Gut microbiota composition links to variation in functional domains across psychiatric disorders

OBJECTIVE

Changes in microbial composition are observed in various psychiatric disorders, but their specificity to certain symptoms or processes remains unclear. This study explores the associations between the gut microbiota composition and the Research Domain Criteria (RDoC) domains of functioning, representing symptom domains, specifically focusing on stress-related and neurodevelopmental disorders in patients with and without psychiatric comorbidity.

METHODS

The gut microbiota was analyzed in 369 participants, comprising 272 individuals diagnosed with a mood disorder, anxiety disorder, attention deficit/hyperactivity disorder, autism spectrum disorder, and/or substance use disorder, as well as 97 psychiatrically unaffected individuals. The RDoC domains were estimated using principal component analysis (PCA) with oblique rotation on a range of psychiatric, psychological, and personality measures. Associations between the gut microbiota and the functional domains were assessed using multiple linear regression and permanova, adjusted for age, sex, diet, smoking, medication use and comorbidity status.

RESULTS

Four functional domains, aligning with RDoC's negative valence, social processes, cognitive systems, and arousal/regulatory systems domains, were identified. Significant associations were found between these domains and eight microbial genera, including associations of negative valence with the abundance of the genera Sellimonas, CHKCI001, Clostridium sensu stricto 1, Oscillibacter, and Flavonifractor; social processes with Sellimonas; cognitive systems with Sporobacter and Hungatella; and arousal/regulatory systems with Ruminococcus torques (all pFDR < 0.05).

CONCLUSION

Our findings demonstrate associations between the gut microbiota and the domains of functioning across patients and unaffected individuals, potentially mediated by immune-related processes. These results open avenues for microbiota-focused personalized interventions, considering psychiatric comorbidity. However, further research is warranted to establish causality and elucidate mechanistic pathways.

Clostridium tanneri sp. nov., isolated from the faecal material of an alpaca

A strictly anaerobic, Gram-stain-negative rod-shaped bacterium, designated A1-XYC3T, was isolated from the faeces of an alpaca (Lama pacos). On the basis of the results of a comparative 16S rRNA gene sequence analysis, the isolate was assigned to the genus Clostridium with the highest sequence similarities to Clostridium magnum DSM 2767T (96.8 %), Clostridium carboxidivorans P7T (96.3 %) and Clostridium aciditolerans JW/YJL-B3T (96.1 %). The average nucleotide identity between A1-XYC3T, C. magnum, C. carboxidivorans and C. aciditolerans was 77.4, 76.1 and 76.6  %, respectively. The predominant components of the cellular fatty acids of A1-XYC3T were C14 : 0, C16 : 0 and summed feature 10, containing C18:0/C17:0 cyclo. The DNA G+C content was 32.4 mol%. On the basis of biochemical, phylogenetic, genotypic and chemotaxonomic criteria, this isolate represents a novel species within Clostridium sensu stricto for which the name Clostridium tanneri sp. nov. is proposed. The type strain of this species is strain A1-XYC3T (=CCM 9376T=NRRL B-65691T).

Clostridium strain FAM25158, a unique endospore-forming bacterium related to Clostridium tyrobutyricum and isolated from Emmental cheese shows low tolerance to salt

The genus Clostridium is a large and diverse group of species that can cause food spoilage, including late blowing defect (LBD) in cheese. In this study, we investigated the taxonomic status of strain FAM25158 isolated from Emmental cheese with LBD using a polyphasic taxonomic and comparative genomic approach. A 16S rRNA gene sequence phylogeny suggested affiliation to the Clostridium sensu stricto cluster, with Clostridium tyrobutyricum DSM 2637T being the closest related type strain (99.16% sequence similarity). Average Nucleotide Identity (ANI) analysis revealed that strain FAM25158 is at the species threshold with C. tyrobutyricum, with ANI values ranging from 94.70 to 95.26%, while the digital DNA-DNA hybridization values were below the recommended threshold, suggesting that FAM25158 is significantly different from C. tyrobutyricum at the genomic level. Moreover, comparative genomic analysis between FAM25158 and its four closest C. tyrobutyricum relatives revealed a diversity of metabolic pathways, with FAM25158 differing from other C. tyrobutyricum strains by the presence of genes such as scrA, srcB, and scrK, responsible for sucrose utilization, and the absence of many important functional genes associated with cold and osmolality adaptation, which was further supported by phenotypic analyses. Surprisingly, strain FAM25158 exhibited unique physiologic traits, such as an optimal growth temperature of 30°C, in contrast to its closest relatives, C. tyrobutyricum species with an optimal growth temperature of 37°C. Additionally, the growth of FAM25158 was inhibited at NaCl concentrations higher than 0.5%, a remarkable observation considering its origin from cheese. While the results of this study provide novel information on the genetic content of strain FAM25158, the relationship between its genetic content and the observed phenotype remains a topic requiring further investigation.

Hathewaya limosa Empyema: A Case Report

Hathewaya limosa, an anaerobic bacterium, has been associated with various infections, including prosthetic valve endocarditis, although its role in empyema remains uncommon. This abstract presents a case report of a patient diagnosed with H. limosa empyema, highlighting the clinical presentation, diagnostic challenges, and successful treatment strategies. The case underscores the importance of considering unusual pathogens in the context of empyema. We discuss the clinical management, microbiological identification, and outcomes of this rare infection to contribute valuable insights for healthcare practitioners encountering similar cases.

Case report and mini-review: Sarcina ventriculi in the stomach of an 80-year-old female

Sarcina ventriculi, also known as Zymosarcina ventriculi and, incorrectly, as Clostridium ventriculi, is rarely encountered in clinical settings. A patient with a complicated gastrointestinal (GI) history, who was acutely presenting with small-bowel obstruction, was found to be colonized by S. ventriculi. The distinctive morphology of this species, with large Gram-variable cocci (up to 3 µm) arranged in two-by-two cuboid clusters reaching up to 20 µm, was key in identifying this bacterium in a stomach biopsy specimen. Sarcina ventriculi appears to be ubiquitously found in nature, and related bacterial species can cause GI-related disease in various animals. Clinical manifestations in humans are broad and often related to other underlying comorbidities. Isolation of S. ventriculi in the laboratory requires anaerobic culture on select media but its absence from standard MALDI-TOF databases complicates identification. Susceptibility data do not exist, so empiric treatment is the only option for this rare pathogen.

Continuous production of high-concentrated ammonia broth through fermentation

Being considered as a valuable resource and energy carrier, extensive research is going on to efficiently extract ammonia (NH3) from anaerobic digestate. However, due to the well-known NH3 inhibition on methanogens, the total NH3 nitrogen (TAN) concentration is typically limited to 1-4 g N/L in digestate, making the NH3 extraction process energy-consumptive. Here, NH3 fermentation, specifically targeting augmented NH3 production through biological reaction, was performed in a continuous mode. With the increase of gelatin input (10 to 150 g COD/L), NH3 concentration and volumetric productivity gradually increased, reaching 12.0 g TAN-N/L and 36.0 g NH3-N/L/d, which were the highest values ever reported. The stepwise increase in NH3 exposure prompted a shift in microbial dominance towards Hathewaya (from 1 % to 68 %), a critical factor for having high NH3 tolerance. Finally, NH3 stripping results suggested that highly concentrated broth could reduce the specific energy consumption for NH3 extraction to 1/3.

Infective Endocarditis by Clostridioides and Clostridium Species-A Narrative Review

Bacteria of the genus Clostridium are anaerobic Gram-positive spore-forming bacilli that include more than 200 species. Some of them are known to cause invasive infections and diseases caused by the production of toxins. Some of the diseases that are mediated by toxins are colitis in patients with specific risk factors, such as previous administration of antimicrobials or foodborne botulism. Invasive diseases include bacteremia, infective endocarditis (IE), clostridial myonecrosis (gas gangrene), and other diseases that involve the destruction of soft tissue due to the local production of toxins. The present study aimed to review all cases of IE by Clostridioides and Clostridium species and describe the epidemiology, clinical characteristics, treatment, and outcomes of these infections. A narrative review was performed based on a search in PubMed and Scopus for studies published until 11 September 2023, providing such data of IE caused by Clostridioides and Clostridium species in humans. A total of 20 studies containing data for 21 patients were included. A prosthetic valve was present in 5 patients (23.8%). The aortic valve was the most commonly involved, followed by the mitral valve. Fever, sepsis, and embolic phenomena were the most common clinical presentations. Beta-lactams and metronidazole were the most commonly used antimicrobials. Surgery was performed in nine patients (45%). Mortality reached 33.3%. IE in multiple valves was associated with increased mortality. Despite the heterogeneous genetic and molecular characteristics that necessitate the taxonomic change of some of this genus's previous members, the clinical syndrome of IE caused by these bacteria seems to have similar characteristics.

