16S rRNA Research Articles

Gut Microbiome Profiles in Colorectal Cancer Patients in Iraq

Colorectal cancer (CRC) is the third most commonly diagnosed cancer globally, and is a significant contributor to both morbidity and mortality rates. Emerging research has promptly highlighted the potential role of the gut microbiome in the development and progression of CRC. This study aims to investigate the differences in gut microbiota between CRC patients and healthy individuals in Iraq, using 16S rRNA metagenomic sequencing on Illumina NovaSeq (PE250-Seq). A total of 21 stool samples were analyzed: 12 from early-stage CRC patients and nine from healthy controls. Bacterial DNA was extracted, followed by 16S rRNA amplicon sequencing to profile the microbial communities. The results indicated significant differences between the fecal microbiome of the two groups. Remarkably, CRC patients exhibited a marked reduction in Bacteroidota and an increase in Verrucomicrobiota compared to healthy controls. At the genus level, Prevotella, Faecalibacterium, Roseburia, Barnesiella, Eubacterium Lachnospiraceae_UCG_004, and Lachnospira were significantly less abundant in CRC patients compared to the healthy individuals, while Actinomyces, Monoglobus, Desulfovibrio, Akkermansia, and Bacteroides were highly enriched. In addition, diversity analyses further indicated decreased α-diversity and distinct β-diversity patterns in the CRC patients, suggesting significant shifts in the gut microbial composition. These findings underscore the potential of microbiome-based diagnostics and therapeutic strategies, with microbial alterations serving as biomarkers for CRC diagnosis. Further research needs to focus on elucidating the causal relationships and therapeutic potential of these microbiome changes in CRC management.

First Report of Bacterial Wilt of Ginger Caused by Ralstonia pseudosolanacearum in the Continental United States

Ginger (Zingiber officinale) is an herbaceous perennial in the Zingiberaceae family grown primarily in tropical to subtropical biomes as a culinary spice, a traditional medicine, and a landscaping plant. While ginger grows at soil temperatures above 20°C, several farmers in the upper Midwestern US farmers grows short-season ginger in high tunnels. In 2023 and 2024, growers in southeastern Minnesota reported a new disease of ginger. USDA traced the origin of the ginger rhizomes imported by these growers to Peru (Soto-Heredia et al., 2024). Plants exhibited wilting, chlorosis, pseudostem collapse, and plant death. Rhizomes were squishy with a fetid, rotting odor. Disease incidence ranged from scattered plants to 50% of the crop. Symptomatic samples tested positive for Ralstonia solanacearum species complex (RSSC) using AgDia ImmunoStrips. Rhizome tissue extracts plated onto CPG + 1% tetrazolium chloride agar and mSMSA agar produced irregular, round-to-fluidal white colonies with pink centers after 48 h of incubation at 28°C (Kelman 1954; Engelbrecht 1994). Diagnostic RSSC phylotype-specific multiplex PCR primers Nmult21:1F, Nmult21:2F, Nmult23:AF, Nmult22:InF, Nmult22:RR, and 759f/760r confirmed isolate identity; two isolates (UMN24-1, UMN24-2) yielded bands at 280 bp and 144 bp, identifying them as RSSC and phylotype I respectively (Fegan and Prior 2005; Opina et al. 1997). Additionally, 16S rRNA PCR of these isolates was sequenced using primers 27F (5’-AGAGTTTGATCMTGGCTCAG-3’)/1492R (5’-TACGGYTACCTTGTTACGACTT-3’) and shared >99% identity (isolate UMN24-1: 99.00% 27F, 99.53% 1492R; UMN24-2: 99.32% 1492R) with R. pseudosolanacearum (Rps) strain Gj707 (GenBank CP104497.1). Eight ginger plants in individual pots were grown in a Conviron growth chamber (28°C, 250 μmol/m2/s, 16 h photoperiod) and inoculated at the six-leaf stage (6 weeks old) by pipetting 109 CFU of the isolate, UMN24-1, suspended in sterile water into a 30°angled 1 cm incision on the pseudostem. We scored disease incidence based on wilted leaves per total leaves on each plant for 14 days post inoculation (dpi). While control plants remained healthy, inoculated plants showed symptoms (wilting, vascular discoloration, chlorosis) at 4 dpi, were 100% wilted by 6 dpi, and all pseudostems completely collapsed by 11 dpi (Fig. S1). Bacteria recovered from the inoculated plants matched the original isolate in appearance and positively identified as RSSC phylotype I using the PCR analyses described above. To confirm taxonomic identification of UMN24-1, the complete genome of this isolate was sequenced using hybrid Illumina and Oxford Nanopore sequencing (NCBI BioProject ID PRJNA1178296, release date upon publication) (Fig. S2). Average nucleotide identity (ANI) analysis of UMN24-1 using KBase’s FastANI app reported 99.8% identity shared with Japanese RSSC phylotype I strain MAFF311693 (GenBank GCF 015698385.1). We also sequenced UMN24-2, and its phylogenetic analysis revealed that the two isolates are clonal (Fig. S2). Hence, we did not submit its sequence to the NCBI. This marks the first documented case of Rps in ginger in the United States. Similar to bacterial wilt in ginger closely related crop like turmeric has been repeatedly reported in northern Europe in recent years (EPPO 2024). While RSSC phylotype I is geographically limited by its minimal cold tolerance, the emergence of a pathogen with a potentially broad host range has worrying implications in a changing climate.

