Phylogenomic analyses of clostridia and identification of novel protein signatures that are specific to the genus Clostridium sensu stricto (cluster I)

Preservation of conjugated primary bile acids by oxygenation of the small intestinal microbiota in vitro

Bile acids play a critical role in the emulsification of dietary lipids, a critical step in the primary function of the small intestine, which is the digestion and absorption of food. Primary bile acids delivered into the small intestine are conjugated to enhance functionality, in part, by increasing aqueous solubility and preventing passive diffusion of bile acids out of the gut lumen. Bile acid function can be disrupted by the gut microbiota via the deconjugation of primary bile acids by bile salt hydrolases (BSHs), leading to their conversion into secondary bile acids through the expression of bacterial bile acid-inducible genes, a process often observed in malabsorption due to small intestinal bacterial overgrowth. By modeling the small intestinal microbiota in vitro using human small intestinal ileostomy effluent as the inocula, we show here that the infusion of physiologically relevant levels of oxygen, normally found in the proximal small intestine, reduced deconjugation of primary bile acids, in part, through the expansion of bacterial taxa known to have a low abundance of BSHs. Further recapitulating the small intestinal bile acid composition of the small intestine, limited conversion of primary into secondary bile acids was observed. Remarkably, these effects were preserved among four separate communities, each inoculated with a different small intestinal microbiota, despite a high degree of taxonomic variability under both anoxic and aerobic conditions. In total, these results provide evidence for a previously unrecognized role that the oxygenated environment of the small intestine plays in the maintenance of normal digestive physiology.

IMPORTANCE

Conjugated primary bile acids are produced by the liver and exist at high concentrations in the proximal small intestine, where they are critical for proper digestion. Deconjugation of these bile acids with subsequent transformation via dehydroxylation into secondary bile acids is regulated by the colonic gut microbiota and reduces their digestive function. Using an in vitro platform modeling the small intestinal microbiota, we analyzed the ability of this community to transform primary bile acids and studied the effect of physiological levels of oxygen normally found in the proximal small intestine (5%) on this metabolic process. We found that oxygenation of the small intestinal microbiota inhibited the deconjugation of primary bile acids in vitro. These findings suggest that luminal oxygen levels normally found in the small intestine may maintain the optimal role of bile acids in the digestive process by regulating bile acid conversion by the gut microbiota.

Revisiting the Intestinal Microbiome and Its Role in Diarrhea and Constipation

The gut microbiota represents a community of microorganisms (bacteria, fungi, archaea, viruses, and protozoa) that colonize the gut and are responsible for gut mucosal structural integrity and immune and metabolic homeostasis. The relationship between the gut microbiome and human health has been intensively researched in the past years. It is now widely recognized that gut microbial composition is highly responsible for the general health of the host. Among the diseases that have been linked to an altered gut microbial population are diarrheal illnesses and functional constipation. The capacity of probiotics to modulate the gut microbiome population, strengthen the intestinal barrier, and modulate the immune system together with their antioxidant properties have encouraged the research of probiotic therapy in many gastrointestinal afflictions. Dietary and lifestyle changes and the use of probiotics seem to play an important role in easing constipation and effectively alleviating diarrhea by suppressing the germs involved. This review aims to describe how probiotic bacteria and the use of specific strains could interfere and bring benefits as an associated treatment for diarrhea and constipation.

Unique Gut Microbiome Signatures among Adult Patients with Moderate to Severe Atopic Dermatitis in Southern Chinese

Imbalance of the immune system caused by alterations of the gut microbiome is considered to be a critical factor in the pathogenesis of infant eczema, but the exact role of the gut microbiome in adult atopic dermatitis (AD) patients remains to be clarified. To investigate the differences of the gut microbiome between adult AD patients and healthy individuals, stool samples of 234 adults, containing 104 AD patients and 130 healthy subjects, were collected for 16S rRNA gene amplicon. Altered structure and metabolic dysfunctions of the gut microbiome were identified in adult AD patients. Our results illustrated that the adult AD patients were more likely to have allergies, particularly non-food allergies. In addition, the gut microbiome composition of the AD and normal groups were considerably different. Moreover, Romboutsia and Clostridi-um_sensu_stricto_1 was enriched in the normal group, whereas Blautia, Butyricicoccus, Lachnoclostridium, Eubacterium_hallii_group, Erysi-pelatoclostridium, Megasphaera, Oscillibacter, and Flavonifractor dominated in the AD group. Additionally, purine nucleotide degradation pathways were significantly enriched in the AD group, and the enrichment of proteinogenic amino acid biosynthesis pathways was found in the normal group. This study provides insights into new therapeutic strategies targeting the gut microbiome for AD and evidence for the involvement of the gut-skin axis in AD patients.

Association between diet and the gut microbiome of young captive red-crowned cranes (Grus japonensis)

BACKGROUND

Exploring the association of diet and indoor and outdoor environments on the gut microbiome of red-crowned cranes. We investigated the microbiome profile of the 24 fecal samples collected from nine cranes from day 1 to 35. Differences in the gut microbiome composition were compared across diet and environments.

RESULTS

A total of 2,883 operational taxonomic units (OTUs) were detected, with 438 species-specific OTUs and 106 OTUs common to the gut microbiomes of four groups. The abundance of Dietzia and Clostridium XI increased significantly when the red-crowned cranes were initially fed live mealworms. Skermanella and Deinococcus increased after the red-crowned cranes were fed fruits and vegetables and placed outdoors. Thirty-three level II pathway categories were predicted. Our study revealed the mechanism by which the gut microbiota of red-crowned cranes responds to dietary and environmental changes, laying a foundation for future breeding, nutritional and physiological studies of this species.

CONCLUSIONS

The gut microbiome of red-crowned cranes could adapt to changes in diet and environment, but the proportion of live mealworms in captive red-crowned cranes can be appropriately reduced at the initial feeding stage, reducing the negative impact of high-protein and high-fat foods on the gut microbiome and growth and development.

Biostimulation of jarosite and iron oxide-bearing mine waste enhances subsequent metal recovery

Novel resource recovery technologies are required for metals-bearing hazardous wastes in order to achieve circular economy outcomes and industrial symbiosis. Iron oxide and co-occurring hydroxysulphate-bearing wastes are globally abundant and often contain other elements of value. This work addresses the biostimulation of indigenous microbial communities within an iron oxide/ hydroxysulphate-bearing waste and its effect on the subsequent recoverability of metals by hydrochloric, sulphuric, citric acids, and EDTA. Laboratory-scale flow-through column reactors were used to examine the effect of using glycerol (10% w/w) to stimulate the in situ microbial community in an iron oxide/ hydroxysulphate-bearing mine waste. The effects on the evolution of leachate chemistry, changes in microbiological community, and subsequent hydrometallurgical extractability of metals were studied. Results demonstrated increased leachability and selectivity of Pb, Cu, and Zn relative to iron after biostimulation with a total of 0.027 kg of glycerol per kg of waste. Biostimulation, which can be readily applied in situ, potentially opens new routes to metal recovery from globally abundant waste streams that contain jarosite and iron oxides.

Study on the preparation and feasibility of a novel adding-type biological slow-release carbon source

The development of slow-release carbon sources is an effective biological treatment to remove nutrients from wastewater with low carbon-to-nitrogen ratio (C/N). Most filling-type slow-release carbon could not fulfil the needs of current wastewater treatment plants (WWTPs) process. And most adding-type slow-release carbon sources were prepared using some expensive chemical materials. In this study, combining the advantages of the aforementioned types, a novel adding-type wastepaper-flora (AT-WF) slow-release carbon source was proposed, aiming to realise wastepaper recycling in WWTPs. The screening and identification of the mixed flora, AT-WF carbon source release behaviour, and denitrification performance were investigated. The results showed that through the proposed screening method, a considerable proportion of cellulose-degradation-related genera was enriched, and the cellulose degradation ability and ratio of readily available carbon sources of flora T4, S4 and S5 were effectively strengthened. AT-WF had significant carbon release ability and stability, with an average total organic carbon (TOC) release of 8.82 ± 2.36 mg/g. Kinetic analysis showed that the entire carbon release process was more consistent with the first-order equation. Piecewise fitting with the Ritger-Peppas equation exhibited that the rapid-release (RR) stage was skeleton dissolution and the slow-release (SR) stage was Fick diffusion. Denitrification efficiency can achieve a high average removal efficiency of 94.17%, which could theoretically contribute 11.2% more to the total inorganic nitrogen (TIN) removal. Thus, this study indicated that AT-WF could be utilised as an alternative carbon source in WWTPs.

