Culture-based Approaches Research Articles

Pathogenic Escherichia coli (E. coli) food borne outbreak: Detection methods and controlling measures

Food-borne illnesses and diseases are major threats to human health. Common food borne pathogens include bacteria such as Escherichia coli Serogroup (O157), Bacillus cereus, Clostridium botulinum, Campylobacter sp., C. perfringens, some Listeria monocytogenes, Salmonella spp., Shigella spp., Staphylococcus aureus, and Vibrio spp. etc. Pathogenic E. coli infection usually causes severe diarrhea. Escherichia coli is the most common cause of acute urinary tract infections as well as urinary tract sepsis. Diarrheagenic E. coli pathotypes can be passed in the feces of humans and other animals. Safeguarding public health during mass gatherings is a big challenge. Despite the recent advances in food preservation techniques and food safety, significant disease outbreaks linked to food borne pathogens such as bacteria, fungi, and viruses still occur worldwide indicating that these pathogens still constitute significant risks to public health. However, at present the conventional method for E. coli detection requires several days, especially in cases where E. coli concentrations are low. Enrichment is a commonly used method for bacterial isolation to increase the cell counts of target bacteria. However, traditional culturing method is also a slow and laborious process requiring a series of steps and may require the use of adjunct methods (e.g. biochemical, serological, nucleic acid-based methods for conclusive identification) and can take up to a week for bacteria. The culture-based approaches coupled with other methods such as PCR, immunoassays, bacteriophages, NGS, Biosensors, and MALDI TOF MS are increasingly being used for the detection and identification of food borne pathogens. Nucleic acid-based methods such as Real-Time PCR and vPCR combined with sequencing approaches are more widely used than immunoassay and NGS-based approaches for pathogen detection. Nanobiotechnology is the latest approach for the detection of pathogens. Bacteriophages are one such unique biological entity that showed excellent host selectivity and have been actively used as recognition probes for pathogen detection. Antibiotics are efficient, powerful, and the most commonly used treatment against pathogenic E. coli. Other ways to treat or prevent E. coli contamination, such as probiotics, antimicrobial nanoparticles, and radiation treatment had been reported.

Evidence for novel polycyclic aromatic hydrocarbon degradation pathways in culturable marine isolates.

Polycyclic aromatic hydrocarbon (PAH) pollution is widespread throughout marine environments and significantly affects native flora and fauna. Investigating microbes responsible for degrading PAHs in these environments provides a greater understanding of natural attenuation in these systems. In addition, the use of culture-based approaches to inform bioinformatic and omics-based approaches is useful in identifying novel mechanisms of PAH degradation that elude genetic biomarker-based investigations. Furthermore, culture-based approaches allow for the study of PAH co-metabolism, which increasingly appears to be a prominent mechanism for PAH degradation in marine microbes.

The Microbial Diversity on the Surface of Smear-Ripened Cheeses and Its Impact on Cheese Quality and Safety.

Smear-ripened cheeses are characterized by a viscous, red-orange surface smear on their rind. It is the complex surface microbiota on the cheese rind that is responsible for the characteristic appearance of this cheese type, but also for the wide range of flavors and textures of the many varieties of smear-ripened cheeses. The surface smear microbiota also represents an important line of defense against the colonization with undesirable microorganisms through various types of interaction, such as competitive exclusion or production of antimicrobial substances. Predominant members of the surface smear microbiota are salt-tolerant yeast and bacteria of the phyla Actinobacteria, Firmicutes, and Proteobacteria. In the past, classical culture-based approaches already shed light on the composition and succession of microorganisms and their individual contribution to the typicity of this cheese type. However, during the last decade, the introduction and application of novel molecular approaches with high-resolution power provided further in-depth analysis and, thus, a much more detailed view of the composition, structure, and diversity of the cheese smear microbiota. This led to abundant novel knowledge, such as the identification of so far unknown community members. Hence, this review is summarizing the current knowledge of the diversity of the surface smear microbiota and its contribution to the quality and safety of smear-ripened cheese. If the succession or composition of the surface-smear microbiota is disturbed, cheese smear defects might occur, which may promote food safety issues. Hence, the discussion of cheese smear defects in the context of an increased understanding of the intricate surface smear ecosystem in this review may not only help in troubleshooting and quality control but also paves the way for innovations that can lead to safer, more consistent, and higher-quality smear-ripened cheeses.