Microbiological and physical-chemical characteristics of the Peruvian fermented beverage "Chicha de siete semillas": Towards the selection of strains with acidifying properties

Traditional fermented beverages have been consumed worldwide for centuries. Such is the case of "Chicha de siete semillas" which is originally from the province of Huanta, in Ayacucho, Peru. In this work we have analyzed the chemical composition and bacterial diversity of products manufactured from six producers, who have used different combinations of cereals, pseudocereals, legumes and aromatic herbs, although maize was present in all of them. The fermented beverages had a low pH, mainly due to the production of lactic acid, whereas ethanol was, in general, present in low concentrations. Most of the products were rich in GABA, the content of biogenic amines being very low, as corresponds to a product with a short maturation time (less than 4 days). A metataxonomic analysis revealed that Streptococcaceae and Leuconostocaceae families were dominant in the majority of the beverages, Streptococcus spp. and Leuconostoc spp. being the representative genera, respectively. The result was corroborated by culture-dependent techniques, since these were the most abundant genera isolated and identified in all samples, with Streptococcus macedonicus and Leuconostoc lactis as representative species. In lower proportions other isolates were identified as Lactobacillus delbrueckii, Lactiplantibacillus plantarum, Furfurilactobacillus rossiae, Weissella confusa and Enterococcus faecium. The genetic profile of 26 S. macedonicus isolates was determined by RAPD-PCR and REP-PCR, showing five different patterns distinguishable with the first technique. One representative strain from each genetic pattern was further characterized and used to ferment a maize-based matrix (with saccharose) in order to know their technological potential. All strains were able to ferment the beverage at 30 °C in a short time (about 6 h) reaching a pH below 4.5 and they remained viable after 24 h; the main organic acid contributing to the pH decrease was lactic acid. Therefore, S. macedonicus is a good candidate for being part of a putative starter culture, since it is a species well adapted to this cereal-based food niche.

Solvent-Producing Clostridia Revisited

The review provides an overview of the current status of the solvent-producing clostridia. The origin and development of industrial clostridial species, as well as the history of the industrial Acetone Butanol Ethanol fermentation process, is reexamined, and the recent resurgence of interest in the production of biobutanol is reviewed. Over 300 fully sequenced genomes for solvent-producing and closely related clostridial species are currently available in public databases. These include 270 genomes sourced from the David Jones culture collection. These genomes were allocated arbitrary DJ codes, and a conversion table to identify the species and strains has now been provided. The expanded genomic database facilitated new comparative genomic and phylogenetic analysis. A synopsis of the common features, molecular taxonomy, and phylogeny of solvent-producing clostridia and the application of comparative phylogenomics are evaluated. A survey and analysis of resident prophages in solvent-producing clostridia are discussed, and the discovery, occurrence, and role of novel R-type tailocins are reported. Prophage genomes with R-type tailocin-like features were detected in all 12 species investigated. The widespread occurrence of tailocins in Gram-negative species is well documented; this survey has indicated that they may also be widespread in clostridia.

Species and Strain Variability among Sarcina Isolates from Diverse Mammalian Hosts

Sarcina spp. has been isolated from the gastrointestinal tracts of diverse mammalian hosts. Their presence is often associated with host health complications, as is evident from many previously published medical case reports. However, only a handful of studies have made proper identification. Most other identifications were solely based on typical Sarcina-like morphology without genotyping. Therefore, the aim of this work was culture detection and the taxonomic classification of Sarcina isolates originating from different mammalian hosts. Sarcina-like colonies were isolated and collected during cultivation analyses of animal fecal samples (n = 197) from primates, dogs, calves of domestic cattle, elephants, and rhinoceroses. The study was carried out on apparently healthy animals kept in zoos or by breeders in the Czech Republic and Slovakia. Selected isolates were identified and compared using 16S rRNA gene sequencing and multi-locus sequence analysis (MLSA; Iles, pheT, pyrG, rplB, rplC, and rpsC). The results indicate the taxonomic variability of Sarcina isolates. S. ventriculi appears to be a common gut microorganism in various captive primates. In contrast, a random occurrence was also recorded in dogs. However, dog isolate N13/4e could represent the next potential novel Sarcina taxonomic unit. Also, a potentially novel Sarcina species was found in elephants, with occurrences in all tested hosts. S. maxima isolates were detected rarely, only in rhinoceroses. Although Sarcina bacteria are often linked to lethal diseases, our results indicate that Sarcina spp. appear to be a common member of the gut microbiota and seem to be an opportunistic pathogen. Further characterization and pathogenic analyses are required.

Profiling of the intestinal community of Clostridia: taxonomy and evolutionary analysis

Aim: Clostridia are relevant commensals of the human gut due to their major presence and correlations to the host. In this study, we investigated intestinal Clostridia of 51 healthy subjects and reconstructed their taxonomy and phylogeny. The relatively small number of intestinal Clostridia allowed a systematic whole genome approach based on average amino acid identity (AAI) and core genome with the aim of revising the current classification into genera and determining evolutionary relationships. Methods: 51 healthy subjects' metagenomes were retrieved from public databases. After the dataset's validation through comparison with Human Microbiome Project (HMP) samples, the metagenomes were profiled using MetaPhlAn3 to identify the population ascribed to the class Clostridia. Intestinal Clostridia genomes were retrieved and subjected to AAI analysis and core genome identification. Phylogeny investigation was conducted with RAxML and Unweighted Pair Group Method with Arithmetic Mean (UPGMA) algorithms, and SplitsTree for split decomposition. Results: 225 out of 406 bacterial taxonomic units were ascribed to Bacillota [Firmicutes], among which 124 were assigned to the class Clostridia. 77 out of the 124 taxonomic units were referred to a species, altogether covering 87.7% of Clostridia abundance. According to the lowest AAI genus boundary set at 55%, 15 putative genera encompassing more than one species (G1 to G15) were identified, while 19 species did not cluster with any other one and each appeared to belong to a diverse genus. Phylogenetic investigations highlighted that most of the species clustered into three main evolutive clades. Conclusion: This study shed light on the species of Clostridia colonizing the gut of healthy adults and pinpointed several gaps in knowledge regarding the taxonomy and the phylogeny of Clostridia.

Comparative genomic analysis and proposal of Clostridium yunnanense sp. nov., Clostridium rhizosphaerae sp. nov., and Clostridium paridis sp. nov., three novel Clostridium sensu stricto endophytes with diverse capabilities of acetic acid and ethanol production

OBJECTIVES

Genus Clostridium sensu stricto is generally regarded as the true Clostridium genus, which includes important human and animal pathogens and industrially relevant microorganisms. Besides, it is also a prominent member of plant-associated endophytes. However, our knowledge of endophytic Clostridium is limited.

METHODS

In this study, the endophytes were isolated under anaerobic condition from the roots of Paris polyphylla Smith var. yunnanensis. Subsequently, a polyphasic taxonomic approach was used to clarify their taxonomic positions. The fermentation products were measured in the isolates with HPLC analysis. Comparative genomics was performed on these new strains and other relatives.

RESULTS

In total, nine endophytic strains belonging to the genus Clostridium sensu stricto were isolated, and three of them were identified as new species. Seven of nine strains could produce acetate, propionate, and butyrate. Only two strains could produce ethanol, although genomics analysis suggested that only two of them were without genes for solventogenesis. Different from the endophytic strains, the phylogenetically closely related non-endophytic strains showed significant enrichment effects on some metabolic pathways involving environmental information processing, carbohydrate, and amino acid metabolisms, etc. It suggests that the genomes of these endophytic strains had undergone subtle changes associated with environmental adaptations.

CONCLUSION

Consequently, strains YIM B02505^T, YIM B02515^T, and YIM B02565^T are proposed to represent a new species of the genus Clostridium sensu stricto, for which the names Clostridium yunnanense sp. nov., Clostridium rhizosphaerae sp. nov., and Clostridium paridis sp. nov. are suggested.