Metabolite-Based Mutualistic Interaction between Two Novel Clostridial Species from Pit Mud Enhances Butyrate and Caproate Production

Pit mud microbial consortia play crucial roles in the formation of Chinese strong-flavor baijiu's key flavor-active compounds, especially butyric and caproic acids. Clostridia, one of the abundant bacterial groups in pit mud, were recognized as important butyric and caproic acid producers. Research on the interactions of the pit mud microbial community mainly depends on correlation analysis at present. Interaction between Clostridium and other microorganisms and its involvement in short/medium-chain fatty acid (S/MCFA) metabolism are still unclear. We previously found coculture of two clostridial strains isolated from pit mud, Clostridium fermenticellae JN500901 (C.901) and Novisyntrophococcus fermenticellae JN500902 (N.902), could enhance S/MCFA accumulation. Here, we investigated their underlying interaction mechanism through the combined analysis of phenotype, genome, and transcriptome. Compared to monocultures, coculture of C.901 and N.902 obviously promoted their growth, including shortening the growth lag phase and increasing biomass, and the accumulation of butyric acid and caproic acid. The slight effects of inoculation ratio and continuous passage on the growth and metabolism of coculture indicated the relative stability of their interaction. Transwell coculture and transcriptome analysis showed the interaction between C.901 and N.902 was accomplished by metabolite exchange, i.e., formic acid produced by C.901 activated the Wood-Ljungdahl pathway of N.902, thereby enhancing its production of acetic acid, which was further converted to butyric acid and caproic acid by C.901 through reverse β-oxidation. This work demonstrates the potential roles of mutually beneficial interspecies interactions in the accumulation of key flavor compounds in pit mud. IMPORTANCE Microbial interactions played crucial roles in influencing the assembly, stability, and function of the microbial community. The metabolites of pit mud microbiota are the key to flavor formation of Chinese strong-flavor baijiu. So far, researches on the interactions of the pit mud microbial community have been mainly based on the correlation analysis of sequencing data, and more work needs to be performed to unveil the complicated interaction patterns. Here, we identified a material exchange-based mutualistic interaction system involving two fatty acid-producing clostridial strains (Clostridium fermenticellae JN500901 and Novisyntrophococcus fermenticellae JN500902) isolated from pit mud and systematically elucidated their interaction mechanism for promoting the production of butyric acid and caproic acid, the key flavor-active compounds of baijiu. Our findings provide a new perspective for understanding the complicated interactions of pit mud microorganisms.

Changes in Lake Sturgeon Gut Microbiomes Relative to Founding Origin and in Response to Chemotherapeutant Treatments

Antibiotics, drugs, and chemicals (collectively referred to as chemotherapeutants) are widely embraced in fish aquaculture as important tools to control or prevent disease outbreaks. Potential negative effects include changes in microbial community composition and diversity during early life stages, which can reverse the beneficial roles of gut microbiota for the maintenance of host physiological processes and homeostatic regulation. We characterized the gut microbial community composition and diversity of an ecologically and economically important fish species, the lake sturgeon (Acipenser fulvescens), during the early larval period in response to weekly treatments using chemotherapeutants commonly used in aquaculture (chloramine-T, hydrogen peroxide, and NaCl₂ followed by hydrogen peroxide) relative to untreated controls. The effects of founding microbial community origin (wild stream vs. hatchery water) were also evaluated. Gut communities were quantified using massively parallel next generation sequencing based on the V4 region of the 16S rRNA gene. Members of the phylum Firmicutes (principally unclassified Clostridiales and Clostridium_sensu_stricto) and Proteobacteria were the dominant taxa in all gut samples regardless of treatment. The egg incubation environment (origin) and its interaction with chemotherapeutant treatment were significantly associated with indices of microbial taxonomic diversity. We observed large variation in the beta diversity of lake sturgeon gut microbiota between larvae from eggs incubated in hatchery and wild (stream) origins based on nonmetric dimensional scaling (NMDS). Permutational ANOVA indicated the effects of chemotherapeutic treatments on gut microbial community composition were dependent on the initial source of the founding microbial community. Influences of microbiota colonization during early ontogenetic stages and the resilience of gut microbiota to topical chemotherapeutic treatments are discussed.

Relationships Between Migration and Microbiome Composition and Diversity in Urban Canada Geese

Microbiome analysis presents an opportunity to understand how urban environments affect avian physiology. For example, habitat use can affect microbiome diversity and composition, and hosts with more diverse gut microbiota are thought to be more resistant to pathogens and have increased fitness. However, the microbiome is an understudied aspect of avian ecology, particularly in the context of migration and urbanization in wild birds. For this study, we hypothesized that, within urban birds, migrants would exhibit greater microbial diversity and inter-individual variation in microbiome composition than residents because they are exposed to more diverse habitats. We focused on Canada geese (Branta canadensis), one of many migratory species that exhibit increasingly more year-round residency in cities. We used 16S rRNA gene amplicon sequencing to quantify microbiome taxonomic composition in fecal samples from 32 GPS-tracked Canada geese, 22 of which were year-round residents of the Chicago area and 10 of which were migrants. Similar to recent studies on wild species feeding near human habitation, urban resident geese had higher gut microbial diversity than migrants. They also had increased inter-individual variation in microbiome composition and, on average, lower relative abundances of bacteria in the phylum Firmicutes, and the genera Terrisporobacter, Turicibacter, and Cellulosilyticum, which all have metabolic functions that may aid in goose digestion. Therefore, the gut microbiome of resident geese may provide fewer potential health benefits. These patterns may be a result of anthropogenic influences on aspects of resident goose ecology, such as diet, as well the influence of migration on migrant goose ecology and biology. Overall, our results suggest that reduced migration for urban-adapted wildlife species may have important consequences for physiology and health.

Social isolation in adolescence and long-term changes in the gut microbiota composition and in the hippocampal inflammation: Implications for psychiatric disorders - Dirk Hellhammer Award Paper 2021

Exposure to early adverse experiences induces persistent changes in physiological, emotional and behavioural functions predisposing the individual to an enhanced vulnerability to develop different disorders during lifespan. The adverse outcomes depend upon the timing of the stressful experiences, and in this contest, adolescence represents a key sensitive period for brain development. Among the biological systems involved, gut microbiota has recently been proposed to act on the interplay between the stress response, brain functions and immune system, through the gut-brain axis communication. In the current study we aimed to evaluate, in a preclinical model, changes over time in the microbiota community structure in physiological condition and in response to stress during adolescence. We also aimed to correlate the microbiota composition to the inflammatory status in brain. We used the preclinical model of social deprivation in rats during adolescence, based on the lack of all social contacts, for four weeks after weaning, followed by re-socialization until adulthood. We collected fecal samples at different post-natal days to investigate the short- and long-lasting effects of social isolation on gut microbiota composition and we collected brain areas (dorsal and ventral hippocampus) samples at killing to measure a panel of inflammatory and microglia activation markers. 16 S metataxonomic sequencing analysis revealed that microbial changes were influenced by age in both isolated and controls rats, regardless of sex, whereas social isolation impacted the microbial composition in a sex-dependent manner. A multivariate analysis showed that social isolation induced short-term gut microbiota alterations in females but not in males. We also identified several stress-related genera associated with social isolation condition. In brain areas we found a specific inflammatory pattern, in dorsal and ventral hippocampus, that significantly correlated with gut microbiota composition. Overall, in this study we reported a novel sex-specific association between gut microbiota composition and inflammatory response related to social isolation paradigm during adolescence, suggesting that stressful experiences during this sensitive period could have a long-lasting impact on the development of different biological systems that could in turn influence the vulnerability to develop mental disorders later in life.

Advantageous microbial community development and improved performance of pilot-scale field systems treating high-risk acid mine drainage with crab shell

Microbial communities are crucial to the effectiveness and stability of bioremediation systems treating acid mine drainage (AMD); however, little research has addressed how they correlate to system performance under changing environmental conditions. In this study, 16S rRNA gene sequencing and quantitative PCR (qPCR) were used to characterize microbial communities within different substrate combinations of crab shell (CS) and spent mushroom compost (SMC) and their association with chemical performance in pilot-scale vertical flow ponds (VFPs) treating high risk AMD in central Pennsylvania over 643 days of operation. As compared to a control containing SMC, VFPs containing CS sustained higher alkalinity, higher sulfate-reducing rates, and more thorough metals removal (>90% for Fe and Al, >50% for Mn and Zn). Correspondingly, CS VFPs supported the growth of microorganisms in key functional groups at increasing abundance and diversity over time, especially more diverse sulfate-reducing bacteria. Through changing seasonal and operational conditions over almost two years, the relative abundance of the core phyla shifted in all reactors, but the smallest changes in functional gene copies were observed in VFPs containing CS. These results suggest that the high diversity and stability of microbial communities associated with CS are consistent with effective AMD treatment.