Assessing Methodological Variability in Gut Microbiome Studies: Lessons from Southeast Asian for Effective Conservation Strategies

Gut microbiome studies have gained significant attention in recent years due to their potential in unveiling the role of microbial communities in animals’ health and ecological processes. However, the lack of standardized protocols in sample handling and processing across studies introduces variability, impeding the comparability of findings. This study addresses this issue by examining methodological variations in gut microbiome research on wildlife and domesticated animals in Southeast Asia. A comprehensive search of 91 relevant studies on the SCOPUS database yielded 54 suitable publications for review, encompassing diverse taxa such as invertebrates (20), fishes (7), reptiles (3), birds (5), and mammals (19). Notably, various methodological approaches were employed to characterize microbial communities, including the source of isolation, various culture-based approaches, sequencing methods, and the targeted markers. Based on the information provided in this study, future studies should strive to develop guidelines and best practices specific to gut microbiome studies. This would enhance comparability and facilitate the integration of findings. Such efforts will also advance our understanding of the microbial diversity associated with wildlife, and its potential implications for their health and conservation.

Optimization of in planta methodology for genome editing and transformation in Citrus.

Genetic transformation of many plant species relies on in vitro tissue culture-based approaches. This can be a labor-intensive process, requiring aseptic conditions and regenerating often recalcitrant species from tissue culture. Here, we have optimized an in planta transformation protocol to rapidly transform commercial citrus cultivars, bypassing the need for tissue culture. As a proof of concept, we used in planta transformation to introduce CRISPR/Cas9 constructs into Limoneira 8A Lisbon lemon and Pineapple sweet orange, cultivars that are challenging to transform with conventional techniques. Using our optimized protocol, the regeneration rate was significantly increased from 4.8% to over 95%, resulting in multiple gene-edited lines in lemon. We also successfully recovered gene-edited Pineapple sweet orange lines using this protocol; the transformation efficiency for these cultivars ranged between 0.63% and 4.17%. Remarkably, these lines were obtained within three months, making this in planta protocol a rapid methodology to obtain transformed citrus plants. This approach can rapidly and effectively introduce key genetic changes into a wide variety of citrus cultivars.

Reducing violent student behavior through culturally based counseling: Mediation analysis of the fairness

This study investigates the impact of Iso Trimorogo counseling, a culture-based counseling approach rooted in Tri Dharma Mangkunegaran Philosophy, on reducing violent behavior in high school students by fostering the character trait of fairness. The research involved 120 high school students from Central Java Province, Indonesia divided into an experimental group receiving Iso Trimorogo counseling and a control group subjected to conventional counseling methods. The efficacy of the counseling was assessed using a fairness character scale and a bullying behavior scale, administered pre- and post-treatment. The study employed bootstrapping analysis with 5000 resampling iterations, maintaining an error threshold of 5% (p < 0.005). The results indicated a significant direct effect of Iso Trimorogo counseling in diminishing violent behavior (F = 9.027) and an indirect effect through the mediation of fairness character development (F = 4.026), with a negative correlation between fairness character and violent behavior (R = 0.389). These findings underscore the importance of integrating character education, particularly focusing on fairness, in counseling strategies to effectively address violent behavior in schools. The study advocates for the adoption of culture-based counseling approaches like Iso Trimorogo in educational settings to enhance student behavior and character development.