Reclassification of Clostridium cocleatum, Clostridium ramosum, Clostridium spiroforme and Clostridium saccharogumia as Thomasclavelia cocleata gen. nov., comb. nov., Thomasclavelia ramosa comb. nov., gen. nov., Thomasclavelia spiroformis comb. nov. and Thomasclavelia saccharogumia comb. nov

The genus Clostridium is phenotypically and genotypically diverse, with many species phylogenetically located outside Clostridium sensu stricto. One such group consists of the species Clostridium cocleatum, Clostridium ramosum, Clostridium spiroforme and Clostridium saccharogumia (formally clostridial rRNA cluster XVIII) [1]. Sequencing of the 16S rRNA and, more recently, the results of genomic analyses have demonstrated that these species represent a coherent cluster separated from other closely related genera located in the family Coprobacillaceae within the order Erysipelotrichales [2]. In addition to phenotypic, phylogenetic and genomic comparisons, chemotaxonomic features were consistent between all four species, the predominant fatty acids were C_16 : 0 and C_18 : 1ω9c, while glucose and ribose were the whole cell sugars present in the cell walls. Furthermore, he results of peptidoglycan analysis indicated that meso-2,6-diaminopimelic acid was present as the diagnostic diamino acid in all four species. Biochemical profiles were also concordant with them being closely related species. Therefore, on the basis of phylogenetic, genomic, phenotypic and chemotaxonomic information, a novel genus, Thomasclavelia gen. nov., is proposed. It is suggested that Clostridium cocleatum, Clostridium ramosum, Clostridium spiroforme and Clostridium saccharogumia be transferred to this genus as Thomasclavelia cocleata comb. nov., Thomasclavelia ramosa comb. nov., Thomasclavelia saccharogumia comb. nov. and Thomasclavelia spiroformis comb. nov. The type species of the genus is Thomasclavelia ramosa CCUG 24038^T (=ATCC 25582^T=DSM 1402^T).

The Effect of Short-Term Consumption of Lactic Acid Bacteria on the Gut Microbiota in Obese People

Obesity is a problem of modern health care that causes the occurrence of many concomitant diseases: arterial hypertension, diabetes mellitus, non-alcoholic fatty liver disease, and cardiovascular diseases. New strategies for the treatment and prevention of obesity are being developed that are based on using probiotics for modulation of the gut microbiota. Our study aimed to evaluate the bacterial composition of the gut of obese patients before and after two weeks of lactic acid bacteria (Lactobacillus acidophilus, Lactiplantibacillus plantarum, Limosilactobacillus fermentum, and Lactobacillus delbrueckii) intake. The results obtained showed an increase in the number of members of the phylum Actinobacteriota in the group taking nutritional supplements, while the number of phylum Bacteroidota decreased in comparison with the control group. There has also been an increase in potentially beneficial groups: Bifidobacterium, Blautia, Eubacterium, Anaerostipes, Lactococcus, Lachnospiraceae ND3007, Streptococcus, Escherichia-Shigella, and Lachnoclostridium. Along with this, a decrease in the genera was demonstrated: Faecalibacterium, Pseudobutyrivibrio, Subdoligranulum, Faecalibacterium, Clostridium sensu stricto 1 and 2, Catenibacterium, Megasphaera, Phascolarctobacterium, and the Oscillospiraceae NK4A214 group, which contribute to the development of various metabolic disorders. Modulation of the gut microbiota by lactic acid bacteria may be one of the ways to treat obesity.

Orlistat and ezetimibe could differently alleviate the high-fat diet-induced obesity phenotype by modulating the gut microbiota

This study aimed to evaluate the possible anti-obesity effects of orlistat and ezetimibe and determine the mechanism by which they alter the composition of gut microbiota and short-chain fatty acids (SCFAs) in mice with a high-fat diet (HFD)-induced obesity. Eighty male, specific pathogen-free C57BL/6J mice aged 3 weeks were divided into four groups (n = 20). The NCD group was fed with a normal diet, and the HFD, HFD+ORL, and HFD+EZE groups were fed with HFD for 20 weeks. From the 13th week onward, the HFD+ORL and HFD+EZE groups were administered with orlistat and ezetimibe, respectively. The glucose and lipid metabolism of the tested mice were evaluated by analyzing blood biochemical indicators during the intervention. Furthermore, the changes in the structure of the fecal microbiota and the fecal SCFA content were analyzed by 16S rRNA sequencing and gas chromatography-mass spectrometry, respectively. HFD induced the obesity phenotype in mice. Compared to the HFD group, the body weight, visceral fat-to-body weight ratio, serum total cholesterol (TC), high-density lipoprotein-cholesterol (HDL-C), and oral glucose tolerance test (OGTT) of the HFD+ORL group significantly decreased, whereas fecal butyric acid levels significantly increased. Ezetimibe intervention significantly reduced the OGTT, serum TC, and HDL-C levels only. The α-diversity of the gut microbiota significantly decreased after intervention with orlistat and ezetimibe. Orlistat altered the relative abundance of some bacteria in the fecal microbiota. The populations of Firmicutes, Alistipes, and Desulfovibrio decreased, whereas those of Verrucomicrobia and Akkermansia significantly increased. Ezetimibe caused changes only in some low-abundance bacteria, as manifested by a decrease in Proteobacteria and Desulfovibrio, and an increase in Bacteroides. The administration of orlistat and ezetimibe can characteristically influence the body weight and serum lipid metabolism, and glucolipid levels in diet-induced obese mice and is accompanied by significant changes in the gut microbiota and SCFAs. These results suggest that the two drugs might exert their own specific anti-obesity effects by modulating the gut microbiota in a different manner. The enhanced health-promoting effect of orlistat might result from its stronger ability to alter the gut microbiota and SCFAs, at least partly.

Probiotic Potential of Clostridium spp.-Advantages and Doubts

Clostridium spp. is a large genus of obligate anaerobes and is an extremely heterogeneous group of bacteria that can be classified into 19 clusters. Genetic analyses based on the next-generation sequencing of 16S rRNA genes and metagenome analyses conducted on human feces, mucosal biopsies, and luminal content have shown that the three main groups of strict extremophile anaerobes present in the intestines are Clostridium cluster IV (also known as the Clostridium leptum group), Clostridium cluster XIVa (also known as the Clostridium coccoides group) and Bacteroides. In addition to the mentioned clusters, some C. butyricum strains are also considered beneficial for human health. Moreover, this bacterium has been widely used as a probiotic in Asia (particularly in Japan, Korea, and China). The mentioned commensal Clostridia are involved in the regulation and maintenance of all intestinal functions. In the literature, the development processes of new therapies are described based on commensal Clostridia activity. In addition, some Clostridia are associated with pathogenic processes. Some C. butyricum strains detected in stool samples are involved in botulism cases and have also been implicated in severe diseases such as infant botulism and necrotizing enterocolitis in preterm neonates. The aim of this study is to review reports on the possibility of using Clostridium strains as probiotics, consider their positive impact on human health, and identify the risks associated with the expression of their pathogenic properties.

Fecal microbiome of horses transitioning between warm-season and cool-season grass pasture within integrated rotational grazing systems

BACKGROUND

Diet is a key driver of equine hindgut microbial community structure and composition. The aim of this study was to characterize shifts in the fecal microbiota of grazing horses during transitions between forage types within integrated warm- (WSG) and cool-season grass (CSG) rotational grazing systems (IRS). Eight mares were randomly assigned to two IRS containing mixed cool-season grass and one of two warm-season grasses: bermudagrass [Cynodon dactylon (L.) Pers.] or crabgrass [Digitaria sanguinalis (L.) Scop.]. Fecal samples were collected during transitions from CSG to WSG pasture sections (C-W) and WSG to CSG (W-C) on days 0, 2, 4, and 6 following pasture rotation and compared using 16S rRNA gene sequencing.

RESULTS

Regardless of IRS or transition (C-W vs. W-C), species richness was greater on day 4 and 6 in comparison to day 0 (P < 0.05). Evenness, however, did not differ by day. Weighted UniFrac also did not differ by day, and the most influential factor impacting β-diversity was the individual horse (R² ≥ 0.24; P = 0.0001). Random forest modeling was unable to accurately predict days within C-W and W-C, but could predict the individual horse based on microbial composition (accuracy: 0.92 ± 0.05). Only three differentially abundant bacterial co-abundance groups (BCG) were identified across days within all C-W and W-C for both IRS (W ≥ 126). The BCG differing by day for all transitions included amplicon sequence variants (ASV) assigned to bacterial groups with known fibrolytic and butyrate-producing functions including members of Lachnospiraceae, Clostridium sensu stricto 1, Anaerovorax the NK4A214 group of Oscillospiraceae, and Sarcina maxima. In comparison, 38 BCG were identified as differentially abundant by horse (W ≥ 704). The ASV in these groups were most commonly assigned to genera associated with degradation of structural carbohydrates included Rikenellaceae RC9 gut group, Treponema, Christensenellaceae R-7 group, and the NK4A214 group of Oscillospiraceae. Fecal pH also did not differ by day.

CONCLUSIONS

Overall, these results demonstrated a strong influence of individual horse on the fecal microbial community, particularly on the specific composition of fiber-degraders. The equine fecal microbiota were largely stable across transitions between forages within IRS suggesting that the equine gut microbiota adjusted at the individual level to the subtle dietary changes imposed by these transitions. This adaptive capacity indicates that horses can be managed in IRS without inducing gastrointestinal dysfunction.

