Bacterial Production Research Articles

A small intestinal bile acid modulates the gut microbiome to improve host metabolic phenotypes following bariatric surgery

Bariatric surgical procedures such as sleeve gastrectomy (SG) provide effective type 2 diabetes (T2D) remission in human patients. Previous work demonstrated that gastrointestinal levels of the bacterial metabolite lithocholic acid (LCA) are decreased after SG in mice and humans. Here, we show that LCA worsens glucose tolerance and impairs whole-body metabolism. We also show that taurodeoxycholic acid (TDCA), which is the only bile acid whose concentration increases in the murine small intestine post-SG, suppresses the bacterial bile acid-inducible (bai) operon and production of LCA both invitro and invivo. Treatment of diet-induced obese mice with TDCA reduces LCA levels and leads to microbiome-dependent improvements in glucose handling. Moreover, TDCA abundance is decreased in small intestinal tissue from T2D patients. This work reveals that TDCA is an endogenous inhibitor of LCA production and suggests that TDCA may contribute to the glucoregulatory effects of bariatric surgery.

Electrochemically synthesized nanostructured gold-bismuth as novel sensor for efficient determination of cefotaxime in aqueous media

Antibiotics are crucial due to their widespread use in human and veterinary medicine. Cefotaxime, a third-generation cephalosporin, prevents bacterial production and treats central nervous system infections like meningitis and septicemia. This study developed a novel electrochemical sensor for detecting Cefotaxime (CFTX) by electrodepositing gold-bismuth nanoparticles (Au-Bi NPs) on a carbon paste electrode (CPE). The electrochemical parameters were optimized for the successful deposition of Au-BiNPs. Morphological and X-ray diffraction (XRD) analyses revealed nanoparticle clusters of cubic Au and stacked monoclinic BiNPs on the CPE surface, with crystallite sizes of 7.5 and 6.3 nm, respectively. Cyclic voltammetry (CV) showed that the sensor had superior electrochemical activity for CFTX oxidation compared to bare CPE, BiNPs/CPE, and AuNPs/CPE, mainly due to the synergetic effect of Au-Bi nanoparticles. Electrochemical impedance spectroscopy (EIS) indicated minimal resistance to electron transfer at Au-BiNPs/CPE. Voltammetric investigations revealed a diffusion-controlled electrooxidation process involving two protons and two electrons, influenced by solution pH and scan rate. The sensor displayed excellent analytical parameters for CFTX detection, including a wide linear range (0.5 μM to 20 μM), high sensitivity (4.55 μAμM−1 cm−2), and a low detection limit (0.094 μM). Density Functional Theory (DFT) calculations provided theoretical insights into the sensor’s performance. The sensor also showed excellent reproducibility, repeatability (RSD values of 3.74 % and 1.71 %, respectively), and long-term stability of about one month, offering a new method for accurate and sensitive CFTX detection.

Migrating ripples create streambed heterogeneity altering microbial diversity and metabolic activity

AbstractSandy sediments of lowland streams are typically transported at low flow in the form of migrating ripples. In these bedforms, microbial communities spanning all trophic guilds (heterotrophic bacteria, fungi, photoautotrophic and phagotrophic protists) are exposed to highly frequent moving–resting cycles of sediment grains. Up to date, it is unknown to what extent ripple migration impacts community metabolism and composition as well as the vertical zonation of sediment‐associated multitrophic microbial communities compared to stationary sediments. We hypothesize that, as a result of mechanical abrasion and limited light supply, migrating ripple sediments have lower microbial abundance, diversity, metabolism and resource acquisition and no vertical zonation compared to stationary sediments. We collected samples from five lowland streams in north‐eastern Germany between May and June 2020. The coarser and better sorted sediments of migrating ripples had a higher oxygen concentration and less organic matter than stationary sediments. Photosynthetic pigments, potential extracellular enzyme activities, bacterial cell counts, and fungal gene copies were lower in migrating ripples than in stationary sediments. In contrast, cell‐specific bacterial production was higher in migrating ripples. Metabarcoding revealed that bedform migration was important in shaping the community structure of bacteria, fungi, and phagotrophic protists. Dry mass‐related net community production, respiration, and bacterial production were higher in superficial compared to underlying layers irrespective of sediment transport. By modulating the abundance, diversity, and structure of different trophic guilds of microbial communities and their resource acquisition, migrating bedforms create streambed heterogeneity, shaping regional biodiversity and the flow of matter through the benthic food web.