Review on Mucormycosis

An increasing number of virulent, angioinvasive spores belonging to the order Mucorales are known to infect individuals who are immunocom promised with potentially fatal diseases. The prognosis for this debilitating infection has improved because of advances in pathophysiology understanding, early detection, and the recent development of active, nontoxic medications. However, due in part to the limited yield and complexity of culture-based and molecular diagnostic approaches, rates of delayed diagnosis and mortality remain high. Novel diagnostic techniques and efficient treatment modalities are thus desperately needed.

Virus-Induced Heritable Gene Editing in Plants.

Gene editing using clustered, regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) nuclease is an excellent tool for assessing gene function in plants. However, delivery of CRISPR/Cas-editing components into plant cells is still a major bottleneck and requires tissue culture-based approaches and regeneration of plants. To overcome this limitation, several plant viral vectors have recently been engineered to deliver single-guide RNA (sgRNA) targets into SpCas9-expressing plants. Here, we describe an optimized, step-by-step protocol based on the tobacco rattle virus (TRV)-based vector system to deliver sgRNAs fused to mobile tRNA sequences for efficient heritable editing in Nicotiana benthamiana and Arabidopsis thaliana model systems. The protocol described here could be adopted to study the function of any gene of interest.

Penile prostheses harbor biofilms driven by individual variability and manufacturer even in the absence of clinical infection.

Culture-based studies have shown that penile prostheses harbor biofilms in the presence and absence of infection, but these findings have not been adequately validated using contemporary microbiome analytic techniques. The study sought to characterize microbial biofilms of indwelling penile prosthesis devices according to patient factors, device components, manufacturer, and infection status. Upon penile prostheses surgical explantation, device biofilms were extracted, sonicated, and characterized using shotgun metagenomics and culture-based approaches. Device components were also analyzed using scanning electron microscopy. Outcomes included the presence or absence of biofilms, alpha and beta diversity, specific microbes identified and the presence of biofilm, and antibiotic resistance genes on each prosthesis component. The average age of participants from whom devices were explanted was 61 ± 11 years, and 9 (45%) of 20 had a diagnosis of diabetes mellitus. Seventeen devices were noninfected, and 3 were associated with clinical infection. Mean device indwelling time prior to explant was 5.1 ± 5.1 years. All analyzed components from 20 devices had detectable microbial biofilms, both in the presence and absence of infection. Scanning electron microscopy corroborated the presence of biofilms across device components. Significant differences between viruses, prokaryotes, and metabolic pathways were identified between individual patients, device manufacturers, and infection status. Mobiluncus curtisii was enriched in manufacturer A device biofilms relative to manufacturer B device biofilms. Bordetella bronchialis, Methylomicrobium alcaliphilum, Pseudoxanthomonas suwonensis, and Porphyrobacter sp. were enriched in manufacturer B devices relative to manufacturer A devices. The most abundant bacterial phyla were the Proteobacteria, Actinobacteria, and Firmicutes. Glycogenesis, the process of glycogen synthesis, was among the predominant metabolic pathways detected across device components. Beta diversity of bacteria, viruses, protozoa, and pathways did not differ among device components. All components of all penile prostheses removed from infected and noninfected patients have biofilms. The significance of biofilms on noninfected devices remains unknown and merits further investigation. Strengths include the multipronged approach to characterize biofilms and being the first study to include all components of penile prostheses in tandem. Limitations include the relatively few number of infected devices in the series, a relatively small subset of devices included in shotgun metagenomics analysis, and the lack of anaerobic and other expanded conditions for culture. Penile prosthesis biofilms are apparent in the presence and absence of infection, and the composition of biofilms was driven primarily by device manufacturer, individual variability, and infection, while being less impacted by device component.