Impact of the Gram-Negative-Selective Inhibitor MAC13243 on In Vitro Simulated Gut Microbiota

New Gram-negative-selective antimicrobials are desirable to avoid perturbations in the gut microbiota leading to antibiotic-induced dysbiosis. We investigated the impact of a prototype drug (MAC13243) interfering with the Gram-negative outer membrane protein LolA on the faecal microbiota. Faecal suspensions from two healthy human donors were exposed to MAC13243 (16, 32, or 64 mg/L) using an in vitro gut model (CoMiniGut). Samples collected 0, 4, and 8 h after exposure were subjected to viable cell counts, 16S rRNA gene quantification and V3-V4 sequencing using the Illumina MiSeq platform. MAC13243 exhibited concentration-dependent killing of coliforms in both donors after 8 h. Concentrations of ≤32 mg/L reduced the growth of aerobic bacteria without influencing the microbiota composition and diversity. An expansion of Firmicutes at the expense of Bacteroidetes and Actinobacteria was observed in the faecal microbiota from one donor following exposure to 64 mg/L of MAC13242. At all concentrations tested, MAC13243 did not lead to the proliferation of Escherichia coli nor a reduced abundance of beneficial bacteria, which are typical changes observed in antibiotic-induced dysbiosis. These results support our hypothesis that a drug interfering with a specific target in Gram-negative bacteria has a low impact on the commensal gut microbiota and, therefore, a low risk of inducing dysbiosis.

Clostridium butyricum, a butyrate-producing potential probiotic, alleviates experimental colitis through epidermal growth factor receptor activation

Inflammatory bowel disease (IBD) is an idiopathic inflammatory bowel disease. Modulation of gut microbiota with dietary and nutritional targets is a feasible strategy for the prevention and treatment of IBD. In this study, we focused on Clostridium butyricum Prazmowski (CB), a butyrate-producing potential probiotic. We found that CB feeding decreased the disease activity index, colon inflammation/injury score and cell apoptosis in an experimental colitis mouse model, as well as elevated the level of SCFAs in cecal feces. CB could also balance the inflammatory cytokines, protect tight junctions, and increase the number of goblet cells and MUC2 production in mice, accompanied by EGFR signaling activation triggered by heparin-binding epidermal growth factor (HB-EGF) and amphiregulin (AREG). From the perspective of mechanism, the CB supernatant (CBS) stimulated EGFR activation in colon epithelial cell lines in concentration-dependent and time-dependent manners. CBS reduced the damage of tight junctions induced by H₂O₂, and inhibition of EGFR could suppress the protective effect of CBS. In conclusion, CB could protect the gut barrier and alleviate experimental colitis through the transactivation of EGFR signaling in intestinal epithelial cells induced by ligands (HB-EGF and AREG). This study identified the potential efficacy of CB as a preventive strategy for IBD and showed the broad prospect of CB as a food supplement.

Roadmap from Microbial Communities to Individuality Modeling for Anaerobic Digestion of Sewage Sludge

Biological models describing anaerobic digestion (AD) of sewage sludge have been widely applied to test various control and operation strategies. Anaerobic digestion model 1 (ADM1) provides a generic platform that includes the main processes of AD, excluding homoacetogenesis and the microbial structure. Homoacetogenic bacteria have been identified as important competitors for hydrogen consumption and acetate production. Although recent advances in meta-omics techniques have improved our characterization of AD microbial communities, conventional models treat functional groups as homogeneous and overlook the physiology and behavior of microbial individuality, limiting insights into mechanisms governing process performance. A novel microbial individuality model (MIM) that integrates kinetics, energetics, and agent-based modeling to describe a microbiome's behavior as heterogenic populations, including homoacetogenesis, was developed. The MIM was validated with two datasets from previous studies through daily biogas production, methane content, compound concentrations, and microbial relative abundance changes. The MIM identified the emergence of Methanosaeta at low concentrations of acetate. Moreover, this simulation supports experimental studies confirming that the overlooked homoacetogenesis is an important hydrogen sink in AD. Validated MIMs are expected to provide insights into syntrophic and competitive interactions among microbiomes in AD systems while testing different operational parameters in a virtual environment. The MIM offers a methodological framework to other biological treatment systems and their microbial community dynamics.

Core-, pan- and accessory genome analyses of Clostridium neonatale: insights into genetic diversity

Clostridium neonatale is a potential opportunistic pathogen recovered from faecal samples in cases of necrotizing enterocolitis (NEC), a gastrointestinal disease affecting preterm neonates. Although the C. neonatale species description and name validation were published in 2018, comparative genomics are lacking. In the present study, we provide the closed genome assembly of the C. neonatale ATCC BAA-265^T (=250.09) reference strain with a manually curated functional annotation of the coding sequences. Pan-, core- and accessory genome analyses were performed using the complete 250.09 genome (4.7 Mb), three new assemblies (4.6–5.6 Mb), and five publicly available draft genome assemblies (4.6–4.7 Mb). The C. neonatale pan-genome contains 6840 genes, while the core-genome has 3387 genes. Pan-genome analysis revealed an ‘open’ state and genomic diversity. The strain-specific gene families ranged from five to 742 genes. Multiple mobile genetic elements were predicted, including a total of 201 genomic islands, 13 insertion sequence families, one CRISPR-Cas type I-B system and 15 predicted intact prophage signatures. Primary virulence classes including offensive, defensive, regulation of virulence-associated genes and non-specific virulence factors were identified. The presence of a tet(W/N/W) gene encoding a tetracycline resistance ribosomal protection protein and a 23S rRNA methyltransferase ermQ gene were identified in two different strains. Together, our results revealed a genetic diversity and plasticity of C. neonatale genomes and provide a comprehensive view of this species genomic features, paving the way for the characterization of its biological capabilities.

Clostridium weizhouense sp. nov., an anaerobic bacterium isolated from activated sludge of petroleum wastewater

A Gram-stain-positive, anaerobic, spore-forming, rod-shaped (0.4–0.6 µm×2.5–3.2 µm), flagellated bacterium, designated strain YB-6T, was isolated from activated sludge of an anaerobic tank at Weizhou marine oil mining wastewater treatment plant in Beihai, Guangxi, PR China. The culture conditions were 25–45 °C (optimum, 37 °C), pH 4–12 (pH 7.0) and NaCl concentration of 0–7 % w/v (0%). Strain YB-6T grew slowly in petroleum wastewater and removed 68.2 % of the total organic carbon in petroleum wastewater within 10 days. Concentrations of naphthalene, anthracene and phenanthrene at an initial concentration of 50 mg l−1 were reduced by 32.8, 40.4 and 14.6 %, respectively, after 7 days. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain YB-6T belongs to Clostridium cluster I and is most closely related to Clostridium uliginosum CK55T (98.5 % similarity). The genome size of strain YB-6T was 3.96 Mb, and the G+C content was 26.5 mol%. The average nucleotide identity value between strain YB-6T and C. uliginosum CK55T was 81.9 %. The major fatty acids in strain YB-6T were C14 : 0 FAME, C16 : 0 FAME and summed feature 4 (unknown 14.762 and/or C15 : 2 FAME). The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, five unidentified aminophospholipids, one unidentified glycolipid and one unidentified aminolipid. Diaminopimelic acid was not detected in the strain YB-6T cell walls. Whole-cell sugars mainly consisted of ribose and galactose. Based on the results of phenotypic and genotypic analyses, strain YB-6T represents a novel species of the genus Clostridium , for which the name Clostridium weizhouense sp. nov. is proposed. The type strain is YB-6T (=GDMCC 1.2529T=JCM 34754T).

Fatal Systemic Infection of Clostridium tarantellae in a Wild Korean Raccoon Dog (Nyctereutes procyonoides koreensis)

Fatal systemic infection by Clostridium tarantellae in a wild Korean raccoon dog (Nyctereutes procyonoides koreensis) was diagnosed based on histopathology, immunofluorescence, PCR, and microbiome taxonomic profiling. Pathologic features were similar to Tyzzer's disease caused by C. piliforme. This is the first report of C. tarantellae infection in Korean raccoon dogs.