Pigments from pathogenic bacteria: a comprehensive update on recent advances.

Bacterial pigments stand out as exceptional natural bioactive compounds with versatile functionalities. The pigments represent molecules from distinct chemical categories including terpenes, terpenoids, carotenoids, pyridine, pyrrole, indole, and phenazines, which are synthesized by diverse groups of bacteria. Their spectrum of physiological activities encompasses bioactive potentials that often confer fitness advantages to facilitate the survival of bacteria amid challenging environmental conditions. A large proportion of such pigments are produced by bacterial pathogens mostly as secondary metabolites. Their multifaceted properties augment potential applications in biomedical, food, pharmaceutical, textile, paint industries, bioremediation, and in biosensor development. Apart from possessing a less detrimental impact on health with environmentally beneficial attributes, tractable and scalable production strategies render bacterial pigments a sustainable option for novel biotechnological exploration for untapped discoveries. The review offers a comprehensive account of physiological role of pigments from bacterial pathogens, production strategies, and potential applications in various biomedical and biotechnological fields. Alongside, the prospect of combining bacterial pigment research with cutting-edge approaches like nanotechnology has been discussed to highlight future endeavours.

Identification of pigmented extremophilic bacteria from mangrove soil with antibiofilm activity on food pathogens

Mangrove ecosystems and associated microorganisms are always a source of curiosity for researchers. Pigment producing bacteria were isolated from the mangrove soil in Kadamakkudi, Cochin, Kerala. The bacteria were biochemically identified and by 16 S rRNA gene sequence. The pigments extracted had been tested for antibiofilm activity against food pathogens Pseudomonas aeruginosa (NCIM 2863), Klebsiella pneumoniae (NCIM 5215), and Escherichia coli (NCIM 2343). Antibiofilm activity was further confirmed by fluorescent and scanning electron microscopy. Six yellow-orange pigmented bacteria (KDR2, KDR3, KDR7, KDR8, KDR14 and KDS1) were isolated. KDR2 was identified as Cellulosimicrobium funkei, KDR7 and KDS1 as Cytobacillus depressus, KDR8 as Bacillus aquimaris, and KDR3 and KDR14 as Halobacillus sp. All of these organisms are known to be extremophiles. The UV-Visible absorption spectrum of all the pigments ranged from 400 nm to 550 nm with different absorbance maxima. All the pigments showed antibiofilm activity against the food pathogens tested.

Diverse bacterial consortia: key drivers of rhizosoil fertility modulating microbiome functions, plant physiology, nutrition, and soybean grain yield