Microbial pyrite formation: mineral morphology and precipitation kinetics

Pyrite (FeS2) is a mineral of wide interest due to its importance in the biogeochemical cycling of Fe and S, which is tied to those of carbon and other trace metals and nutrients. The mineral itself has potential applications as biosignatures, for environmental remediation and as semiconductors. Despite being a common authigenic mineral in sedimentary environments, most laboratory-based experiments have failed to form pyrite in microbial cultures at ambient temperatures. To fill this knowledge gap, we have employed cultivation-based approaches, using different combinations of microorganisms (Fe(III)- and S0-reducers; S0-disproportionaters) and initial Fe and S sources to identify the conditions that are optimal for pyrite formation. Scanning electron microscopy (SEM), Raman spectroscopy and X-ray diffraction (XRD) demonstrate that pyrite is not formed within ~3 years at circumneutral pH when oxidants (e.g., Fe(III) minerals, elemental sulfur, S0) are exhausted. In contrast, pyrite is formed within months when S0 and Fe(III) minerals are both present. The precipitation timescale is consistent with those expected in sedimentary environments Mansor and Fantle 2019), albeit some natural pyrite framboids are expected to form even faster Rickard 2019). The pyrite crystals formed in our experiments are in the low micrometer range, with either a spherical or euhedral morphology depending on the initial crystallinity of the supplied Fe(III) minerals. Framboids are not formed in our system, perhaps due to the relatively slow precipitation kinetics. Time-based sampling indicates mackinawite (FeS) as the first product, with rare (and minor) detection of greigite (Fe3S4) and vivianite [Fe3(PO4)2.8H2O]. We hypothesize that pyrite formation and growth proceed mainly from transformation of precursor minerals, with potential contributions via dissolution-precipitation and/or particle attachment pathways. Our preliminary study is the first step in optimizing a system for microbial pyrite formation, with the intention of investigating the properties and the reactivity of the mineral with implications for biosignatures, environmental remediation and industrial applications.

Metagenomic and Culture-Based Analyses of Microbial Communities from Petroleum Reservoirs with High-Salinity Formation Water, and Their Biotechnological Potential.

The reserves of light conditional oil in reservoirs with low-salinity formation water are decreasing worldwide, necessitating the extraction of heavy oil from petroleum reservoirs with high-salinity formation water. As the first stage of defining the microbial-enhanced oil recovery (MEOR) strategies for depleted petroleum reservoirs, microbial community composition was studied for petroleum reservoirs with high-salinity formation water located in Tatarstan (Russia) using metagenomic and culture-based approaches. Bacteria of the phyla Desulfobacterota, Halanaerobiaeota, Sinergistota, Pseudomonadota, and Bacillota were revealed using 16S rRNA-based high-throughput sequencing in halophilic microbial communities. Sulfidogenic bacteria predominated in the studied oil fields. The 75 metagenome-assembled genomes (MAGs) of prokaryotes reconstructed from water samples were assigned to 16 bacterial phyla, including Desulfobacterota, Bacillota, Pseudomonadota, Thermotogota, Actinobacteriota, Spirochaetota, and Patescibacteria, and to archaea of the phylum Halobacteriota (genus Methanohalophilus). Results of metagenomic analyses were supported by the isolation of 20 pure cultures of the genera Desulfoplanes, Halanaerobium, Geotoga, Sphaerochaeta, Tangfeifania, and Bacillus. The isolated halophilic fermentative bacteria produced oil-displacing metabolites (lower fatty acids, alcohols, and gases) from sugar-containing and proteinaceous substrates, which testify their potential for MEOR. However, organic substrates stimulated the growth of sulfidogenic bacteria, in addition to fermenters. Methods for enhanced oil recovery should therefore be developed, combining the production of oil-displacing compounds with fermentative bacteria and the suppression of sulfidogenesis.

Diversity analysis of hilsa (Tenualosa ilisha) gut microbiota using culture-dependent and culture-independent approaches.

