the new isolate and N. succinicivorans type strain ADV 07/08/06-B-1388^T is 52.5 ± 2.7%. Strain Marseille-P2082 has a genome of 1,360,589 bp with a 51.1% G+C content. Its major fatty acids were identified as C_18:1n9, C_18:0 and C_16:0. Based on its phenotypic, genomic and phylogenetic characteristics, strain Marseille-P2082^T [= CSURP2082 (Collection de Souches de l'Unité des Rickettsies) = DSM 100853] is proposed as the type strain of the novel species Negativicoccus massiliensis sp. nov. The 16S rRNA gene sequence and whole-genome shotgun sequence have been deposited in EMBL-EBI under accession numbers LN876651 and LT700188, respectively.

From Culturomics to Clinical Microbiology and Forward

Culturomics has permitted discovery of hundreds of new bacterial species isolated from the human microbiome. Profiles generated by using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry have been added to the mass spectrometer database used in clinical microbiology laboratories. We retrospectively collected raw data from MALDI-TOF mass spectrometry used routinely in our laboratory in Marseille, France, during January 2012-March 2018 and analyzed 16S rDNA sequencing results from misidentified strains. During the study period, 744 species were identified from clinical specimens, of which 21 were species first isolated from culturomics. This collection involved 105 clinical specimens, accounting for 98 patients. In 64 cases, isolation of the bacteria was considered clinically relevant. MALDI-TOF mass spectrometry was able to identify the species in 95.2% of the 105 specimens. While contributing to the extension of the bacterial repertoire associated with humans, culturomics studies also enlarge the spectrum of prokaryotes involved in infectious diseases.

Naming microorganisms: the contribution of the IHU Méditerranée Infection, Marseille, France

The number of isolated new microorganisms has dramatically increased after the readaption of culture using the culturomics approach. Each of these microorganisms is deposited in an international strain collection institute, with its name being attributed and published by the scientist who isolated it. The attributed name is of Latin or Latinized origin and chosen on the basis of the geographical location of the sample collection, the institute or geographical region where the project was being performed, the name of a concerned scientist, and characteristics of the sample or the microorganism. Our institution has played an important role in the isolation of new microorganisms, with the first effort reporting 468 new bacterial species (3% of the bacterial species isolated at least once worldwide) and 327 species isolated for the first time from human beings, which in turn resulted in an increase of 30% of the total number of microorganisms isolated. Additionally, more than 100 giant viruses, including seven new species, have been isolated at our institute. In the present work, after recalling the rules of nomenclature, we detail the naming of the new microorganisms chosen at our laboratory. The most common species name was massiliensis, attributed 161 times. We consider it imperative for the cultivators, who have frequently made considerable efforts in the field of microbial culture, to be the ones who name the newly isolated microorganisms, taking into consideration the Latinized nomenclature standards.