Leveraging Fecal Microbial Markers to Improve the Diagnostic Accuracy of the Fecal Immunochemical Test for Advanced Colorectal Adenoma

INTRODUCTION

Fecal immunochemical tests (FITs) detect colorectal adenoma inefficiently. The gut microbiota participates in colorectal cancer development. We aimed to explore fecal microbial signatures for advanced adenomas and evaluate their diagnostic value and complementary capacity to FIT.

METHODS

Using 16S rRNA sequencing, we studied gut microbiota in feces from 1,546 subjects in a screening setting, including 268 patients with advanced adenomas, 490 patients with nonadvanced adenomas, and 788 healthy subjects. Feature selections were performed using linear discriminant analysis effect size, multivariate association with linear models, and least absolute shrinkage and selection operator. The diagnostic performance of microbial signatures and their auxiliary role to FITs and the added value of the Asia-Pacific Colorectal Screening score were evaluated. We applied 0.632+ bootstrapping to adjust the potential overfitting.

RESULTS

We identified 13 microbial signatures to show the joint diagnostic value for advanced adenoma, with genus Tyzzerella 4 demonstrating the highest adjusted area under the curve (AUC) of 0.545 (95% confidence interval [CI], 0.520-0.610). The 13-bacteria increased the adjusted AUC to 0.607 (95% CI, 0.548-0.660). Compared with individual FIT (adjusted AUC = 0.527; 95% CI, 0.519-0.571), 13-bacteria and FITs collectively reached an adjusted AUC of 0.641 (95% CI, 0.579-0.691). At cutoff values yielding specificities of 90% and 80%, the adjusted sensitivities were 28.4% (95% CI, 19.3-36.8) and 41.1% (95% CI, 29.9-49.4), respectively. The Asia-Pacific Colorectal Screening score further boosted the adjusted AUC to 0.706 (95% CI, 0.648-0.750).

DISCUSSION

In this study using fecal samples from a screening setting, the identified microbial signatures could complement FITs for detecting advanced adenomas. Gut microbiota can act as a promising tool to optimize the current colorectal cancer screening modalities.

Bacterial Diversity of Water and Sediment Samples from Gull Point State Park (West Okoboji, Iowa) Determined Using 16S rRNA Gene Amplicon Sequencing

Gull Point State Park is located on a peninsula on the west shore of West Okoboji Lake (Iowa, USA). It is the primary state park in the Iowa Great Lakes region. Sediment and water samples from three locations at the Gull Point pond were analyzed for their microbial composition.

Mining the Factors Driving the Evolution of the Pit Mud Microbiome under the Impact of Long-Term Production of Strong-Flavor Baijiu

The mud cellar creates a unique microenvironment for the fermentation of strong-flavor baijiu (SFB). Recent research and long-term practice have highlighted the key roles of microbes inhabiting pit mud in the formation of SFB’s characteristic flavor. A positive correlation between the quality of SFB and cellar age was extracted from practice; however, the evolutionary patterns of pit mud microbiome and driving factors remain unclear. Here, based on the variation regularity analysis of microbial community structure and metabolites of samples from cellars of different ages (∼30/100/300 years), we further investigated the effects of lactate and acetate (main microbial metabolites in fermented grains) on modulating the pit mud microbiome. Esters (50.3% to 64.5%) dominated the volatile compounds identified in pit mud, and contents of the four typical acids (lactate, hexanoate, acetate, and butyrate) increased with cellar age. Bacteria (9.5 to 10.4 log₁₀ [lg] copies/g) and archaea (8.3 to 9.1 lg copies/g) mainly constituted pit mud microbiota, respectively dominated by Clostridia (39.7% to 81.2%) and Methanomicrobia (32.8% to 92.9%). An upward trend with cellar age characterized the relative and absolute abundance of the most predominant bacterial and archaeal genera, Caproiciproducens and Methanosarcina. Correlation analysis revealed significantly (P < 0.05) positive relationships between the two genera and major metabolites. Anaerobic fermentation with acetate and lactate as carbon sources enhanced the enrichment of Clostridia, and furthermore, the relative abundance of Caproiciproducens (40.9%) significantly increased after 15-day fed-batch fermentation with lactate compared with the initial pit mud (0.22%). This work presents a directional evolutionary pattern of pit mud microbial consortia and provides an alternative way to accelerate the enrichment of functional microbes.

IMPORTANCE The solid-state anaerobic fermentation in a mud cellar is the most typical feature of strong-flavor baijiu (SFB). Metabolites produced by microbes inhabiting pit mud are crucial to create the unique flavor of SFB. Accordingly, craftspeople have always highlighted the importance of the pit mud microbiome and concluded by centuries of practice that the production rate of high-quality baijiu increases with cellar age. To deepen the understanding of the pit mud microbiome, we determined the microbial community and metabolites of different-aged pit mud, inferred the main functional groups, and explored the forces driving the microbial community evolution through metagenomic, metabolomic, and multivariate statistical analyses. The results showed that the microbial consortia of pit mud presented a regular and directional evolutionary pattern under the impact of continuous batch-to-batch brewing activities. This work provides insight into the key roles of the pit mud microbiome in SFB production and supports the production optimization of high-quality pit mud.

Correlations between maximum reductive dechlorination rates and specific biomass parameters in Dehalococcoides mccartyi consortia enriched on chloroethenes PCE, TCE and cis-1,2-DCE

One of the challenges to implementing the modeling of the biological reductive dechlorination (RD) process is the evaluation of biological parameters that represent the abundance/activity levels of the microorganisms involved in the biodegradation of chloroethenes. Here we report a combined analysis of kinetic and specific biomass parameters conducted on three dechlorinating consortia enriched on PCE, TCE and cis-1,2-DCE. In these consortia, Dehalococcoides mccartyi (Dhc) represented ≥70% of the bacterial population identified via 16S rRNA gene amplicon sequencing. Quantitative biomolecular methods were used to generate specific biomass parameters targeting either the Dhc population (16S rRNA genes or cells) or specific genes encoding RD process-involved reductive dehalogenases. The correlation factor between the abundance of active Dhc cells or tceA gene copies and maximum RD rates allowed to predict an increment of 7E+09 of active Dhc cells or 5E+09 tceA gene copies/L under controlled conditions. Diversely, the utilization of gene transcripts as biomass parameters for RD modeling did not provide reliable correlations with kinetic performances. This study provides valuable insights for further modeling of the RD process through the utilization of specific biomass parameters.

Co-exposure to inorganic arsenic and fluoride prominently disrupts gut microbiota equilibrium and induces adverse cardiovascular effects in offspring rats

Co-exposure to inorganic arsenic (iAs) and fluoride (F^-) and their collective actions on cardiovascular systems have been recognized as a global public health concern. Emerging studies suggest an association between the perturbation of gut bacterial microbiota and adverse cardiovascular effects (CVEs), both of which are the consequence of iAs and F^- exposure in human and experimental animals. The aim of this study was to fill the gap of understanding the relationship among co-exposure to iAs and F^-, gut microbiota perturbation, and adverse CVEs. We systematically assessed cardiac morphology and functions (blood pressure, echocardiogram, and electrocardiogram), and generated gut microbiota profiles using 16S rRNA gene sequencing on rats exposed to iAs (50 mg/L NaAsO₂), F^- (100 mg/L NaF) or combined iAs and F^- (50 mg/L NaAsO₂ + 100 mg/L NaF), in utero and during early postnatal periods (postnatal day 90). Correlation analysis was then performed to examine relationship between significantly altered microbiota and cardiac performance indices. Our results showed that co-exposure to iAs and F^- resulted in more prominent effects in CVEs and perturbation of gut microbiota profiles, compared to iAs or F^- treatment alone. Furthermore, nine bacterial genera (Adlercreutzia, Clostridium sensu stricto 1, Coprococcus 3, Romboutsia, [Bacteroides] Pectinophilus group, Lachnospiraceae NC2004 group, Desulfovibrio, and two unidentified genera in Muribaculaceae and Ruminococcaceae family), which differed significantly in relative abundance between control and iAs and F^- co-exposure group, were strongly correlated with the higher risk of CVEs (correlation coefficient = 0.70-0.88, p < 0.05). Collectively, these results suggest that co-exposure to iAs and F^- poses a higher risk of CVEs, and the part of the mode of action is potentially through inducing gut microbiota disruption, and the strong correlations between them indicate a high potential for the development of novel microbiome-based biomarkers of iAs and/or F^- associated CVEs.