The bacterial communities associated with the gastrointestinal tract are primarily involved in digestion, physiology and immune response against pathogenic bacteria for the overall development and health of the host. Hilsa shad (Tenualosa ilisha), a tropical anadromous fish, found predominantly in Bangladesh and India, has so far been poorly investigated for its gut bacterial communities. In this study, both culture-based and metagenomic approaches were used to detect intestinal isolates of hilsa, captured from both freshwater and seawater to investigate the community structure of intestinal microbiota. Culture-dependent approach allowed to isolate a total of 23 distinct bacterial species comprising sixteen Gram-negative, and seven Gram-positive isolates, where Proteobacteria and Firmicutes were identified as the two most dominant phyla. While metagenomic approach explored a wide range of important gastrointestinal bacteria, primarily dominated by Proteobacteria, Firmicutes and Bacteroidetes, with Proteobacteria and Firmicutes, being the most abundant in freshwater and seawater samples, respectively. A combination of these approaches provided the differential gastrointestinal-associated bacterial diversity in freshwater and seawater hilsa with the prediction of overall functional potential.

Microbiological Non-Culture-Based Methods for Diagnosing Invasive Pulmonary Aspergillosis in ICU Patients.

The diagnosis of invasive pulmonary aspergillosis (IPA) in intensive care unit (ICU) patients is crucial since most clinical signs are not specific to invasive fungal infections. To detect an IPA, different criteria should be considered. Next to host factors and radiological signs, microbiological criteria should be fulfilled. For microbiological diagnostics, different methods are available. Next to the conventional culture-based approaches like staining and culture, non-culture-based methods can increase sensitivity and improve time-to-result. Besides fungal biomarkers, like galactomannan and (1→3)-β-D-glucan as nonspecific tools, molecular-based methods can also offer detection of resistance determinants. The detection of novel biomarkers or targets is promising. In this review, we evaluate and discuss the value of non-culture-based microbiological methods (galactomannan, (1→3)-β-D-glucan, Aspergillus PCR, new biomarker/targets) for diagnosing IPA in ICU patients.

A comparative approach to confirm antibiotic-resistant microbes in the cryosphere.

Antibiotic-resistant microbes pose one of the biggest challenges of the current century. While areas with proximity to human impact are closely studied, a lot is yet to learn about antimicrobial resistance in remote regions like the cryosphere. Nowadays, antibiotic (AB) resistance is considered a pollution that has reached the Earth's most pristine areas. However, monitoring of resistant environmental bacteria therein faces several challenges that inhibit scientific progress in this field. Due to many cultivation-based antibiotic susceptibility tests being optimized for mesophilic pathogenic microorganisms, many researchers opt for expensive molecular biological approaches to detect antibiotic resistance in the cryosphere. However, some disadvantages of these methods prohibit effective comprehensive monitoring of resistant bacteria in pristine areas, hence we suggest established cultivation-based approaches when looking for antimicrobial resistance in the cryosphere. In this study, we compared two common antibiotic susceptibility tests and optimized them to meet the needs of psychrophilic microorganisms. The resulting cultures thereof originated from cryospheric habitats with differing anthropogenic impacts. The results show that these methods are applicable to detect antibiotic resistance in cryospheric habitats and could potentially increase the comparability between studies.

Large-Scale Integration of Amplicon Data Reveals Massive Diversity within Saprospirales, Mostly Originating from Saline Environments.

The order Saprospirales, a group of bacteria involved in complex degradation pathways, comprises three officially described families: Saprospiraceae, Lewinellaceae, and Haliscomenobacteraceae. These collectively contain 17 genera and 31 species. The current knowledge on Saprospirales diversity is the product of traditional isolation methods, with the inherited limitations of culture-based approaches. This study utilized the extensive information available in public sequence repositories combined with recent analytical tools to evaluate the global evidence-based diversity of the Saprospirales order. Our analysis resulted in 1183 novel molecular families, 15,033 novel molecular genera, and 188 K novel molecular species. Of those, 7 novel families, 464 novel genera, and 1565 species appeared in abundances at ≥0.1%. Saprospirales were detected in various environments, such as saline water, freshwater, soil, various hosts, wastewater treatment plants, and other bioreactors. Overall, saline water was the environment showing the highest prevalence of Saprospirales, with bioreactors and wastewater treatment plants being the environments where they occurred with the highest abundance. Lewinellaceae was the family containing the majority of the most prevalent species detected, while Saprospiraceae was the family with the majority of the most abundant species found. This analysis should prime researchers to further explore, in a more targeted way, the Saprospirales proportion of microbial dark matter.