Soybean cultivation in tropical regions relies on symbioses with nitrogen-fixing Bradyrhizobium and plant growth-promoting bacteria (PGPBs), reducing environmental impacts of N fertilizers and pesticides. We evaluate the effects of soybean inoculation with different bacterial consortia combined with PGPBs or microbial secondary metabolites (MSMs) on rhizosoil chemistry, plant physiology, plant nutrition, grain yield, and rhizosphere microbial functions under field conditions over three growing seasons with four treatments: standard inoculation of Bradyrhizobium japonicum and Bradyrhizobium diazoefficiens consortium (SI); SI plus foliar spraying with Bacillus subtilis (SI + Bs); SI plus foliar spraying with Azospirillum brasilense (SI + Az); and SI plus seed application of MSMs enriched in lipo-chitooligosaccharides extracted from B. diazoefficiens and Rhizobium tropici (SI + MSM). Rhizosphere microbial composition, diversity, and function was assessed by metagenomics. The relationships between rhizosoil chemistry, plant nutrition, grain yield, and the abundance of microbial taxa and functions were determined by generalized joint attribute modeling. The bacterial consortia had the most significant impact on rhizosphere soil fertility, which in turn affected the bacterial community, plant physiology, nutrient availability, and production. Cluster analysis identified microbial groups and functions correlated with shifts in rhizosoil chemistry and plant nutrition. Bacterial consortia positively modulated specific genera and functional pathways involved in biosynthesis of plant secondary metabolites, amino acids, lipopolysaccharides, photosynthesis, bacterial secretion systems, and sulfur metabolism. The effects of the bacterial consortia on the soybean holobiont, particularly the rhizomicrobiome and rhizosoil fertility, highlight the importance of selecting appropriate consortia for desired outcomes. These findings have implications for microbial-based agricultural practices that enhance crop productivity, quality, and sustainability.Graphical

Clostridial Myonecrosis: A Comprehensive Review of Toxin Pathophysiology and Management Strategies.

Clostridial myonecrosis, commonly known as gas gangrene (GG), is a rapidly progressing and potentially fatal bacterial infection that primarily affects muscle and soft tissue. In the United States, the incidence of GG is roughly 1000 cases per year, while, in developing countries, the incidence is higher. This condition is most often caused by Clostridium perfringens, a Gram-positive, spore-forming anaerobic bacterium widely distributed in the environment, although other Clostridium species have also been reported to cause GG. The CP genome contains over 200 transport-related genes, including ABC transporters, which facilitate the uptake of sugars, amino acids, nucleotides, and ions from the host environment. There are two main subtypes of GG: traumatic GG, resulting from injuries that introduce Clostridium spores into deep tissue, where anaerobic conditions allow for bacterial growth and toxin production, and spontaneous GG, which is rarer and often occurs in immunocompromised patients. Clostridium species produce various toxins (e.g., alpha, theta, beta) that induce specific downstream signaling changes in cellular pathways, causing apoptosis or severe, fatal immunological conditions. For example, the Clostridium perfringens alpha toxin (CPA) targets the host cell's plasma membrane, hydrolyzing sphingomyelin and phosphatidylcholine, which triggers necrosis and apoptosis. The clinical manifestations of clostridial myonecrosis vary. Some patients experience the sudden onset of severe pain, swelling, and muscle tenderness, with the infection progressing rapidly to widespread tissue necrosis, systemic toxicity, and, if untreated, death. Other patients present with discharge, pain, and features of cellulitis. The diagnosis of GG primarily involves clinical evaluation, imaging studies such as X-rays, computer tomography (CT) scans, and culture. The treatment of GG involves surgical exploration, broad-spectrum antibiotics, antitoxin, and hyperbaric oxygen therapy, which is considered an adjunctive treatment to inhibit anaerobic bacterial growth and enhance the antibiotic efficacy. Early recognition and prompt, comprehensive treatment are critical to improving the outcomes for patients affected by this severe and life-threatening condition.

Propolis: as an Additive in Bacterial Cellulose Production

Propolis: as an Additive in Bacterial Cellulose Production

D-Methionine-induced DNases disperse established Burkholderia pseudomallei biofilms and promotes ceftazidime susceptibility