Mechanistic Insight into the Fragmentation of Type I Collagen Fibers into Peptides and Amino Acids by a Vibrio Collagenase

Vibrio collagenases of the M9A subfamily are closely related to Vibrio pathogenesis for their role in collagen degradation during host invasion. Although some Vibrio collagenases have been characterized, the collagen degradation mechanism of Vibrio collagenase is still largely unknown. Here, an M9A collagenase, VP397, from marine Vibrio pomeroyi strain 12613 was characterized, and its fragmentation pattern on insoluble type I collagen fibers was studied. VP397 is a typical Vibrio collagenase composed of a catalytic module featuring a peptidase M9N domain and a peptidase M9 domain and two accessory bacterial prepeptidase C-terminal domains (PPC domains). It can hydrolyze various collagenous substrates, including fish collagen, mammalian collagens of types I to V, triple-helical peptide [(POG)₁₀]₃, gelatin, and 4-phenylazobenzyloxycarbonyl-Pro-Leu-Gly-Pro-o-Arg (Pz-peptide). Atomic force microscopy (AFM) observation and biochemical analyses revealed that VP397 first assaults the C-telopeptide region to dismantle the compact structure of collagen and dissociate tropocollagen fragments, which are further digested into peptides and amino acids by VP397 mainly at the Y-Gly bonds in the repeating Gly-X-Y triplets. In addition, domain deletion mutagenesis showed that the catalytic module of VP397 alone is capable of hydrolyzing type I collagen fibers and that its C-terminal PPC2 domain functions as a collagen-binding domain during collagenolysis. Based on our results, a model for the collagenolytic mechanism of VP397 is proposed. This study sheds light on the mechanism of collagen degradation by Vibrio collagenase, offering a better understanding of the pathogenesis of Vibrio and helping in developing the potential applications of Vibrio collagenase in industrial and medical areas. IMPORTANCE Many Vibrio species are pathogens and cause serious diseases in humans and aquatic animals. The collagenases produced by pathogenic Vibrio species have been regarded as important virulence factors, which occasionally exhibit direct pathogenicity to the infected host or facilitate other toxins' diffusion through the digestion of host collagen. However, our knowledge concerning the collagen degradation mechanism of Vibrio collagenase is still limited. This study reveals the degradation strategy of Vibrio collagenase VP397 on type I collagen. VP397 binds on collagen fibrils via its C-terminal PPC2 domain, and its catalytic module first assaults the C-telopeptide region and then attacks the Y-Gly bonds in the dissociated tropocollagen fragments to release peptides and amino acids. This study offers new knowledge regarding the collagenolytic mechanism of Vibrio collagenase, which is helpful for better understanding the role of collagenase in Vibrio pathogenesis and for developing its industrial and medical applications.

Sphingobacterium hungaricum sp. nov. a novel species on the borderline of the genus Sphingobacterium

A Gram-reaction-negative bacterial strain, designated Kb22^T, was isolated from agricultural soil and characterized using a polyphasic approach to determine its taxonomic position. On the basis of 16S rRNA gene sequence analysis, the strain shows highest similarity (94.39 %) to Sphingobacterium nematocida M-SX103^T. The highest average nucleotide identity value (71.83 %) was found with Sphingobacterium composti T5-12^T, and the highest amino acid identity value (66.65 %) was found with Sphingobacterium olei HAL-9^T. Cells are aerobic, non-motile rods. The isolate was found to be positive for catalase and oxidase tests. The assembled genome of strain Kb22^T has a total length of 4,06 Mb, the DNA G+C content is 38.1 mol%. The only isoprenoid quinone is menaquinone 7 (MK-7). The major fatty acids are iso-C_15:0 (28.4%), summed feature 3 (C_16:1 ω7c and/or iso-C_15:0 2-OH) (25.7 %) and iso-C_17:0 3-OH (19.7 %). Based on phenotypic characteristics and phylogenetic results, it is concluded that strain Kb22^T is a member of the genus Sphingobacterium and represents a novel species for which the name Sphingobacterium hungaricum sp. nov. is proposed. The type strain of the species is strain Kb22^T (=LMG 31574^T=NCAIM B.02638^T).

Sarcina ventriculi a rare pathogen

Sarcina ventriculi is a gram-positive bacterium, able to survive in extreme low pH environment. It’s first description dates from 1842, by John Goodsir. Since then, just a few cases have been reported. In veterinary medicine, especially in ruminants, it causes bloating, vomiting, gastric perforation and death of the animal. It is commonly associated with delayed gastric emptying or obstruction to gastric outlet, although it’s pathogenicity in humans is not fully understood. We report two cases with identification of the bacteria in gastric specimens stained with hematoxylin-eosin staining, in different clinical settings. The first patient is a young female patient, presenting cardiac arrest and death after gastric perforation and the second patient an adult male presenting with gastric adenocarcinoma, treated with partial gastrectomy followed by adjuvant chemoradiation. In our literature review, we identified forty-five cases reporting Sarcina ventriculi appearance, with a sudden increase since 2010.

Enhanced trichloroethylene biodegradation: Roles of biochar-microbial collaboration beyond adsorption

Trichloroethylene (TCE) is a pollutant widely found in groundwater, especially in the heavily contaminated industrial sites. Biological dechlorination method is environmentally friendly and low-cost. However, microorganisms grow slowly and their activity is susceptible to environmental fluctuations. This study used biochar as an additive to promote anaerobic biodegradation of TCE with mixed culture. Results showed that biochar with dose of 0.1-0.4% (w/v) brought a rapid initial decrease of TCE concentration by 39.4-88.8% in 24 h via adsorption mechanism. Biochar produced at 500 °C pyrolysis temperature (BC500) achieved the highest TCE adsorption in comparison to BC300 and BC700. Subsequently, a significantly shortened microbial stagnation phase (from 85 h to 37 h) was observed in the system with the presence of biochar. During the exponential growth phase, BC700 outperformed BC300 and BC500 in terms of TCE degradation efficiency. Electrochemical analysis demonstrated that BC700 possessed the greatest electron transfer capability. Finally, biochar shortened the time for achieving 100% removal of TCE by 54.5-69.7% (from approximate 330 h to 100-150 h). Even at high concentration of TCE (20-30 mg·L^-1) that could lead to serious microbial growth inhibition, the TCE degradation efficiency could be recovered in the presence of BC500. The high-throughput sequencing data revealed that biochar promoted the relative abundance of co-metabolizing dechlorinating microorganisms (Pseudomonas, Burkholderia) in the aqueous solution, and simultaneously led to the selective colonization of reductive dechlorinating microorganisms (Enterobacteriaceae, Clostridium) attached on biochar surface. On the other hand, biochar addition decreased the relative abundance of hydrogen-competing microorganisms, thereby forming an efficient co-metabolism-reductive dechlorination system. These findings allow a better understanding of the promotion mechanism of biochar for microbial dechlorination technology supporting the biochar-assisted bioremediation in practice.

Whole Genome Sequence-Based Identification of Clostridium estertheticum Complex Strains Supports the Need for Taxonomic Reclassification Within the Species Clostridium estertheticum

Isolates within the Clostridium estertheticum complex (CEC) have routinely been identified through the 16S rRNA sequence, but the high interspecies sequence similarity reduces the resolution necessary for species level identification and often results in ambiguous taxonomic classification. The current study identified CEC isolates from meat juice (MJS) and bovine fecal samples (BFS) and determined the phylogeny of species within the CEC through whole genome sequence (WGS)-based analyses. About 1,054 MJS were screened for CEC using quantitative real-time PCR (qPCR). Strains were isolated from 33 MJS and 34 BFS qPCR-positive samples, respectively. Pan- and core-genome phylogenomics were used to determine the species identity of the isolates. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) were used to validate the species identity. The phylogeny of species within the CEC was determined through a combination of these methods. Twenty-eight clostridia strains were isolated from MJS and BFS samples out of which 13 belonged to CEC. At 95% ANI and 70% dDDH thresholds for speciation, six CEC isolates were identified as genomospecies2 (n=3), Clostridium tagluense (n=2) and genomospecies3 (n=1). Lower thresholds of 94% ANI and 58% dDDH were required for the classification of seven CEC isolates into species C. estertheticum and prevent an overlap between species C. estertheticum and Clostridium frigoriphilum. Combination of the two species and abolishment of current subspecies classification within the species C. estertheticum are proposed. These data demonstrate the suitability of phylogenomics to identify CEC isolates and determine the phylogeny within CEC.

Clostridium chrysemydis sp. nov., isolated from the faecal material of a painted turtle

A strict anaerobic, Gram-stain-positive rod-shaped bacterium, designated PT^T, was isolated from the faecal material of a painted turtle (Chrysemys picta). Based on a comparative 16S rRNA gene sequence analysis, the isolate was assigned to Clostridium sensu stricto with the highest sequence similarities to Clostridium moniliforme (97.4 %), Clostridium sardiniense (97.2 %) and the misclassified organism Eubacterium multiforme (97.1 %). The predominant cellular fatty acids of strain PT^T were C_14 : 0, C_16 : 0 and an unidentified product with an equivalent chain length of 14.969. The G+C content determined from the genome was 28.8 mol%. The fermentation end products from glucose were acetate and butyrate with no alcohols detected and trace amounts of CO₂ and H₂ also detected; no respiratory quinones were detected. Based on biochemical, phylogenetic, genotypic and chemotaxonomic criteria, the isolate represents a novel species of the genus Clostridium for which the name Clostridium chrysemydis sp. nov. is proposed. The type strain is strain PT^T (=CCUG 74180^T=ATCC TSD-219^T).