Gut dysbiosis is associated with difficult-to-treat rheumatoid arthritis

BackgroundDifficult-to-treat rheumatoid arthritis (D2T RA) refers to a subset of patients who fail to achieve adequate disease control after the use of two or more biological or targeted synthetic disease-modifying antirheumatic drugs (b/tsDMARDs) with different mechanisms of action, while maintaining active inflammatory disease. This presents a therapeutic challenge and highlights the need to explore contributing factors such as the potential role of the gut microbiota. Therefore, the aim of this study was to analyze the gut microbiota and inflammation in patients with D2T RA in comparison to patients with easy-to-treat RA (E2T RA).ObjectiveTo analyze the gut microbiota and inflammation in patients with D2T RA.MethodsWe performed an observational study of a prospective cohort between 2007 and 2011 and analyzed the gut microbiota. In 2022, we identified 2 extreme patient phenotypes: (1) D2T RA, which was defined as failure of ≥2 biological or targeted synthetic disease-modifying antirheumatic drugs (b/tsDMARDs) (with different mechanisms of action) plus signs of active disease; and (2) easy-to-treat RA (E2T RA), i.e., stable disease managed with a single treatment. The gut microbiota was analyzed using 16S rRNA gene sequencing; bioinformatics analysis was performed using QIIME2, and its functionality was inferred through PICRUSt. We recorded data on clinical findings, inflammation, and cytokines. A Cox multivariate analysis was performed to identify factors related to D2T RA.ResultsThe study population comprised 39 patients: 13 (33%) with D2T RA and 26 (66%) with E2T RA. The families Lachnospiraceae and Pasteurellaceae, and their genera Coprococcus and Haemophilus were more abundant in E2T RA patients, while the genus Megasphaera was more abundant in D2T RA patients. The Firmicutes/Bacteroidetes ratio decreased in D2T RA patients. The metabolic profile of the gut microbiota was characterized by differences in Degradation/Utilization/Assimilation pathway and the Biosynthesis pathway. The factors associated with D2T RA were inflammatory activity according to DAS28-ESR (HR, 2.649; p = 0.013), prednisone (HR, 3.794; p = 0.008), and the Firmicutes/Bacteroidetes ratio (HR, 0.288; p = 0.033).ConclusionThe composition of the gut microbiota of patients with D2T RA differed from that of E2T RA patients, as did the metabolic pathways.

The Positive Regulatory Effect of DBT on Lipid Metabolism in Postpartum Dairy Cows

Background/Objectives: The transition from a non-lactating to a lactating state is a critical period for lipid metabolism in dairy cows. Danggui Buxue Tang (DBT), stimulating energy metabolism, ameliorates diseases related to lipid metabolism disorders and is expected to be an effective supplement for alleviating excessive lipid mobilisation in periparturient dairy cows. This study aimed to investigate the effects of supplemental DBT on serum biochemical indices, faecal microbial communities, and plasma metabolites in dairy cows. Methods: Thirty cows were randomly divided into three groups: H-DBT group, L-DBT group, and control group. DBT administration was started on the day of calving and continued once daily for seven days. Faecal and blood samples were collected on calving day, 7 days after calving, and 14 days after calving. The levels of serum biochemical indices were measured at three time points in the three groups using commercial kits. Cows in the H-DBT group and control group were selected for metabolome and 16S rRNA amplicon sequencing. Results: Our research shows that, in dairy cows 7 days postpartum, DBT significantly reduced serum 3-hydroxybutyric acid (BHB) concentrations and the number of cows with BHB concentrations ≥ 1 mmol/L. Additionally, DBT increased serum total cholesterol contents at both 7 and 14 days postpartum. Analysis of the microbiota community showed that DBT modulated the composition and structure of the hindgut microbiota. Metabolomic analysis revealed decreased plasma acetylcarnitine, 2-hydroxybutyric acid, and BHB levels 7 days postpartum, whereas the TCA cycle was enhanced. At 14 days postpartum, DBT altered the plasma bile acid profile, especially glycine-conjugated bile acids, including GCDCA, GUDCA, and GDCA. Correlation analyses showed that the relative abundances of Bacillus, Solibacillus, Dorea, and Romboutsia were strongly correlated with the differential metabolites, which is crucial for the beneficial effects of DBT. Conclusions: DBT improves energy status and lipid metabolism in postpartum dairy cows by modulating hindgut microbiota and serum lipid metabolites.