Burkholderia pseudomallei biofilm is correlated with pathogenesis, antibiotic resistance, and relapsing cases of melioidosis, leading to challenges in clinical management. There is increasing interest in employing biofilm dispersal agents as adjunctive treatments for biofilm-associated infections. Methionine (Met) has shown promise as an anti-biofilm agent by inducing bacterial DNase production, resulting in the degradation of extracellular DNA (eDNA) and dispersion of bacterial biofilm. In this study, we investigated the impact of 0.05–50 μM D-Met and L-Met on the 24-h established biofilm of a clinical isolate, B. pseudomallei H777. Our findings revealed the ability of D-Met and L-Met to disperse the established biofilm in a non-dose-dependent manner accompanied by eDNA depletion. Real-time PCR analysis further identified an up-regulation of bacterial nuclease genes, including recJ, eddB, nth, xth, and recD, in the presence of 0.05 μM D-Met. Similarly, recJ and eddB in B. pseudomallei were up-regulated in response to the presence of 0.05 μM L-Met. Notably, D-Met enhanced the susceptibility of B. pseudomallei H777 biofilm cells to ceftazidime. Our findings indicate a correlation between methionine supplementation and the up-regulation of nuclease genes, leading to eDNA depletion and the dispersal of preformed B. pseudomallei H777 biofilm. This enhances the susceptibility of biofilm cells to ceftazidime, showing promise in combating biofilm-associated B. pseudomallei infections.

Production optimization and antioxidant potential of exopolysaccharide produced by a moderately halophilic bacterium Virgibacillus dokdonensis VITP14

This study aimed to enhance the extracellular polymeric substances (EPS) production of Virgibacillus dokdonensis VITP14 and explore its antioxidant potential. EPS and biomass production by VITP14 strain were studied under different culture parameters and media compositions using one factor at a time method. Among different nutrient sources, glucose and peptone were identified as suitable carbon and nitrogen sources. Furthermore, the maximum EPS production was observed at 5% of inoculum size, 5 g/L of NaCl, and 96 h of fermentation. Response surface methodology was employed to augment EPS production and investigate the optimal levels of nutrient sources with their interaction. The strain was observed to produce actual maximum EPS of about 26.4 g/L for finalized optimum medium containing glucose 20 g/L, peptone 10 g/L, and NaCl 50 g/L while the predicted maximum EPS was 26.5 g/L. There was a nine fold increase in EPS production after optimization study. Additionally, EPS has exhibited significant scavenging, reducing, and chelating potential (>85%) at their higher concentration. This study imparts valuable insights into optimizing moderately halophilic bacterial EPS production and evaluating its natural antioxidant properties. According to findings, V. dokdonensis VITP14 was a promising isolate that will provide significant benefits to biopolymer producing industries.

Bacterially expressed full length Hemagglutinin of Avian Influenza Virus H5N1 forms oligomers and exhibits hemagglutination

Avian influenza poses a significant global health threat, with the potential for widespread pandemics and devastating consequences. Hemagglutinin (HA), a critical surface glycoprotein of influenza viruses, plays a pivotal role in viral entry and serves as a primary target for subunit vaccine development. In this study, we successfully cloned, expressed, and purified hemagglutinin from the circulating strain of H5N1 influenza virus using a robust molecular biology approach. The cloning process involved insertion of the synthetic HA gene into the pET21b vector, confirmed through double digestion and sequencing. SDS-PAGE analysis confirmed the presence of the expected 60 kDa protein band post-induction. Following expression, the protein was subjected to purification via Ni-NTA affinity chromatography, yielding pure protein fractions. Native PAGE analysis confirmed the protein's oligomeric forms, essential for optimal antigenicity. Western blot analysis further validated protein identity using anti-His and anti-HA antibodies. MALDI-TOF analysis confirmed the protein's sequence integrity, while hemagglutination assay demonstrated its biological activity in binding to N-acetyl neuraminic acid. These findings underscore the potential of recombinant hemagglutinin as a valuable antigen for diagnosis and biochemical assays as well as for vaccine development against avian influenza. In conclusion, this study represents a critical guide for bacterial production of H5N1 HA, which can be a cost-effective and simpler strategy compared to mammalian protein expression. Further research into optimizing vaccine candidates and production methods will be essential in combating the ongoing threat of avian influenza pandemics.

Identification of Kibdelomycin and Related Biosynthetic Gene Clusters and Characterization of the C-Branching of Amycolose.