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.

Molecular characterization of bacteria and archaea in a bioaugmented zero-water exchange shrimp pond

In the zero-water exchange shrimp culture pond maintained with the application of indigenous bioaugmentor, low levels of total ammonia–nitrogen were reported, indicating the relevance of indigenous microbial communities. Sediments (0–5 cm layer) were sampled from the pond (85th day) and the bacterial and archaeal communities; specifically, the ammonia oxidizers (ammonia-oxidizing bacteria, ammonia-oxidizing archaea, and anaerobic ammonia-oxidizing bacteria) in the sediment metagenome of the pond were analysed using the 16S rRNA and functional genes. Bacterial and archaeal 16S rRNA genes showed the relative abundance of Delta-Proteobacteria and Bacteroidetes groups performing sulphur respiration and organic matter degradation, archaeal groups of anaerobic sulphur respiring Crenarchaeotae, and chemolithoautotrophic ammonia oxidizers belonging to Thaumarchaeota. The presence of these diverse bacterial and archaeal communities denotes their significant roles in the cycling the carbon, nitrogen, and sulphur thereby bringing out efficient bioremediation in the bioaugmented zero-water exchange shrimp culture pond. Similarly, the functional gene-specific study showed the predominance of Nitrosomonas sp. (ammonia-oxidizing bacteria), Nitrosopumilus maritimus (ammonia-oxidizing archaea), and Candidatus Kuenenia (anaerobic ammonia-oxidizing bacteria) in the system, which points to their importance in the removal of accumulated ammonia. Thus, this study paves the way for understanding the microbial communities, specifically the ammonia oxidizers responsible for maintaining healthy and optimal environmental conditions in the bioaugmented zero-water exchange shrimp culture pond.

Effects of integrated biocontrol on bacterial wilt and rhizosphere bacterial community of tobacco

Bacterial wilt as a soil-borne disease was caused by Ralstonia solanacearum, and seriously damages the growth of tobacco. Integrated biocontrol method was explored to control bacterial wilt. Nevertheless, the long-term effects of the integrated biocontrol method on soil bacterial community, soil physicochemical properties and the incidence of bacterial wilt are not well understood. In this study, B. amyoliquefaciens ZM9, calcium cyanamide and rice bran were applied to tobacco fields in different ways. The disease index and incidence of tobacco bacterial wilt (TBW), soil physicochemical properties, colonization ability of B. amyoliquefaciens ZM9, and rhizopshere bacterial community were investigated. The results showed that the integrated application of B. amyoliquefaciens ZM9, rice bran and calcium cyanamide had the highest control efficiency of TBW and bacteria community diversity. Additionally, the integrated biocontrol method could improve the colonization ability of B. amyoliquefaciens ZM9. Furthermore, the integrated biocontrol method could effectively suppress TBW by regulating soil physicochemical properties, promoting beneficial bacteria and antagonistic bacteria of rhizopshere soil. This strategy has prospect of overcoming the defects in application of a single antagonistic bacteria and provides new insights to understand how to improve the colonization capacity of antagonistic bacteria and control efficacy for TBW.

Robust demarcation of 17 distinct Bacillus species clades, proposed as novel Bacillaceae genera, by phylogenomics and comparative genomic analyses: description of Robertmurraya kyonggiensis sp. nov. and proposal for an emended genus Bacillus limiting it only to the members of the Subtilis and Cereus clades of species

To clarify the evolutionary relationships and classification of Bacillus species, comprehensive phylogenomic and comparative analyses were performed on >300 Bacillus/Bacillaceae genomes. Multiple genomic-scale phylogenetic trees were initially reconstructed to identify different monophyletic clades of Bacillus species. In parallel, detailed analyses were performed on protein sequences of genomes to identify conserved signature indels (CSIs) that are specific for each of the identified clades. We show that in different reconstructed trees, most of the Bacillus species, in addition to the Subtilis and Cereus clades, consistently formed 17 novel distinct clades. Additionally, some Bacillus species reliably grouped with the genera Alkalicoccus, Caldalkalibacillus, Caldibacillus, Salibacterium and Salisediminibacterium. The distinctness of identified Bacillus species clades is independently strongly supported by 128 identified CSIs which are unique characteristics of these clades, providing reliable means for their demarcation. Based on the strong phylogenetic and molecular evidence, we are proposing that these 17 Bacillus species clades should be recognized as novel genera, with the names Alteribacter gen. nov., Ectobacillus gen. nov., Evansella gen. nov., Ferdinandcohnia gen. nov., Gottfriedia gen. nov., Heyndrickxia gen. nov., Lederbergia gen. nov., Litchfieldia gen. nov., Margalitia gen. nov., Niallia gen. nov., Priestia gen. nov., Robertmurraya gen. nov., Rossellomorea gen. nov., Schinkia gen. nov., Siminovitchia gen. nov., Sutcliffiella gen. nov. and Weizmannia gen. nov. We also propose to transfer 'Bacillus kyonggiensis' to Robertmurraya kyonggiensis sp. nov. (type strain: NB22=JCM 17569^T=DSM 26768). Additionally, we report 31 CSIs that are unique characteristics of either the members of the Subtilis clade (containing the type species B. subtilis) or the Cereus clade (containing B. anthracis and B. cereus). As most Bacillus species which are not part of these two clades can now be assigned to other genera, we are proposing an emended description of the genus Bacillus to restrict it to only the members of the Subtilis and Cereus clades.

Role of the microbiota in ileitis of a mouse model of inflammatory bowel disease-Glutathione peroxide isoenzymes 1 and 2-double knockout mice on a C57BL background

C57Bl6 (B6) mice devoid of glutathione peroxidases 1 and 2 (Gpx1/2-DKO) develop ileitis after weaning. We previously showed germ-free Gpx1/2-DKO mice of mixed B6.129 background did not develop ileocolitis. Here, we examine the composition of the ileitis provoking microbiota in B6 Gpx1/2-DKO mice. DNA was isolated from the ileum fecal stream and subjected to high-throughput sequencing of the V3 and V4 regions of the 16S rRNA gene to determine the abundance of operational taxonomic units (OTUs). We analyzed the role of bacteria by comparing the microbiomes of the DKO and pathology-free non-DKO mice. Mice were treated with metronidazole, streptomycin, and vancomycin to alter pathology and correlate the OTU abundances with pathology levels. Principal component analysis based on Jaccard distance of abundance showed 3 distinct outcomes relative to the source Gpx1/2-DKO microbiome. Association analyses of pathology and abundance of OTUs served to rule out 7-11 of 24 OTUs for involvement in the ileitis. Collections of OTUs were identified that appeared to be linked to ileitis in this animal model and would be classified as commensals. In Gpx1/2-DKO mice, host oxidant generation from NOX1 and DUOX2 in response to commensals may compromise the ileum epithelial barrier, a role generally ascribed to oxidants generated from mitochondria, NOX2 and endoplasmic reticulum stress in response to presumptive pathogens in IBD. Elevated oxidant levels may contribute to epithelial cell shedding, which is strongly associated with progress toward inflammation in Gpx1/2-DKO mice and predictive of relapse in IBD by allowing leakage of microbial components into the submucosa.

The Role of Intestinal Microbiota and Mast Cell in a Rat Model of Visceral Hypersensitivity

Background/Aims

To explore the role of intestinal flora and mast cells in visceral hypersensitivity (VH).

Methods

The experimental animals were divided into 4 groups: control group, VH group, VH + VSL#3 group, and VH + ketotifen group. Stool samples were collected from each group (n = 3) for a further analysis using 16S ribosomal DNA gene sequence. Visceral sensitivity was evaluated by abdominal withdrawal reflex (AWR) score. Colon tissues of rats were obtained from each group. Mast cells were detected by toluidine blue staining. The degranulation of mast cells was assessed by transmission electron microscopy.

Results

VH rat model could successfully be induced by acetic acid enema combined with partial limb restraint method. Compared with rats in the control group, AWR score, number of mast cells, and degranulation of mast cells were increased in the VH rats, which could be reduced by administration of ketotifen or probiotic VSL#3. Clostridium sensu stricto 1 abundance was higher in the VH group compared to the control group, which could be restored by application of probiotic VSL#3.