Effects of Chinese Herbal Medicines on Growth Performance, Antioxidant Capacity, and Liver and Intestinal Health of Hybrid Snakehead (Channa maculata ♀ × Channa. argus ♂)

Chinese herbal medicines have become a new green feed additive in the aquaculture industry. The aim of this study is to investigate the effects of traditional Chinese herbal medicines (Isatidis radix, Forsythia suspensa, and Schisandra chinensis) on the growth performance, antioxidant capacity, and intestinal microbiota of hybrid snakehead (Channa maculata ♀ × Channa argus ♂). A total of 600 fish (mean weight: 15.85 ± 0.15 g) were randomly assigned to five groups, including the control group (CG), I. radix extract group (IRE), F. suspensa extract group (FSE), S. chinensis extract group (SCE), and the Chinese herbal medicine mixture group (CHMM; a mixture of extracts of I. radix, F. suspensa, and S. chinensis at the ratio of 1:1:1) for 6 weeks. The results show that the IRE-supplemented diet improved the survival rate (SR), feed efficiency ratio (FE), and condition factor (CF) compared to others. Compared to the control group, the activity of superoxide dismutase (SOD) in plasma and intestine was significantly increased in the FSE and CHMM groups, whereas the content of malondialdehyde (MDA) in plasma and liver was significantly reduced in the SCE group. A 16s rRNA analysis indicates that dietary supplementation with FSE significantly promoted the proliferation of Fusobacteriota, while IRE supplementation increased the alpha diversity of intestinal bacteria. In conclusion, the addition of I. radix to the diet of hybrid snakehead improves growth, antioxidant capacity, and liver and intestine health, and modulates the intestinal microbiota of snakehead positively.

16S rRNA and metabolomics reveal the key microbes and key metabolites that regulate diarrhea in Holstein male calves

IntroductionDiarrhea is a prevalent disease among calves, which significantly hinders their growth and development, thereby impacting farm productivity and revenue. This study aimed to investigate the impact of diarrhea on calf growth.MethodsHolstein male calves with similar birth weight (39.5 ± 4.2 kg) were included in this study, and key parameters such as fecal score, diarrhea incidence, and growth performance from birth to weaning were measured. Rectal fecal samples from both diarrheic (n = 24) and healthy calves (n = 24) aged 1–4 weeks were analyzed using 16S rRNA gene sequencing and untargeted metabolomics.ResultsOur findings indicated a high prevalence of diarrhea among calves between 1–4 weeks of age on pasture, which led to a marked decrease in growth performance, including average daily gain. At the genus level, the relative abundance of GCA-900066575 in one-week-old diarrheic calves was significantly higher; Escherichia-Shigella and Pseudoflavonifractor were more abundant in two-week-old calves; while Tyzzerella and Lachnospiraceae_UCG-004 increased significantly in four-week-old calves, and correlated negatively with average daily gain, suggesting that these bacteria may promote the occurrence of diarrhea. Correlation analysis revealed that fecal metabolites such as arachidonic acid, cis-vaccenic acid, oleic acid, choline, creatinine, and others were significantly negatively correlated with calf growth performance and were significantly increased in diarrheic calves. WGNCA identified that dark magenta module metabolites were significantly associated with diarrhea traits from 1–4 weeks. Thirteen metabolites, including glycerophospholipids (such as 1-stearoyl-2-hydroxy-sn-glycero-3-phosphoethanolamine), fatty acids (such as dodecanoic acid), and arachidonic acid, were positively correlated with GCA-900066575, Escherichia-shigella, Tyzzerella, and Clostridium_butyricum, but negatively correlated with UBA1819, Lachnoclostridium_sp_YL32, and Clostridium_scindens.DiscussionTherefore, GCA-900066575, Escherichia-shigella, Lachnospiraceae_UCG-004, and Tyzzerella are likely key bacterial genera causing diarrhea in calves, while arachidonic acid, glycerol phospholipids, and fatty acids are critical metabolites associated with this condition. These alterations in the fecal microbiota and metabolite composition were found to be the principal contributors to growth retardation in diarrheic calves.