Many bacterial natural products contain C-branched sugars, including components from the outer cell wall or antibiotically active metabolites. The enzymatic C-branching of keto sugars leading to longer side chains (≥C2) is catalyzed by thiamine diphosphate (ThDP)-dependent enzymes. Chiral tertiary α-hydroxy ketones are formed in this process. The ThDP-dependent enzymes that catalyze C-branching reactions belong to one of three enzymatic superfamilies: decarboxylases, transketolases, and α-ketoacid dehydrogenases 2, but branching of keto sugars has only been demonstrated for decarboxylases. In this study, we showed that an α-ketoacid dehydrogenase is responsible for C-branching of the deoxyketo sugar amycolose in the biosynthesis of kibdelomycin in Kibdelosporangium sp. MA7385. In addition, we characterized an amino transferase in the same biosynthetic gene cluster (BGC) that accepts a sterically demanding tertiary α-hydroxy ketone in a downstream reaction. Subsequently, we identified approximately 400 similar BGCs in silico, suggesting that there is a large diversity of possible ThDP-dependent enzymes catalyzing the C-branching of keto sugars and subsequent modifications.

The effectiveness of garlic extracts on biogenic amine formation by foodborne pathogens and fish spoilage bacteria

SummaryImpacts of aqueous and ethanolic extracts of garlic were investigated in suppressing bacterial growth and biogenic amine (BA) formation by selected foodborne pathogens (Candida albicans, Salmonella paratyphi A, Escherichia coli and Staphylococcus aureus) and fish spoilage bacteria (Enterococcus faecalis, Photobacterium damselae and Pseudomonas luteola). The spread‐plate method was used to monitor bacterial growth in histidine decarboxylase broth (HDB), whereas the rapid high‐performance liquid chromatographic (HPLC) method was used for BA analysis. Bacterial growth and their ammonia and BA production were monitored using HDB. The results showed that bacterial growth on HDB was in the range from 9.13, for P. luteola, to 9.54 log CFU (colony‐forming units) mL−1, for S. aureus and C. albicans. The presence of garlic extracts in HDB resulted considerably in lowering bacterial growth and BA formation (P < 0.05). The highest inhibitory activities of ethanolic and water garlic extracts were obtained for Gram‐positive S. aureus with 1.4 and 1.5 logarithmic reduction on bacterial growth, followed by Gram‐negative Salmonella Paratyphi A and E. coli. Application of garlic extracts, mainly ethanolic ones, showed a significant inhibitory effect on bacterial ammonia production, with 4‐100‐fold lower ammonia accumulation (P < 0.05). Bacteria produced all tested BAs, mainly dopamine, agmatine and tryptamine. The highest levels of histamine and tyramine (61.99 and 36.45 mg L−1) were produced by S. aureus. In the presence of aqueous or ethanolic garlic extracts, putrescine production by E. faecalis was around 110‐fold lower than that of the control group. Results revealed that both garlic extracts are potent antimicrobials that can control the growth of foodborne pathogens and their harmful BA formation.

Hyaluronic acid production by Streptococcus zooepidemicus MW26985 using potato peel waste hydrolyzate.

In this research, we examined the production of hyaluronic acid (HA) by Streptococcus zooepidemicus strain MW26985 using different substrates and potato peel waste (PPW) as an affordable substrate. First, culture medium components, including carbon and nitrogen sources, were optimized for bacterial HA production. Five different carbon sources (glucose, sucrose, lactose, sago starch, and potato starch, at a concentration of 30g/L) and three distinct nitrogen sources (peptone, yeast extract, and ammonium sulfate, at a concentration of 10g/L) were investigated. Glucose, among the carbon sources, and yeast extract, among nitrogen sources, produced the most HA which was determined as 1.41g/L. Afterward, potato peel sugars were extracted by dilute acid and enzymatic hydrolysis and then employed as a cost-effective carbon source for the growth of S. zooepidemicus. Based on the results, the fermentation process yielded 0.59g/L HA from potato peel sugars through acid hydrolysis and 0.92g/L HA from those released by enzymatic hydrolysis. The supplementation of both hydrolyzates with glucose as an additional carbon source enhanced HA production to 0.95g/L and 1.18g/L using acidic and enzymatic hydrolyzates, respectively. The cetyltrimethylammonium bromide (CTAB) turbidimetric method was used to evaluate the concentration of HA in the fermentation broth using the colorimetric method. Also, the peaks observed by Fourier transform infrared (FTIR) spectroscopy confirmed that the exopolysaccharide (EPS) was composed of HA. These observations demonstrate that potato peel residues can be a novel alternative as a carbon source for the economical production of HA by S. zooepidemicus.