Conclusions

Probiotic VSL#3 decreases visceral sensitivity in VH rats. The mechanism may be related to mast cell and intestinal flora. Change of Clostridium sensu stricto 1 abundance may be a basis for VH observed in irritable bowel syndrome and may be prevented by specific probiotic administration.

Concurrent use of methanol and ethanol for chain-elongating short chain fatty acids into caproate and isobutyrate

Microbial chain elongation (MCE) is a bioprocess that could utilise a mixed-culture fermentation to valorise organic waste. MCE converting ethanol and short chain fatty acids (SCFA; derived from organic waste) to caproate has been studied extensively and implemented. Recent studies demonstrated the conversion of SCFAs and methanol or ethanol into isomerised fatty acids as novel products, which may expand the MCE application and market. Integrating caproate and isomerised fatty acid production in one reactor system is theoretically feasible given the employment of a mixed culture and may increase the economic competence of MCE; however, the feasibility of such has never been demonstrated. This study investigated the feasibility of using two electron donors, i.e. methanol and ethanol, for upgrading SCFAs into isobutyrate and caproate concurrently in MCE Results show that supplying methanol and ethanol in MCE simultaneously converted acetate and/or butyrate into caproate and isobutyrate, by a mixed-culture microbiome. The butyrate supplement stimulated the caproate production rate from 1.5 to 2.6 g/L.day and induced isobutyrate production (1.5 g/L.day). Further increasing ethanol feeding rate from 140 to 280 mmol carbon per litre per day enhanced the direct use of butyrate for caproate production, which improved the caproate production rate to 5.9 g/L.day. Overall, the integration of two electron donors, i.e. ethanol and methanol, in one chain-elongation reactor system for upgrading SCFAs was demonstrated. As such, MCE could be applied to valorise organic waste (water) streams into a wider variety of value-added biochemical.

Oral Administration of Heat-Treated Lactobacilli Modifies the Murine Microbiome and Reduces Citrobacter Induced Colitis

Significant evidence supports a relationship between the gut microbiome, inflammation, host response, and health, including the finding that a number of disorders are associated with disruption of the microbiome. In these disorders, a number of dietary interventions (including prebiotics, live probiotics, or heat-killed microbes) have been proposed to be curative or preventative agents. The use of heat-killed microbes has a number of benefits over living organisms, including reduced infection risk in vulnerable individuals, extended shelf life and the potential for use in combination with antimicrobial agents. We previously reported that murine chow supplemented with 5% ADR-159, a heat-treated fermentate generated by two Lactobacillus strains, altered both behavior and the microbiome of male mice. Now we show that ADR-159 fed female mice also display a similar microbiome shift as determined by 16S rDNA analysis. In particular, we observed a reduction of levels of Turicibacter and Clostridium sensu stricto. These subtle changes in the bacterial component of the microbiome were mirrored by changes in the virome. Extended consumption of the ADR-159 diet had no negative effect on general health and lipocalin 2 levels (LCN2; a proxy for inflammation), but we observed increased IL-17f and decreased IL-12α expression in the colon and decreased short chain fatty acid levels in the ADR-159 fed animals. Four weeks into the diet, half of the animals were dosed with Citrobacter to determine the effect of ADR-159 on infection and on pathogen induced colitis. Overall, our results suggest that while the ADR-159 diet does not prevent Citrobacter infection, it had an effect on Citrobacter-induced inflammation. In contrast to animals fed standard chow, ADR-159 fed animals did not show a reduction of small intestine length and increase of colon crypt depth, which occurred in control mice. These microbiological, histological, and immunological results provide evidence to support the impact of heat-treated microorganisms and their metabolites on the murine microbiome and health.

Stimulation of optimized influent C:N ratios on nitrogen removal in surface flow constructed wetlands: Performance and microbial mechanisms

Exploring optimal C:N ratio is necessary to ensure balanced microbial nitrification and denitrification in constructed wetlands (CWs), which has become an important management practice for more efficient nitrogen removal and sustainability of CWs. Surface flow constructed wetlands (SFCWs) vegetated with Myriophyllum aquaticum were designed to investigate the effects of five different influent C:N ratios (0:1, 2.5:1, 5:1, 10:1, and 15:1) on nitrogen removal performance and microbial communities over a 175-day experimental period. Compared to the influent C:N ratios of 0:1, higher NH₄⁺-N, NO₃^--N, and total nitrogen (TN) removal efficiencies and lower NO₃^--N accumulation were observed at influent C:N ratios higher than 5:1. In addition, the highest TN removal efficiency (70.4%) and the lowest nitrous oxide emission flux (4.12 mg m^-2 d^-1) were obtained at the influent C:N ratio of 5:1. High-throughput sequencing revealed that influent C:N ratios altered the distribution and composition of microbial communities in the sediment, which resulted in a dynamic interplay between N-transforming functional microbes and NH₄⁺-N and NO₃^--N removal. In particular, the dominant denitrifiers, including Desulfovibrio, Zoogloea, and Dechloromonas, were more abundant in the sediment with an influent C:N ratio of 5:1, which contributed to the high N removal rate. These findings may be used to screen for an optimum influent C:N ratio to maintain the sustainability of SFCWs with higher N removal efficiency.

Enhanced butyrate production by transition metal particles during the food waste fermentation

Butyrate is an important precursor for fine chemicals and biofuels. The aim of this study is to investigate butyrate production as affected by transition metal addition of food waste fermentation including, nickel, Raney nickel and copper particles. Performance of fermentation showed nickel particles achieved the highest butyrate concentration, 7.3 g/L, which was 38.5% higher than that in the control trial. Raney nickel also showed similar effect on the enhancement of butyrate production. However, increased dosage of transition metal particle addition led to decreased butyrate production. The theoretical link between metal-assisted dark fermentation and butyrate production was tentatively explored. Redox potential affected by nickel addition was assumed to be an essential factor for butyrate production. Microbial community analysis found Clostridium sensu stricto 11 may be the dominant functional species for butyrate production. The study demonstrates that development on transition metal catalyst may contribute to waste biorefinery for added value products/energy production.

Specific detection of "Clostridium autoethanogenum", Clostridium ljungdahlii and Clostridium carboxidivorans in complex bioreactor samples

The high genetic similarity between some carboxydotrophic bacteria does not allow for the use of common sequencing techniques targeting the 16S rRNA gene for species identification. 16S rRNA sequencing fails to discriminate among Clostridium ljungdahlii and 'Clostridium autoethanogenum', despite this two species exhibit significant differences in CO2 assimilation and alcohol production. In this work we designed PCR primers targeting for the DNA gyrase subunit A (gyrA) and a putative formate/nitrite transporter (fnt) to specifically detect the presence of 'C. autoethanogenum', C. ljungdahlii or Clostridium carboxidivorans. We could confirm the simultaneous presence of C. ljungdahlii and 'C. autoethanogenum' in different bioreactors, and a preference of the latter for high CO2 content.

Identification of Molecular Markers That Are Specific to the Class Thermoleophilia

The class Thermoleophilia is one of the deep-rooting lineages within the Actinobacteria phylum and metagenomic investigation of microbial diversity suggested that species associated with the class Thermoleophilia are abundant in hot spring and soil samples. However, very few species of this class have been cultivated and characterized. Our understanding of the phylogeny and taxonomy of Thermoleophilia is solely based on 16S rRNA sequence analysis of limited cultivable representatives, but no other phenotypic or genotypic characteristics are known that can clearly discriminate members of this class from the other taxonomic units within the kingdom bacteria. This study reports phylogenomic analysis for 12 sequenced members of this class and clearly resolves the interrelationship of not yet cultivated species with reconstructed genomes and known type species. Comparative genome analysis discovered 12 CSIs in different proteins and 32 CSPs that are specific to all species of this class. In addition, a large number of CSIs or CSPs were identified to be unique to certain lineages within this class. This study represents the first and most comprehensive phylogenetic analysis of the class Thermoleophilia, and the identified CSIs and CSPs provide valuable molecular markers for the identification and delineation of species belonging to this class or its subordinate taxa.