Microbiota of Cow's Milk with Udder Pathologies

Mastitis is the most common disease for cattle, causing great economic losses for the global dairy industry. Recent studies indicate the multi-agent and microbiome diversity of this disease. To understand the nature of mastitis and investigate the role of the microbiome in the development of pathologies in the udder of bovines, we performed NGS sequencing of the 16S rRNA gene of cow’s milk with pathologies of the udder. The obtained data show a significant increase in the Cutibacterium, Blautia, Clostridium sensu stricto 2, Staphylococcus, Streptococcus and Microbacterium genera for groups of cows with udder pathologies. Increasing relative abundance of the Staphylococcus and Streptococcus genera was associated with subclinical mastitis. Our data show that a relative increase in abundance of the Staphylococcus and Microbacterium genera may be an early sign of infection. We have shown, for the first time, an increase in the Colidextribacter, Paeniclostridium and Turicibacter genera in groups of cows with mastitis. These results expand our understanding of the role of the microbiome in the development of bovine mastitis.

Mixed Acid Fermentation of Carbohydrate-Rich Dairy Manure Hydrolysate

Dairy manure (DM) is an abundant agricultural residue that is largely composed of lignocellulosic biomass. The aim of this study was to investigate if carbon derived from DM fibers can be recovered as medium-chain fatty acids (MCFAs), which are mixed culture fermentation products of economic interest. DM fibers were subjected to combinations of physical, enzymatic, chemical, and thermochemical pretreatments to evaluate the possibility of producing carbohydrate-rich hydrolysates suitable for microbial fermentation by mixed cultures. Among the pretreatments tested, decrystalization dilute acid pretreatment (DCDA) produced the highest concentrations of glucose and xylose, and was selected for further experiments. Bioreactors fed DCDA hydrolysate were operated. Acetic acid and butyric acid comprised the majority of end products during operation of the bioreactors. MCFAs were transiently produced at a maximum concentration of 0.17 mg COD_MCFAs/mg COD_Total. Analyses of the microbial communities in the bioreactors suggest that lactic acid bacteria, Megasphaera, and Caproiciproducens were involved in MCFA and C4 production during DCDA hydrolysate metabolism.

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.

Diversity and Evolution of Clostridium beijerinckii and Complete Genome of the Type Strain DSM 791T

Clostridium beijerinckii is a relatively widely studied, yet non-model, bacterium. While 246 genome assemblies of its various strains are available currently, the diversity of the whole species has not been studied, and it has only been analyzed in part for a missing genome of the type strain. Here, we sequenced and assembled the complete genome of the type strain Clostridium beijerinckii DSM 791T, composed of a circular chromosome and a circular megaplasmid, and used it for a comparison with other genomes to evaluate diversity and capture the evolution of the whole species. We found that strains WB53 and HUN142 were misidentified and did not belong to the Clostridium beijerinckii species. Additionally, we filtered possibly misassembled genomes, and we used the remaining 237 high-quality genomes to define the pangenome of the whole species. By its functional annotation, we showed that the core genome contains genes responsible for basic metabolism, while the accessory genome has genes affecting final phenotype that may vary among different strains. We used the core genome to reconstruct the phylogeny of the species and showed its great diversity, which complicates the identification of particular strains, yet hides possibilities to reveal hitherto unreported phenotypic features and processes utilizable in biotechnology.

Lipid diversity in clostridia

Studies of the lipidomes of twenty-one species of clostridia have revealed considerable diversity. Even among those species now defined as Clostridium sensu stricto, which are related to Clostridium butyricum, the type species, lipid analysis has shown that a number of distinct clades have characteristic polar lipids. All species of Clostridium sensu stricto have phosphatidylethanolamine, phosphatidylglycerol and cardiolipin which are present as all acyl or alk-1'-enyl acyl (plasmalogen) species. In addition, almost every clade has specialized polar lipids. For example, the group closely related to Clostridium beijerinckii and several other solventogenic species has glycerol acetals of plasmenylethanolamine, which protects the membrane bilayer arrangement when the lipids are highly unsaturated or in the presence of solvents. The group related to Clostridium novyi has aminoacyl-phosphatidylglycerol, which protects these pathogens from cationic antimicrobial peptides (CAMPs) of innate immunity. Clostridium botulinum species, which fall into several groups, align with these clades, and have the same specific lipids. This review will present the current state of knowledge on clostridial lipids.

Sporulation in solventogenic and acetogenic clostridia

The Clostridium genus harbors compelling organisms for biotechnological production processes; while acetogenic clostridia can fix C1-compounds to produce acetate and ethanol, solventogenic clostridia can utilize a wide range of carbon sources to produce commercially valuable carboxylic acids, alcohols, and ketones by fermentation. Despite their potential, the conversion by these bacteria of carbohydrates or C1 compounds to alcohols is not cost-effective enough to result in economically viable processes. Engineering solventogenic clostridia by impairing sporulation is one of the investigated approaches to improve solvent productivity. Sporulation is a cell differentiation process triggered in bacteria in response to exposure to environmental stressors. The generated spores are metabolically inactive but resistant to harsh conditions (UV, chemicals, heat, oxygen). In Firmicutes, sporulation has been mainly studied in bacilli and pathogenic clostridia, and our knowledge of sporulation in solvent-producing or acetogenic clostridia is limited. Still, sporulation is an integral part of the cellular physiology of clostridia; thus, understanding the regulation of sporulation and its connection to solvent production may give clues to improve the performance of solventogenic clostridia. This review aims to provide an overview of the triggers, characteristics, and regulatory mechanism of sporulation in solventogenic clostridia. Those are further compared to the current knowledge on sporulation in the industrially relevant acetogenic clostridia. Finally, the potential applications of spores for process improvement are discussed.Key Points• The regulatory network governing sporulation initiation varies in solventogenic clostridia.• Media composition and cell density are the main triggers of sporulation.• Spores can be used to improve the fermentation process.

Clostridium fungisolvens sp. nov., a new β-1,3-glucan-decomposing bacterium isolated from anoxic soil subjected to biological soil disinfestation

Biological soil disinfestation (BSD) or reductive soil disinfestation (RSD) is a bioremediation method used to suppress or eliminate soil-borne plant pathogens by stimulating activities of indigenous anaerobic bacteria of the soil. An anaerobic bacterial strain (TW1^T) was isolated from an anoxic soil sample subjected to the BSD treatment and comprehensively characterized. Cells of the strain were Gram-stain-positive, slightly curved and motile rods producing terminal spores. The strain was aerotolerant. Strain TW1^T was saccharolytic and produced acetate, butyrate, H₂ and CO₂ as fermentation end products. Strain TW1^T decomposed β-1,3-glucan (curdlan and laminarin) and degraded mycelial cells of an ascomycete Fusarium plant pathogen. Major cellular fatty acids of strain TW1^T were C_14 : 0, C_14 : 0 dimethylacetal (DMA), C_16 : 0 aldehyde and C_16 : 0 DMA. Strain TW1^T made a group on the phylogenetic tree constructed based on 16S rRNA gene sequences with species such as Clostridium fallax (96.3 %) and Clostridium polyendosporum (96.0 %). Whole genome analysis of strain TW1^T showed that the total length of the genome was 5.28 Mb with the DNA G+C content of 31.3 mol%. The average nucleotide identity (ANIb) between strain TW1^T and C. fallax was 71.2 %. Presence of the genes encoding laminarinase or GH16 β-glucosidase was confirmed from the genome analysis of strain TW1^T. Based on the genomic, phylogenetic and phenotypic properties obtained, we propose strain TW1^T should be assigned in the genus Clostridium in the family Clostridiaceae as Clostridium fungisolvens sp. nov. The type strain TW1^T (=NBRC 112097^T=DSM 110791^T).

Safety and efficacy of the feed additive consisting of Clostridium butyricum FERM BP-2789 (Miya-Gold® S) for chickens for fattening, chickens reared for laying, turkeys for fattening, turkeys reared for breeding, minor avian species (excluding laying birds), piglets (suckling and weaned) and minor porcine species (Miyarisan Pharmaceutical Co. Ltd.)