Effects of bacterial products, inflammatory mediators, and insulin on the phosphorylation of RPS6 and STAT3 in equine epidermal cells

Effects of bacterial products, inflammatory mediators, and insulin on the phosphorylation of <scp>RPS6</scp> and <scp>STAT3</scp> in equine epidermal cells

Bacterial Filaments Induced by Antibiotic Minimal Inhibitory Concentrations in Persister Cells

Background: The ability of minor subpopulations among clonal populations to survive antibiotics is referred to as bacterial persistence. It is believed that persisters come from latent cells, where antibiotic target areas are less active and incapable of being affected. Objective: 112 clinical Escherichia coli isolates were acquired out of diverse medical samples and genetically identified using the uspA gene, which is part of the housekeeping genes. Methods: The examination of persister cells was carried out by subjecting isolates of E. coli in the exponential phase with high dose of ciprofloxacin (20 fold MIC) and calculating the surviving persister cells using CFU (colony forming units) counts. The detection and measurement of bacterial filament production was done using scanning electron and light microscopy. Results: Results showed that the bacterial filament cells kept on lengthen but cease to divide (no septa formation) at sub-minimal inhibitory doses of ciprofloxacin. Persistent isolates were shown to exhibit a wide range of form and size variations, with cells up to 4.5 times longer than usual. Conclusions: The results showed the importance of antibiotic stress on persisted cells that result in the production of filaments as a means of survival and the need to examine these rare phenotypic variations. These occurrences may be the beginning of the spread of bacterial resistance.

Sigma S Involved in Bacterial Survival of Ralstonia pseudosolanacearum

Ralstonia pseudosolanacearum, a plant pathogenic bacterium that can survive for a long time in soil and water, causes lethal wilt in the Solanaceae family. Sigma S is a part of the RNA polymerase complex, which regulates gene expression during bacterial stress response or stationary phase. In this study, we investigated the role of sigma S in R. pseudosolanacearum under stress conditions using a rpoS-defective mutant strain of R. pseudosolanacearum and its wild-type strain. The phenotypes of rpoS-defective mutant were complemented by introducing the original rpoS gene. There were no differences observed in bacterial growth rate and exopolysaccharide production between the wild-type strain and the rpoS mutant. However, the wild-type strain responded more sensitively to nutrient deficiency compared to the mutant strain. Under the nutrient deficiency, the rpoS mutant maintained a high bacterial viability for a longer period, while the viability of the wild-type strain declined rapidly. Furthermore, a significant difference in pH was observed between the culture supernatant of the wild-type strain and the mutant strain. The pH of the culture supernatant for the wild-type strain decreased rapidly during bacterial growth, leading to medium acidification. The rapid decline in the wild-type strain’s viability may be associated with medium acidification and bacterial sensitivity to acidity during transition to the stationary phase. Interestingly, the rpoS mutant strain cannot utilize acetic acid, D-alanine, D-trehalose, and L-histidine. These results suggest that sigma S of R. pseudosolanacearum regulates the production or utilization of organic acids and controls cell death during stationary phase under nutrient deficiency.