Identification of fungal associates of the swamp helmet orchid (Corybas carsei), a threatened (nationally critical) species

ABSTRACT Corybas carsei is one of New Zealand’s most endangered orchids, with a single remaining population in the Whangamarino Wetland (North Island). Although orchid mycorrhizae have proved a critical aspect of orchid conservation globally, until now mycorrhizal fungi of C. carsei have not been identified or utilised for conservation. This study investigated fungal associates of C. carsei using three culture-based approaches: fungi grown directly from fragments of root tissue, from pelotons isolated from root-collars, and directly from macerated protocorm tissue. Fungi were cultured and identified as a diverse array of fungi through Sanger sequencing of the internal transcribed spacer region. This included the fungus Pleurotus purpureo-olivaceus (Basidiomycota; Agaricales), which belongs to a genus containing putative orchid mycorrhizal fungi, and the ericoid mycorrhizal fungus Oidiodendron eucalypti (Ascomycota; Leotiomycetes incertae sedis). No Rhizoctonia-like fungi, typical of orchid mycorrhizae, were found through any approach and fungi cultured in the present study likely represent endophytes, rather than mycorrhizal fungi. The potential of C. carsei having unculturable mycorrhizal associations, and the challenge this presents to conservation efforts, is discussed.

Identification of Antibiotic Resistance Gene Hosts in Treatment Wetlands Using a Single-Cell Based High-Throughput Approach

Determining the prevalence of antimicrobial resistance (AMR) in non-clinical settings is vital for better management of the global AMR crisis. Untreated and even treated wastewaters are important sources that release AMR into the environment. Methodologically, it is difficult to generate a comprehensive in situ profile of antibiotic resistance gene hosts. Here, we used epicPCR (emulsion, paired isolation, and concatenation PCR) as a cultivation-independent method to reveal the host profiles of the AMR indicator genes intI1, sul1, sul2, and dfrA1 in two constructed wetlands treating municipal wastewater. Overall, the epicPCR analysis revealed a profile of AMR indicator gene hosts that is consistent with literature data from cultivation-based approaches. Most carriers of antibiotic resistance (AR) genes and likely of class 1 integrons belonged to the Gammaproteobateria, particularly the Burkholderiaceae and Rhodocyclaceae families, followed by members of the Campylobacterota, Desulfobacterota, and Firmicutes. The analysis also identified several novel hosts for the indicator genes widely distributed in the wetlands, including the genera Legionella and Ralstonia. Therefore, the application of epicPCR has produced an expanded insight into the in situ indicator gene host profile, while highlighting the role of the environment as a reservoir for AMR.

Yeast diversity in pit mud and related volatile compounds in fermented grains of chinese strong-flavour liquor