Profiling the Clostridia with butyrate-producing potential in the mud of Chinese liquor fermentation cellar

Butyrate and its derivates pertain to the key aroma contributors of strong-flavour baijiu, a kind of Chinese liquors, that is produced from grains by solid-state multispecies anaerobic fermentation in a mud cellar. Microbes inhabiting in the fermentation pit mud largely determines baijiu's flavour and quality. In order to shed light on the microbial functional groups driving butyrate production in pit mud, clone library analysis was firstly performed and the results demonstrated that Clostridia (relative abundance: 50%) and Bacilli (37%) were major groups possessing butyrate kinase (buk) pathway and Clostridia (98%) dominated butyryl-CoA:acetate CoA-transferase (but) pathway. According to Clostridial specific-16S rRNA gene sequencing analysis, we found the resilience character of Clostridial community in pit mud. Amongst Clostridial groups, 32.0% of the sequences were grouped into Clostridiales incertae sedis, followed by Heliobacteriaceae (18.3%) and Clostridiaceae 1 (8.4%). Moreover, Hydrogenispora, Sedimentibacter and Clostridium were the top three abundant genera. Relative abundance of Hydrogenispora was higher in the late days of fermentation, while Sedimentibacter exhibited higher proportion in the early days. Different from the previous studies using universal bacterial primer sets, Hydrogenispora was first reported as one dominant genus in pit mud. As for the reported potential butyrate producer Clostridium, nineteen species were obtained and ten of them were first isolated from the pit mud. Amongst them, buk was identified in eleven species by PCR analysis, while but was identified in the other seven, indicating the species-specific butyrate synthesis pathways of Clostridium. This study provides a perspective on targeting and isolating specific functional microbes in baijiu microbiota with the gene sequence-based medium prediction method.

Clostridium fermenticellae sp. nov., isolated from the mud in a fermentation cellar for the production of the Chinese liquor, baijiu

A novel Gram-stain-positive, rod-shaped, obligately anaerobic, non-motile, spore-forming and binary fission encapsulated bacterium, designated strain JN500901^T, was isolated from a mud cellar which has been continuously used for the fermentation of Chinese strong-flavour baijiu for over 100 years. Growth of JN500901^Toccurred at pH 4.5-8.0 (optimum, pH 5.0), 20-40 °C (37 °C), 0-2 % (w/v) NaCl and 0-10 % (v/v) ethanol. The Biolog assay revealed that strain JN500901^T metabolized d-fructose, l-fucose, isomaltulose and l-rhamnose among the 95 studied carbon sources. p-Cresol was the predominant volatile metabolite in the fermentation broth of strain JN500901^T incubated in liquid reinforced clostridial medium under anaerobic conditions. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain JN500901^T belongs to Clostridiumsensu stricto, and shared the highest sequence similarity to Clostridiumcarboxidivorans DSM 15243^T (94.2 %), followed by Clostridiumscatologenes DSM 757^T (94.1 %). The dominant cellular fatty acids (>10 %) were C16 : 0 FAME (36.6 %), C19 : 0 cyc 9,10 DMA (19.8 %) and C16 : 1 cis 9 DMA (11.8 %). The complete genome of strain JN500901^T contained a circular chromosome of 2.812 Mb with 2611 genes and 31.0 mol% G+C content. Comparative genome analysis of the strain JN500901^T, Clostridiumcarboxidivorans DSM 15243^T and Clostridiumscatologenes DSM 757^T revealed 74.5 and 74.8 % average nucleotide identity, respectively. Based on the phenotypic, biochemical and phylogenetic analyses presented here, strain JN500901^T is considered to be a novel species of the genus Clostridiumsensustricto, for which the name Clostridium fermenticellae sp. nov. is proposed. The type strain is JN500901^T (=CICC 24501^T=JCM 32827^T).

High-Throughput Sequence Analyses of Bacterial Communities and Multi-Mycotoxin Profiling During Processing of Different Formulations of Kunu, a Traditional Fermented Beverage

Kunu is a traditional fermented single or mixed cereals-based beverage popularly consumed in many parts of West Africa. Presently, the bacterial community and mycotoxin contamination profiles during processing of various kunu formulations have never been comprehensively studied. This study, therefore, investigated the bacterial community and multi-mycotoxin dynamics during the processing of three kunu formulations using high-throughput sequence analysis of partial 16S rRNA gene (hypervariable V3-V4 region) and liquid chromatography tandem mass spectrometry (LC-MS/MS), respectively. A total of 2,303 operational taxonomic units (OTUs) were obtained across six processing stages in all three kunu formulations. Principal coordinate analysis biplots of the Bray-Curtis dissimilarity between bacterial communities revealed the combined influences of formulations and processing steps. Taxonomically, OTUs spanned 13 phyla and 486 genera. Firmicutes (phylum) dominated (relative abundance) most of the processing stages, while Proteobacteria dominated the rest of the stages. Lactobacillus (genus taxa level) dominated most processing stages and the final product (kunu) of two formulations, whereas Clostridium sensu stricto (cluster 1) dominated kunu of one formulation, constituting a novel observation. We further identified Acetobacter, Propionibacterium, Gluconacetobacter, and Gluconobacter previously not associated with kunu processing. Shared phylotypes between all communities were dominated by lactic acid bacteria including species of Lactobacillus, Lactococcus, Leuconostoc, Pediococcus, and Weissella. Other shared phylotypes included notable acetic acid bacteria and potential human enteric pathogens. Ten mycotoxins [3-Nitropropionic acid, aflatoxicol, aflatoxin B1 (AFB1), AFB2, AFM1, alternariol (AOH), alternariolmethylether (AME), beauvericin (BEAU), citrinin, and moniliformin] were quantified at varying concentrations in ingredients for kunu processing. Except for AOH, AME, and BEAU that were retained at minimal levels of < 2 μg/kg in the final product, most mycotoxins in the ingredients were not detectable after processing. In particular, mycotoxin levels were substantially reduced by fermentation, although simple dilution and sieving also contributed to mycotoxin reduction. This study reinforces the perception of kunu as a rich source of bacteria with beneficial attributes to consumer health, and provides in-depth understanding of the microbiology of kunu processing, as well as information on mycotoxin contamination and reduction during this process. These findings may aid the development of starter culture technology for safe and quality kunu production.

Different Influences of Bacterial Communities on Fe (III) Reduction and Phosphorus Availability in Sediments of the Cyanobacteria- and Macrophyte-Dominated Zones

Little is known about the effects of bacterial community on iron (Fe) and phosphorus (P) cycles in sediments under different primary producer habitats in different seasons. Lake Taihu has both the cyanobacteria- and macrophyte-dominated lake zones. In this work, the abundance and structure of bacterial community was investigated using qPCR and 16S rRNA gene high throughput sequencing, respectively. Compared with the sediments in the cyanobacteria-dominated lake zone, sediments in the macrophyte-dominated lake zone had higher TP, TOC and TN contents but lower DO and Eh values. Dissolved reactive P, dissolved Fe, and their molar ratios (Fe/P) were lower in the sediments of the cyanobacteria-dominated lake zone than those in the macrophyte-dominated lake zone. Consistent with this was the significantly lower abundance of total and typical Fe redox transforming bacteria in the sediment of the cyanobacteria-dominated lake zone than those in the macrophyte-dominated lake zone. Correlation analyses also revealed positive influence of abundances of total bacteria and typical Fe reducing bacteria on dissolved Fe and Fe/P ratio. The results showed that, in the cyanobacteria-dominated open water zone, Acidimicrobiaceae was capable of Fe metabolism, contributing to higher P flux in summer. In the cyanobacteria-dominated bay, Sva0081 sediment group and Desulfobulbaceae could transform sulfate to sulfide, which resulted in the reduction of Fe (III), while in the macrophyte-dominated zones, Clostridium sensu stricto 1 could couple oxidation of organic carbon with the reduction of Fe (III). The present study adds new knowledge linking the bacterial communities with the physicochemical cycles of Fe and P in sediments under different primary producer habitats.

Opportunistic bacteria confer the ability to ferment prebiotic starch in the adult cystic fibrosis gut

Chronic disruption of the intestinal microbiota in adult cystic fibrosis (CF) patients is associated with local and systemic inflammation, and has been linked to the risk of serious comorbidities. Supplementation with high amylose maize starch (HAMS) might provide clinical benefit by promoting commensal bacteria and the biosynthesis of immunomodulatory metabolites. However, whether the disrupted CF gut microbiota has the capacity to utilise these substrates is not known. We combined metagenomic sequencing, in vitro fermentation, amplicon sequencing, and metabolomics to define the characteristics of the faecal microbiota in adult CF patients and assess HAMS fermentation capacity. Compared to healthy controls, the faecal metagenome of adult CF patients had reduced bacterial diversity and prevalence of commensal fermentative clades. In vitro fermentation models seeded with CF faecal slurries exhibited reduced acetate levels compared to healthy control reactions, but comparable levels of butyrate and propionate. While the commensal genus Faecalibacterium was strongly associated with short chain fatty acid (SCFA) production by healthy microbiota, it was displaced in this role by Clostridium sensu stricto 1 in the microbiota of CF patients. A subset of CF reactions exhibited enterococcal overgrowth, resulting in lactate accumulation and reduced SCFA biosynthesis. The addition of healthy microbiota to CF faecal slurries failed to displace predominant CF taxa, or substantially influence metabolite biosynthesis. Despite significant microbiota disruption, the adult CF gut microbiota retains the capacity to exploit HAMS. Our findings highlight the potential for taxa associated with the altered CF gut microbiotato mediate prebiotic effects in microbial systems subject to ongoing perturbation, irrespective of the depletion of common commensal clades.