The feed additive under assessment (trade name: Miya-Gold® S) is based on viable spores of Clostridium butyricum FERM BP-2789. It is authorised for use in minor avian species (excluding laying birds), weaned piglets and minor weaned porcine species, chickens reared for laying, turkeys for fattening and turkeys reared for breeding. This opinion concerns the request for renewal of the authorisation of Miya-Gold® S for the species/categories for which an authorisation exists, the use in chickens for fattening, for which the previous authorisation had expired, and the extension of use to suckling piglets and suckling minor porcine species. The applicant provided evidence that the additive currently in the market complies with the conditions of authorisation. There is no new evidence that would lead the Panel to reconsider previous conclusions that Miya-Gold® S remains safe for the animal species/categories, the consumer and the environment under the current and previously authorised conditions of use. This conclusion applies also to the new target species for which a request of use is made. Regarding the safety for the user, the Panel concluded that the additive is not irritant to skin and eyes and that sensitisation via respiratory route cannot be excluded. There is no need for assessing the efficacy of Miya-Gold® S in the context of the renewal of the authorisation in chickens reared for laying, turkeys for fattening and reared for breeding, minor avian species (excluding laying birds), weaned piglets and weaned minor porcine species. The additive has the potential to be efficacious in chickens for fattening, suckling piglets and suckling minor porcine species at the level of 2.5 × 108 CFU/kg complete feedingstuff. Miya-Gold® S is compatible with decoquinate, diclazuril, lasalocid, maduramicin ammonium, narasin, narasin/nicarbazin, monensin sodium, robenidine, salinomycin sodium and semduramicin.

Antibiotic susceptibility screening of primate-associated Clostridium ventriculi

Clostridium ventriculi (syn. Sarcina ventriculi) is a Gram-positive opportunistic pathogen with sarcina morphology. In the case of gastrointestinal disorders, the treatment is often empirical. Due to the common occurrence in primates and the potential risk of dysbiosis; the antibiotic susceptibility screening of C. ventriculi strains isolated from guenon monkeys and crested gibbons to 58 antibiotics was performed to reduce potentially ineffective antibiotic use in case of disease. Isolates were found to be susceptible to the majority of the tested antibiotics, mainly to (fluoro)quinolones, macrolides, penicillins, and tetracyclines. The susceptibility profiles were similar despite the hosts. Tested strains showed also natural resistance to a few antibiotics on the genus level. Detected in vitro antibiotic efficiency is consistent with documented human treatment cases.

A Sarcina bacterium linked to lethal disease in sanctuary chimpanzees in Sierra Leone

Human and animal infections with bacteria of the genus Sarcina (family Clostridiaceae) are associated with gastric dilation and emphysematous gastritis. However, the potential roles of sarcinae as commensals or pathogens remain unclear. Here, we investigate a lethal disease of unknown etiology that affects sanctuary chimpanzees (Pan troglodytes verus) in Sierra Leone. The disease, which we have named “epizootic neurologic and gastroenteric syndrome” (ENGS), is characterized by neurologic and gastrointestinal signs and results in death of the animals, even after medical treatment. Using a case-control study design, we show that ENGS is strongly associated with Sarcina infection. The microorganism is distinct from Sarcina ventriculi and other known members of its genus, based on bacterial morphology and growth characteristics. Whole-genome sequencing confirms this distinction and reveals the presence of genetic features that may account for the unusual virulence of the bacterium. Therefore, we propose that this organism be considered the representative of a new species, named “Candidatus Sarcina troglodytae”. Our results suggest that a heretofore unrecognized complex of related sarcinae likely exists, some of which may be highly virulent. However, the potential role of “Ca. S. troglodytae” in the etiology of ENGS, alone or in combination with other factors, remains a topic for future research.

Infections with bacteria of the genus Sarcina are associated with gastric diseases of unclear etiology. Here, Owens et al. show that infection with a distinct Sarcina species is strongly associated with a lethal disease that affects sanctuary chimpanzees in Sierra Leone.

Detection of Psychrophilic Clostridium spp. in Fecal Samples from Cattle of Different Ages Sampled at the Slaughterhouse Level

ABSTRACT

Clostridium estertheticum and C. estertheticum-like spp. are obligate anaerobic psychrophiles causing "blown pack" spoilage of chilled vacuum-packed meat. The present study aimed at detecting and isolating these spoilage bacteria in fecal samples of cattle of different ages at the slaughterhouse level. One hundred two swab fecal samples were obtained and enriched anaerobically in prereduced peptone-yeast-glucose-starch (PYGS) medium for 3 weeks at 4°C and then screened for C. estertheticum and C. estertheticum-like spp. by using a 16S rRNA gene-based real-time PCR (RT-PCR) assay. The RT-PCR-positive samples were further enriched for 3 weeks in prereduced PYGS medium and then subjected to an ethanol (50%, v/v) and lysozyme (4 mg/mL) treatment. Isolation was carried out anaerobically on Columbia agar with 5% defibrinated sheep blood at 4°C for 3 weeks. Isolated strains were identified morphologically and by the 16S rRNA gene. Forty (39%) of 102 samples were RT-PCR positive. The frequency of positive samples was the following: 9 (45%) of 20 in calves (aged ≤160 days), 23 (43%) of 54 in young cattle (aged 161 to 1,000 days), and 8 (29%) of 28 in cows or bulls (aged >1,000 days). Six strains were isolated from 6 of 40 RT-PCR-positive samples. Of these, five were from the calves (n = 1) and young cattle (n = 4). The six isolates were identified as C. estertheticum (n = 1), Clostridium frigoriphilum (n = 1), and C. estertheticum-like spp. (n = 4). The present findings confirm that feces of cattle are an important source of psychrophilic Clostridium spp. The fecal carriage among livestock animals at slaughter is strongly correlated with the risk of carcass contamination. Therefore, the maintenance of slaughter hygiene is of central importance.

HIGHLIGHTS

Clostridium manihotivorum sp. nov., a novel mesophilic anaerobic bacterium that produces cassava pulp-degrading enzymes

BACKGROUND

Cassava pulp is a promising starch-based biomasses, which consists of residual starch granules entrapped in plant cell wall containing non-starch polysaccharides, cellulose and hemicellulose. Strain CT4T, a novel mesophilic anaerobic bacterium isolated from soil collected from a cassava pulp landfill, has a strong ability to degrade polysaccharides in cassava pulp. This study explored a rarely described species within the genus Clostridium that possessed a group of cassava pulp-degrading enzymes.

METHODS

A novel mesophilic anaerobic bacterium, the strain CT4T, was identified based on phylogenetic, genomic, phenotypic and chemotaxonomic analysis. The complete genome of the strain CT4T was obtained following whole-genome sequencing, assembly and annotation using both Illumina and Oxford Nanopore Technology (ONT) platforms.

RESULTS

Analysis based on the 16S rRNA gene sequence indicated that strain CT4T is a species of genus Clostridium. Analysis of the whole-genome average amino acid identity (AAI) of strain CT4T and the other 665 closely related species of the genus Clostridium revealed a separated strain CT4T from the others. The results revealed that the genome consisted of a 6.3 Mb circular chromosome with 5,664 protein-coding sequences. Genome analysis result of strain CT4T revealed that it contained a set of genes encoding amylolytic-, hemicellulolytic-, cellulolytic- and pectinolytic enzymes. A comparative genomic analysis of strain CT4T with closely related species with available genomic information, C. amylolyticum SW408T, showed that strain CT4T contained more genes encoding cassava pulp-degrading enzymes, which comprised a complex mixture of amylolytic-, hemicellulolytic-, cellulolytic- and pectinolytic enzymes. This work presents the potential for saccharification of strain CT4T in the utilization of cassava pulp. Based on phylogenetic, genomic, phenotypic and chemotaxonomic data, we propose a novel species for which the name Clostridium manihotivorum sp. nov. is suggested, with the type strain CT4T (= TBRC 11758T = NBRC 114534T).

Phenotypic and genomic analysis of isopropanol and 1,3-propanediol producer Clostridium diolis DSM 15410

Clostridium diolis DSM 15410 is a type strain of solventogenic clostridium capable of conducting isopropanol-butanol-ethanol fermentation. By studying its growth on different carbohydrates, we verified its ability to utilize glycerol and produce 1,3-propanediol and discovered its ability to produced isopropanol. Complete genome sequencing showed that its genome is a single circular chromosome and belongs to the cluster I (sensu scricto) of the genus Clostridium. By cultivation analysis we highlighted its specific behavior in comparison to two selected closely related strains. Despite the fact that several CRISPR loci were found, 16 putative prophages showed the ability to receive foreign DNA. Thus, the strain has the necessary features for future engineering of its 1,3-propanediol biosynthetic pathway and for the possible industrial utilization in the production of biofuels.

Effect of oral administration of omeprazole on the microbiota of the gastric glandular mucosa and feces of healthy horses

BACKGROUND

Omeprazole administration is associated with changes in gastric and fecal microbiota and increased incidence of Clostridioides difficile enterocolitis in humans and dogs.