Chinese strong-flavour liquor is produced via a traditional solid-state fermentation strategy facilitated by live microorganisms in pit mud-based cellars. For the present analysis, pit mud samples from different spatial locations within fermentation cellars were collected, and the yeast communities therein were assessed via culture-based and denaturing gradient gel electrophoresis (DGGE) approaches. These analyses revealed significant differences in the composition of yeast communities present in different layers of pit mud. In total, 29 different yeast species were detected, and principal component analyses revealed clear differences in microbial diversity in pit mud samples taken from different cellar locations. Culture-dependent strategies similarly detected 20 different yeast species in these samples. However, while Geotrichum silvicola, Torulaspora delbrueckii, Hanseniaspora uvarum, Saturnispora silvae, Issatchenkia orientalis, Candida mucifera, Kazachstania barnettii, Cyberlindnera jadinii, Hanseniaspora spp., Alternaria tenuissima, Cryptococcus laurentii, Metschnikowia spp., and Rhodotorula dairenensis were detected via a PCR-DGGE approach, they were not detectable in culture-dependent analyses. In contrast, culture-based approaches led to the identification of Schizosaccharomyces pombe and Debaryomyces hansenii in these pit mud samples, whereas they were not detected using DGGE fingerprints profiles. An additional HS-SPME-GC-MS-based analysis of the volatile compounds present in fermented grains samples led to the identification of 66 such compounds, with the highest levels of volatile acids, esters, and alcohols being detected in fermented grains from lower layer samples. A canonical correspondence analysis (CCA) suggested they were significant correlations between pit mud yeast communities and associated volatile compounds in fermented grains.

A culture-based assessment of the microbiota of conventional and free-range chicken meat from Irish processing facilities.

Chicken meat is the most popularly consumed meat worldwide, with free-range and ethically produced meat a growing market among consumers. However, poultry is frequently contaminated with spoilage microbes and zoonotic pathogens which impact the shelf-life and safety of the raw product, constituting a health risk to consumers. The free-range broiler microbiota is subject to various influences during rearing such as direct exposure to the external environment and wildlife which are not experienced during conventional rearing practices. Using culture-based microbiology approaches, this study aimed to determine whether there is a detectable difference in the microbiota from conventional and free-range broilers from selected Irish processing plants. This was done through analysis of the microbiological status of bone-in chicken thighs over the duration of the meat shelf-life. It was found that the shelf-life of these products was 10 days from arrival in the laboratory, with no statistically significant difference (P > 0.05) evident between free-range and conventionally raised chicken meat. A significant difference, however, was established in the presence of pathogenesis-associated genera in different meat processors. These results reinforce past findings which indicate that the processing environment and storage during shelf-life are key determinants of the microflora of chicken products reaching the consumer.

Insight into gut dysbiosis of patients with inflammatory bowel disease and ischemic colitis.

The collection of whole microbial communities (bacteria, archaea, fungi, and viruses) together constitutes the gut microbiome. Diet, age, stress, host genetics, and diseases cause increases or decreases in the relative abundance and diversity of bacterial species (dysbiosis). We aimed to investigate the gut microbial composition at different taxonomic levels of healthy controls (HCs) with active Crohn's disease (CD), ulcerative colitis (UC), and ischemic colitis (IC) using culture- and non-culture-based approaches and identify biomarkers to discriminate CD, UC, or IC. We determined the specific changes in the gut microbial profile using culture-independent (16S rRNA gene amplicon sequencing) as well as culture-based (culturomic) approaches. Biomarkers were validated using quantitative Real-Time PCR (qPCR). In both methods, bacterial diversity and species richness decreased in disease-associated conditions compared with that in HCs. Highly reduced abundance of Faecalibacterium prausnitzii and Prevotella sp. and an increased abundance of potentially pathogenic bacteria such as Enterococcus faecium, Enterococcus faecalis, and Escherichia coli in all CD, UC, or IC conditions were observed. We noted a high abundance of Latilactobacillus sakei in CD patients; Ligilactobacillus ruminis in UC patients; and Enterococcus faecium, Escherichia coli, and Enterococcus faecalis in IC patients. Highly reduced abundance of Faecalibacterium prausnitzii in all cases, and increased abundance of Latilactobacillus sakei and Enterococcus faecium in CD, Ligilactobacillus ruminis and Enterococcus faecium in UC, and Enterococcus faecium, Escherichia coli, and Enterococcus faecalis in IC could be biomarkers for CD, UC, and IC, respectively. These biomarkers may help in IBD (CD or UC) and IC diagnosis.