Genome-Based Comparison of Clostridioides difficile: Average Amino Acid Identity Analysis of Core Genomes

Infections due to Clostridioides difficile (previously known as Clostridium difficile) are a major problem in hospitals, where cases can be caused by community-acquired strains as well as by nosocomial spread. Whole genome sequences from clinical samples contain a lot of information but that needs to be analyzed and compared in such a way that the outcome is useful for clinicians or epidemiologists. Here, we compare 663 public available complete genome sequences of C. difficile using average amino acid identity (AAI) scores. This analysis revealed that most of these genomes (640, 96.5%) clearly belong to the same species, while the remaining 23 genomes produce four distinct clusters within the Clostridioides genus. The main C. difficile cluster can be further divided into sub-clusters, depending on the chosen cutoff. We demonstrate that MLST, either based on partial or full gene-length, results in biased estimates of genetic differences and does not capture the true degree of similarity or differences of complete genomes. Presence of genes coding for C. difficile toxins A and B (ToxA/B), as well as the binary C. difficile toxin (CDT), was deduced from their unique PfamA domain architectures. Out of the 663 C. difficile genomes, 535 (80.7%) contained at least one copy of ToxA or ToxB, while these genes were missing from 128 genomes. Although some clusters were enriched for toxin presence, these genes are variably present in a given genetic background. The CDT genes were found in 191 genomes, which were restricted to a few clusters only, and only one cluster lacked the toxin A/B genes consistently. A total of 310 genomes contained ToxA/B without CDT (47%). Further, published metagenomic data from stools were used to assess the presence of C. difficile sequences in blinded cases of C. difficile infection (CDI) and controls, to test if metagenomic analysis is sensitive enough to detect the pathogen, and to establish strain relationships between cases from the same hospital. We conclude that metagenomics can contribute to the identification of CDI and can assist in characterization of the most probable causative strain in CDI patients.

Novel Insight from Computational Virtual Screening Depict the Binding Potential of Selected Phytotherapeutics Against Probable Drug Targets of Clostridium difficile

This study explores computational screening and molecular docking approaches to screen novel herbal therapeutics against probable drug targets of Clostridium difficile. The essential genes were predicted by comparative genome analysis of C. difficile and best homologous organisms using BLAST search at database of essential genes (DEG). The functions of these genes in various metabolic pathways were predicted and some of these genes were considered as potential targets. Three major proteins were selected as putative targets, namely permease IIC component, ABC transporter and histidine kinase. The three-dimensional structures of these targets were predicted by molecular modelling. The herbal bioactive compounds were screened by computer-aided virtual screening and binding potentials against the drug targets were predicted by molecular docking. Quercetin present in Psidium guajava (binding energy of -9.1 kcal/mol), Ellagic acid found in Punica granatum and Psidium guajava (binding energy -9.0 kcal/mol) and Curcumin, present in Curcuma longa (binding energy -7.8 kcal/mol) demonstrated minimum binding energy and more number of interacting residues with the drug targets. Further, comparative study revealed that phytoligands demonstrated better binding affinities to the drug targets in comparison with usual ligands. Thus, this investigation explores the therapeutic probabilities of selected phytoligands against the putative drug targets of C. difficile.

Bioaugmentation with Clostridium tyrobutyricum to improve butyric acid production through direct rice straw bioconversion

One-pot bioconversion is an economically attractive biorefinery strategy to reduce enzyme consumption. Direct conversion of lignocellulosic biomass for butyric acid production is still challenging because of competition among microorganisms. In a consolidated hydrolysis/fermentation bioprocessing (CBP) the microbial structure may eventually prefer the production of caproic acid rather than butyric acid production. This paper presents a new bioaugmentation approach for high butyric acid production from rice straw. By dosing 0.03 g/L of Clostridium tyrobutyricum ATCC 25755 in the CBP, an increase of 226% higher butyric acid was yielded. The selectivity and concentration also increased to 60.7% and 18.05 g/L, respectively. DNA-sequencing confirmed the shift of bacterial community in the augmented CBP. Butyric acid producer was enriched in the bioaugmented bacterial community and the bacteria related to long chain acids production was degenerated. The findings may be useful in future research and process design to enhance productivity of desired bio-products.

Exogenous N-acyl homoserine lactones facilitate microbial adhesion of high ammonia nitrogen wastewater on biocarrier surfaces

Startup of biofilm process triggered by initial adhesion of bacteria is difficult in high ammonia nitrogen wastewater treatment. In this study, the influence of two commonly used N-acyl homoserine lactones (AHLs), N-Hexanoyl-l-homoserine lactone (C6-HSL) and N-Octanoyl-l-homoserine lactone (C8-HSL), on the adhesion of soluble macromolecules and bacteria in four types of high ammonia nitrogen wastewater to surfaces of model biocarriers (i.e. polystyrene, polyamide and polyethylene terephthalate) was investigated by using a quartz crystal microbalance with dissipation (QCM-D) monitoring technology. Results showed that the adhesion was enhanced by the addition of exogenous AHLs and there was more microbial retention attributed by C8-HSL. Greater deposition amount was generally found on PS and better enhanced performances of the adhesion were found on PA surface. Furthermore, viscoelastic film formed under synchronous high-low salinity and organic content and dominant bacteria of real wastewater determined the role of exogenous AHLs. The method of adding moderate amount of exogenous AHLs into bioreactors has important implications for accelerating the startup process treating high ammonia nitrogen wastewater by biofilm process.

A Phylogenomic and Molecular Markers Based Analysis of the Class Acidimicrobiia

Recent metagenomic surveys of microbial community suggested that species associated with the class Acidimicrobiia are abundant in diverse aquatic environments such as acidic mine water, waste water sludge, freshwater, or marine habitats, but very few species have been cultivated and characterized. The current taxonomic framework of Acidimicrobiia is solely based on 16S rRNA sequence analysis of few cultivable representatives, and no molecular, biochemical, or physiological characteristics are known that can distinguish species of this class from the other bacteria. This study reports the phylogenomic analysis for 20 sequenced members of this class and reveals another three major lineages in addition to the two recognized families. Comparative analysis of the sequenced Acidimicrobiia species identified 15 conserved signature indels (CSIs) in widely distributed proteins and 26 conserved signature proteins (CSPs) that are either specific to this class as a whole or to its major lineages. This study represents the most comprehensive phylogenetic analysis of the class Acidimicrobiia and the identified CSIs and CSPs provide useful molecular markers for the identification and delineation of species belonging to this class or its subgroups.

The effect of Clostridium butyricum on symptoms and fecal microbiota in diarrhea-dominant irritable bowel syndrome: a randomized, double-blind, placebo-controlled trial

Irritable bowel syndrome (IBS) is a common disorder in gastrointestinal system and impairs the quality of life of the patients. Clostridium butyricum (CB) is a probiotics that has been used in several gastrointestinal diseases. The efficacy of CB in treating IBS is still unknown. This prospective, multi-centre, randomized, double-blind, placebo-controlled trial aimed to assess the efficacy and safety of CB in treating diarrhea-predominant IBS (IBS-D) and analyze the fecal microbiota after treatment. Two hundred patients with IBS-D were recruited and were given CB or placebo for 4 weeks. End points included change from baseline in IBS symptoms, quality of life, stool consistency and frequency. Compared with placebo, CB is effective in improving the overall IBS-D symptoms (-62.12 ± 74.00 vs. -40.74 ± 63.67, P = 0.038) as well as quality of life (7.232 ± 14.06 vs. 3.159 ± 11.73, P = 0.032) and stool frequency (-1.602 ± 1.416 vs. -1.086 ± 1.644, P = 0.035). The responder rates are found higher in CB compared with the placebo (44.76% vs. 30.53%, P = 0.042). The change in fecal microbiota was analyzed and function pathways of CB in treating IBS-D were predicted. In conclusion, CB improves overall symptoms, quality of life and stool frequency in IBS-D patients and is considered to be used as a probiotics in treating IBS-D clinically.