Optimization of Culture Conditions and Characterization of Pectinase from Isolated Bacteria and Application in Juice Clarificationz`

Microbial pectinase has high demand in different industries. Pectinase producing bacteria were isolated and purified from soil samples and screened by primary and secondary screening for pectinase production. Out of the 13 bacterial samples, sample 4.1(S4.1) showed consistent enzyme activity. Optimum production of pectinase was high when incubated at 24-hour at 37°C with 2% substrate concentration maintaining pH6. Optimum pectinase activity was observed at temperature 37°C and pH 6. Cu++ was found as activator and Zn++, Ca++ as inhibitors of pectinases. The values for Km and Vmax were found to be 1.181mg/ml and 471.69µM/min respectively. Pectinase was efficiently partially purified by 90% acetone saturation. Specific enzyme activity for partially purified enzyme with acetone was 96870 U/mg and purification fold was 35.41. The utilization of low-cost agro-industrial wastes as substrates has been preferable in pectinase production. The sweet lemon and lemon fruit peel powder was observed good substrate for pectinase production. Furthermore, the yield and clarity of sweet lemon juice increased as the concentration of pectinase increased, indicating its potential use in juice processing. Experimental results suggest pectinases from S4.1 was of high value and can be utilized for fruit juice clarification.

Chemoenzymatic synthesis of 7-chloro-4-Dimethylallyl-L-Tryptophan, a fragment of krisynomycin

The krisynomycins are macrocyclic depsipeptide natural products from Streptomyces that act as imipenem potentiators against methicillin-resistant Staphylococcus aureus (MRSA). The flagship molecule of this family, krisynomycin, features a unique 7-chloro-4-dimethylallyl-l-tryptophan (7-Cl-4-Pren-Trp) fragment that is both essential for biological activity and unprecedented among bacterial natural products. In silico analysis of the putative biosynthetic gene cluster revealed an aromatic prenyltransferase and a tryptophan halogenase, though the precise reaction order en route to 7-Cl-4-Pren-Trp remained ambiguous. We report herein a brief chemoenzymatic synthesis of 7-Cl-4-Pren-Trp through a prenylation-chlorination sequence, which contains the first ever C4 prenylation of tryptophan by a bacterial enzyme. Furthermore, our efforts provide tentative evidence that the same reaction sequence is operative in the biosynthesis of krisynomycin.

Cabozantinib and nivolumab with or without live bacterial supplementation in metastatic renal cell carcinoma: a randomized phase 1 trial

Supplementation with CBM588, a bifidogenic live bacterial product, has been associated with improved clinical outcomes in persons with metastatic renal cell carcinoma (mRCC) receiving nivolumab and ipilimumab. However, its effect on those receiving tyrosine kinase inhibitor-based combinations is unknown. In this open-label, randomized, investigator-initiated, phase 1 study, 30 participants with locally advanced or mRCC with histological confirmation of clear cell, papillary or sarcomatoid component were randomized in a 2:1 fashion to receive cabozantinib (an inhibitor of vascular endothelial growth factor receptor, MET and AXL) and nivolumab (anti-programmed cell death protein 1) with or without CBM588 as first-line treatment. Metagenomic sequencing was performed on stool samples to characterize their gut microbiome at baseline and 13 weeks into treatment. The primary endpoint was a change in the relative abundance of Bifidobacterium spp.; secondary endpoints included objective response rate (ORR), progression-free survival (PFS) and toxicity profile. The primary endpoint of the study was not met and the addition of CBM588 to cabozantinib and nivolumab did not result in a difference in the relative abundance of Bifidobacterium spp. or alpha diversity (as measured by the Shannon index). However, ORR was significantly higher in participants treated with CBM588 compared to those in the control arm (14 of 19, 74% versus 2 of 10, 20%; P = 0.01). PFS at 6 months was 84% (16 of 19) and 60% (6 of 10) in the experimental and control arms, respectively. No significant difference in toxicity profile was seen between the study arms. Our results provide a preliminary signal of improved clinical activity with CBM588 in treatment-naive participants with mRCC receiving cabozantinib and nivolumab. Further investigation is needed to confirm these findings and better characterize the underlying mechanism driving this effect.ClinicalTrials.gov identifier: NCT05122546