HYPOTHESIS/OBJECTIVES

Study purpose was to assess the effect of omeprazole on gastric glandular and fecal microbiota in healthy adult horses.

ANIMALS

Eight healthy horses stabled on straw and fed 100% haylage.

METHODS

Prospective controlled study. Transendoscopic gastric glandular biopsies, gastric fluid, and fecal samples were obtained from each horse twice at a 7-day interval before the administration of omeprazole. Samples were taken on the same horses before and after a 7-day administration of omeprazole (4 mg/kg PO q24h). pH was assessed on fresh gastric fluid and other samples were kept at -20°C until analysis. Bacterial taxonomy profiling was obtained by V1V3 16S amplicon sequencing from feces and gastric glandular biopsies. Analysis of alpha, beta diversity, and comparison between time points were performed with MOTHUR and results were considered significant when P < .05.

RESULTS

Gastric pH increased significantly after 7 days of omeprazole administration (P = .006). Omeprazole did not induce significant major changes in composition of fecal or gastric glandular microbiota, however, after administration, certain microbial genera became more predominant in the gastric glandular mucosa (lower Simpson's evenness, P = .05). Only the genus Clostridium sensu strictu_1 had a significant shift in the glandular gastric mucosa after omeprazole administration (P = .002). No population shifts were observed in feces.

CONCLUSIONS AND CLINICAL IMPORTANCE

Oral administration of omeprazole could have fewer effects in gastrointestinal microbiota in the horse compared to other species.

Description of Clostridium cagae sp. nov., Clostridium rectalis sp. nov. and Hathewaya massiliensis sp. nov., new anaerobic bacteria isolated from human stool samples

Using culturomics methods, three strains were isolated, identified and characterized following the taxonogenomics concept. Clostridium cagae strain Marseille-P4344T (=CSURP4344), Clostridium rectalis strain Marseille-P4200T (=CSURP4200) and Hathewaya massiliensis strain Marseille-P3545T (=CSURP3545) were isolated from human stool samples. The phylogenetic reconstruction, phenotypic criteria and genomic analyses were carried out and demonstrated that these three bacteria are different from previously known bacterial species with standing in nomenclature and were classified as new members of the Clostridiaceae family.

Characterization of Peptacetobacter hominis gen. nov., sp. nov., isolated from human faeces, and proposal for the reclassification of Clostridium hiranonis within the genus Peptacetobacter

A novel, Gram-stain-positive, rod-shaped, non-motile, non-spore-forming, obligately anaerobic bacterium, designated strain ZHW00191^T, was isolated from human faeces and characterized by using a polyphasic taxonomic approach. Growth occurred at 25-45 °C (optimum, 37-42 °C), at pH 5.5-10.0 (optimum, pH 6.5-7.0) and with 0-2 % (w/v) NaCl (optimum, 0 %). The end products of glucose fermentation were acetic acid, isobutyric acid and isovaleric acid and a small amount of propionic acid. The dominant cellular fatty acids (>10 %) of strain ZHW00191^T were C_16 : 0, C_18 : 1 ω9с and C_18 : 2ω6,9с. Its polar lipid profile comprised diphosphatidylglycerol, phosphatidylglycerol, three unidentified phospholipids and ten unidentified glycolipids. Respiratory quinones were not detected. The cell-wall peptidoglycan contained meso-2,6-diaminopimelic acid, and the whole-cell sugars were ribose and glucose. The genomic DNA G+C content was 32.8 mol%. Analysis of the 16S rRNA gene sequence indicated that ZHW00191^T was most closely related to Clostridium hiranonis TO-931^T (95.3 % similarity). Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) analyses with closely related reference strains indicated that reassociation values were both well below the thresholds of 95-96% and 70 % for species delineation, respectively. Based on phenotypic, chemotaxonomic and genetic studies, a novel genus, Peptacetobacter gen. nov., is proposed. The novel isolate ZHW00191^T (=JCM 33482^T=GDMCC 1.1530^T) is proposed as the type strain of the type species Peptacetobacter hominis gen. nov., sp. nov. of the proposed new genus. Furthermore, it is proposed that Clostridium hiranonis be transferred to this novel genus, as Peptacetobacter hiranonis comb. nov.

Isolation of Clostridium from Yunnan-Tibet hot springs and description of Clostridium thermarum sp. nov. with lignocellulosic ethanol production

Lignocellulose is considered a major source of renewable energy that serve as an alternative to the fossil fuels. Members of the genus Clostridium are some of the many microorganisms that have the ability to degrade lignocellulose efficiently to sugar, which can be further converted to biofuel. In this study, we isolated twelve Clostridium strains from hot spring samples of Yunnan and Tibet, of which isolates SYSU GA15002^T and SYSU GA17076 showed low 16S rRNA gene sequence identity profiles to any of the validly named Clostridium strains (<94.0%). Studies using a polyphasic taxonomy approach concluded that the two isolates represent one novel species of the genus Clostridium, for which we propose the name Clostridium thermarum sp. nov., with SYSU GA15002^T as the type strain of the species. Isolate SYSU GA15002^T has an optimum growth temperature at 45°C. Fermentation of the substrates cellobiose, cellulose, xylan and untreated straw powder by this strain results in the production of ethanol, along with acetate and formate. The complete pathways for the conversion of cellulose and xylan to ethanol is also predicted from the genome of isolate SYSU GA15002^T, which revealed a single step conversion of lignocellulosic biomass through consolidated bioprocessing. This paper is a comprehensive study encompassing isolation, polyphasic taxonomy, lignocellulose biodegradation and the genomic information of Clostridium in Yunnan-Tibet hot springs.

N-Aryl-3-mercaptosuccinimides as Antivirulence Agents Targeting Pseudomonas aeruginosa Elastase and Clostridium Collagenases

In light of the global antimicrobial-resistance crisis, there is an urgent need for novel bacterial targets and antibiotics with novel modes of action. It has been shown that Pseudomonas aeruginosa elastase (LasB) and Clostridium histolyticum (Hathewaya histolytica) collagenase (ColH) play a significant role in the infection process and thereby represent promising antivirulence targets. Here, we report novel N-aryl-3-mercaptosuccinimide inhibitors that target both LasB and ColH, displaying potent activities in vitro and high selectivity for the bacterial over human metalloproteases. Additionally, the inhibitors demonstrate no signs of cytotoxicity against selected human cell lines and in a zebrafish embryo toxicity model. Furthermore, the most active ColH inhibitor shows a significant reduction of collagen degradation in an ex vivo pig-skin model.

Shift in bacterial diversity in acidogenesis of gelatin and gluten seeded with various anaerobic digester inocula

The aim of this study was to investigate divergence of bacteria degrading model proteins of food-processing wastewater. Gelatin and gluten were used as substrate to represent animal and plant proteins from food wastes, respectively. The inocula were obtained from eight full-scale anaerobic digestion reactors. Food-to-microorganism ratio was 3 g chemical oxygen demand equivalent of substrate per 1 g volatile suspended solids of inoculum. A first-order reaction model revealed reaction constants ranged 1.34 ≤ k ≤ 2.30 d-1 for gelatin and 0.63 ≤ k ≤ 1.69 d-1 for gluten. Metagenomic analysis of 16s rRNA sequences showed that dominant bacteria after gelatin degradation batch were different for each inocula. Klebsiella aerogenes, Hathewaya, Peptoclostridium, or Clostridium collagenovorans were most abundant. Klebsiella aerogenes was the most abundant species after gluten degradation for all inocula.

A meta-analysis of the bovine gastrointestinal tract microbiota

The bovine gastrointestinal (GI) tract microbiota has important influences on animal health and production. Presently, a large number of studies have used high-throughput sequencing of the archaeal and bacteria 16S rRNA gene to characterize these microbiota under various experimental parameters. By aggregating publically available archaeal and bacterial 16S rRNA gene datasets from 52 studies we were able to determine taxa that are common to nearly all microbiota samples from the bovine GI tract as well as taxa that are strongly linked to either the rumen or feces. The methanogenic genera Methanobrevibacter and Methanosphaera were identified in nearly all fecal and rumen samples (> 99.1%), as were the bacterial genera Prevotella and Ruminococcus (≥ 92.9%). Bacterial genera such as Alistipes, Bacteroides, Clostridium, Faecalibacterium and Escherichia/Shigella were associated with feces and Fibrobacter, Prevotella, Ruminococcus and Succiniclasticum with the rumen. As expected, individual study strongly affected the bacterial community structure, however, fecal and rumen samples did appear separated from each other. This meta-analysis provides the first comparison of high-throughput sequencing 16S rRNA gene datasets generated from the bovine GI tract by multiple studies and may serve as a foundation for improving future microbial community research with cattle.