The Gut Microbiome in Neuromyelitis Optica

Neuromyelitis optica (NMO) is a rare, disabling, sometimes fatal central nervous system inflammatory demyelinating disease that is associated with antibodies ("NMO IgG") that target the water channel protein aquaporin-4 (AQP4) expressed on astrocytes. There is considerable interest in identifying environmental triggers that may elicit production of NMO IgG by AQP4-reactive B cells. Although NMO is considered principally a humoral autoimmune disease, antibodies of NMO IgG are IgG1, a T-cell-dependent immunoglobulin subclass, indicating that AQP4-reactive T cells have a pivotal role in NMO pathogenesis. When AQP4-specific proliferative T cells were first identified in patients with NMO it was discovered that T cells recognizing the dominant AQP4 T-cell epitope exhibited a T helper 17 (Th17) phenotype and displayed cross-reactivity to a homologous peptide sequence within a protein of Clostridium perfringens, a commensal bacterium found in human gut flora. The initial analysis of gut microbiota in NMO demonstrated that, in comparison to healthy controls (HC) and patients with multiple sclerosis, the microbiome of NMO is distinct. Remarkably, C. perfringens was the second most significantly enriched taxon in NMO, and among bacteria identified at the species level, C. perfringens was the one most highly associated with NMO. Those discoveries, along with evidence that certain Clostridia in the gut can regulate the balance between regulatory T cells and Th17 cells, indicate that gut microbiota, and possibly C. perfringens itself, could participate in NMO pathogenesis. Collectively, the evidence linking microbiota to humoral and cellular immunity in NMO underscores the importance for further investigating this relationship.

Comparative pathogenomics of Clostridium tetani

Clostridium tetani and Clostridium botulinum produce two of the most potent neurotoxins known, tetanus neurotoxin and botulinum neurotoxin, respectively. Extensive biochemical and genetic investigation has been devoted to identifying and characterizing various C. botulinum strains. Less effort has been focused on studying C. tetani likely because recently sequenced strains of C. tetani show much less genetic diversity than C. botulinum strains and because widespread vaccination efforts have reduced the public health threat from tetanus. Our aim was to acquire genomic data on the U.S. vaccine strain of C. tetani to better understand its genetic relationship to previously published genomic data from European vaccine strains. We performed high throughput genomic sequence analysis on two wild-type and two vaccine C. tetani strains. Comparative genomic analysis was performed using these and previously published genomic data for seven other C. tetani strains. Our analysis focused on single nucleotide polymorphisms (SNP) and four distinct constituents of the mobile genome (mobilome): a hypervariable flagellar glycosylation island region, five conserved bacteriophage insertion regions, variations in three CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) systems, and a single plasmid. Intact type IA and IB CRISPR/Cas systems were within 10 of 11 strains. A type IIIA CRISPR/Cas system was present in two strains. Phage infection histories derived from CRISPR-Cas sequences indicate C. tetani encounters phages common among commensal gut bacteria and soil-borne organisms consistent with C. tetani distribution in nature. All vaccine strains form a clade distinct from currently sequenced wild type strains when considering variations in these mobile elements. SNP, flagellar glycosylation island, prophage content and CRISPR/Cas phylogenic histories provide tentative evidence suggesting vaccine and wild type strains share a common ancestor.

Variation of bacterial communities in water and sediments during the decomposition of Microcystis biomass

The bacterial community composition in water and sediment samples during the decomposition of Microcystis biomass were analyzed using the 454 pyrosequencing technique. We found dramatic shifts in the bacterial community composition of water and sediments after the addition of Microcystis biomass. Among all the detected phyla, only Firmicutes was found to be dominant in both water and sediment samples. The genus Clostridium sensu stricto was the absolutely dominant group in Firmicutes and showed drastic variations with incubation time during the decomposition process. Peak values in relative abundance of Clostridium sensu stricto appeared in the first few days for water and sediment samples. Environmental factors such as pH, dissolved oxygen (DO), and dissolved organic carbon (DOC) in water samples showed drastic variations during the decomposing process, which might be the prominent forces driving the variation of bacterial communities. The abundant genus, Clostridium sensu stricto, were thought to be well adapted to higher DOC and turbidity and lower pH and DO conditions. Compared with the sediment samples, the decomposition of Microcystis biomass had greater influence on the bacterial community composition in water and Clostridium sensu stricto might play important roles in the process of Microcystis biomass decomposition.

Variability in DPA and Calcium Content in the Spores of Clostridium Species

Spores of a number of clostridial species, and their resistance to thermal treatment is a major concern for the food industry. Spore resistance to wet heat is related to the level of spore hydration, which is inversely correlated with the content of calcium and dipicolinic acid (DPA) in the spore core. It is widely believed that the accumulation of DPA and calcium in the spore core is a fundamental component of the sporulation process for all endospore forming species. We have noticed heterogeneity in the heat resistance capacity and overall DPA/calcium content among the spores of several species belonging to Clostridium sensu stricto group: two C. acetobutylicum strains (DSM 792 and 1731), two C. beijerinckii strains (DSM 791 and NCIMB 8052), and a C. collagenovorans strain (DSM 3089). A C. beijerinckii strain (DSM 791) and a C. acetobutylicum strain (DSM 792) display low Ca and DPA levels. In addition, these two species, with the lowest average Ca/DPA content amongst the strains considered, also exhibit minimal heat resistance. There appears to be no correlation between the Ca/DPA content and the phylogenetic distribution of the C. acetobutylicum and C. beijerinckii species based either on the 16S rRNA or the spoVA gene. This finding suggests that a subset of Clostridium sensu stricto species produce spores with low resistance to wet heat. Additionally, analysis of individual spores using STEM-EDS and STXM revealed that DPA and calcium levels can also vary amongst individual spores in a single spore population.

Priority of the genus name Clostridium Prazmowski 1880 (Approved Lists 1980) vs Sarcina Goodsir 1842 (Approved Lists 1980) and the creation of the illegitimate combinations Clostridium maximum (Lindner 1888) Lawson and Rainey 2016 and Clostridium ventriculi (Goodsir 1842) Lawson and Rainey 2016 that may not be used

In a recent publication that attempts to deal with the growing problem of taxa being added to the genus Clostridium that are outside of Clostridium (16S rRNA) group I, a solution is proposed that seeks to limit the genus Clostridium Prazmowski 1880 (Approved Lists 1980) to a small number of species 'related' to the type species, Clostridium butyricum Prazmowski 1880 (Approved Lists 1980). It has been proposed that this genus should also include members of the genus Sarcina Goodsir 1842 (Approved Lists 1980), Sarcinamaxima Lindner 1888 (Approved Lists 1980) and Sarcinaventriculi Goodsir 1842 (Approved Lists 1980), the latter being the nomenclatural type of the genus Sarcina Goodsir 1842 (Approved Lists 1980). In making proposals to treat the genus name Sarcina Goodsir 1842 (Approved Lists 1980) as a synonym of ClostridiumPrazmowski 1880 (Approved Lists 1980), reference is made to the wording of the International Code of Nomenclature of Bacteria. However, while that wording is factually correct, other parts of the Code are relevant to this issue and clearly indicate that the proposed course of action is not sanctioned by texts that have not been directly made reference to. Rather than avoiding confusion it has been contributed to, and it is necessary to document where the problems lie.

Impact of genomics on the understanding of microbial evolution and classification: the importance of Darwin's views on classification

Analyses of genome sequences, by some approaches, suggest that the widespread occurrence of horizontal gene transfers (HGTs) in prokaryotes disguises their evolutionary relationships and have led to questioning of the Darwinian model of evolution for prokaryotes. These inferences are critically examined in the light of comparative genome analysis, characteristic synapomorphies, phylogenetic trees and Darwin's views on examining evolutionary relationships. Genome sequences are enabling discovery of numerous molecular markers (synapomorphies) such as conserved signature indels (CSIs) and conserved signature proteins (CSPs), which are distinctive characteristics of different prokaryotic taxa. Based on these molecular markers, exhibiting high degree of specificity and predictive ability, numerous prokaryotic taxa of different ranks, currently identified based on the 16S rRNA gene trees, can now be reliably demarcated in molecular terms. Within all studied groups, multiple CSIs and CSPs have been identified for successive nested clades providing reliable information regarding their hierarchical relationships and these inferences are not affected by HGTs. These results strongly support Darwin's views on evolution and classification and supplement the current phylogenetic framework based on 16S rRNA in important respects. The identified molecular markers provide important means for developing novel diagnostics, therapeutics and for functional studies providing important insights regarding prokaryotic taxa.