Resistance to medically important antimicrobials in broiler and layer farms in Cameroon and its relation with biosecurity and antimicrobial use

IntroductionPoultry production accounts for 42% of Cameroonian meat production. However, infectious diseases represent the main hindrance in this sector, resulting in overuse and misuse of antimicrobials that can contribute to the emergence and dissemination of antimicrobial resistance (AMR). This study aimed to evaluate the prevalence of antimicrobial resistance genes (ARGs) conferring resistance to carbapenems (blaVIM-2 and blaNDM), (fluoro) quinolones (qnrS, qnrA, and qnrB), polymyxins (mcr1 to mcr5), and macrolides (ermA and ermB) in the poultry farm environment. Additionally, the study examined the relationship between these ARGs and biosecurity implementation, as well as farmers’ knowledge, attitudes, and practices toward antimicrobial use (AMU) and AMR, including their perception of AMR risk.Materials and methodsFecal, drinking water, and biofilm samples from drinking water pipelines were collected from 15 poultry farms and subsequently analyzed by real-time PCR and 16S rRNA NGS.ResultsAll samples tested positive for genes conferring resistance to (fluoro) quinolones, 97.8% to macrolides, 64.4% to polymyxins, and 11.1% to carbapenems. Of concern, more than half of the samples (64.4%) showed a multi-drug resistance (MDR) pattern (i.e., resistance to ≥3 antimicrobial classes). Drinking water and biofilm microbial communities significantly differed from the one of the fecal samples, both in term of diversity (α-diversity) and composition (β-diversity). Furthermore, opportunistic pathogens (i.e., Comamonadaceae and Sphingomonadaceae) were among the most abundant bacteria in drinking water and biofilm. The level of biosecurity implementation was intermediate, while the knowledge and attitude of poultry farmers toward AMU were insufficient and unsuitable, respectively. Good practices toward AMU were found to be correlated with a reduction in polymyxins and MDR.DiscussionThis study provides valuable information on resistance to medically important antimicrobials in poultry production in Cameroon and highlights their potential impact on human and environmental health.

Margaropus Karsch, 1879 is not closely related to Boophilus Curtice, 1891 (Acari: Ixodidae)

Margaropus Karsch, 1879 and Boophilus Curtice, 1891 have been thought to be sister-taxa for over 75 years since these ticks share features like circular spiracles, no festoons, no distinct grooves behind the anus and one-host life cycles. We inferred the first phylogeny with Margaropus from 4,218 bp of mitochondrial (cox 1, 12S) and nuclear DNA (ITS2, 18S rRNA). Margaropus is not the sister-group to Boophilus or even closely related to Boophilus, but rather Margaropus is either the sister-group to, or embedded in, the genus Rhipicephalus.

Ecological and Functional Changes in the Hindgut Microbiome of Holstein Cows at High Altitudes

The extreme environmental conditions of the Qinhai–Tibetan Plateau (QTP) challenge livestock survival and productivity, yet little is known about how high-altitude environments impact the gut microbiota of dairy cows. To fill this gap, we systematically investigated the differences in the hindgut microbiome between 87 plateau Holstein cows and 72 plain Holstein cows using 16S rRNA gene sequencing. Our analysis revealed that the hindgut microbiota of the plateau group exhibited lower species richness but higher evenness than that in the plain group. Additionally, significant separation in hindgut microbiota composition between the two groups was observed based on altitude, while parity, days in milk, and age did not show a comparable impact. Moreover, altitude had a lasting impact on bacterial communities and their co-occurrence networks, resulting in reduced microbial interactions and lower modularity in the plateau group. Furthermore, we identified four key microbial taxa, the Bacteroidaceae and Rikenellaceae families, as well as the Prevotella and Treponema genera, which were associated with the regulation of carbohydrate digestion and energy metabolism and might help the Holstein cows adapt to the plateau environment. Our findings provide insights into strategies for enhancing the adaptability of dairy cows to high-altitude environments through microbiota modulation, which could ultimately contribute to improving livestock management and sustainability in these extreme environments.

Probiotic characterisation of lactic acid bacteria isolated from pickles and their potential application as presumptive probiotic starter culture in cucumber pickles

Abstract This study aimed to isolate lactic acid bacteria (LAB) from traditional pickles, analyse their probiotic properties, identify them and evaluate their potential use in the production of cucumber pickles. The majority of the isolates (65) demonstrated survival at pH 3.0, while only three isolates exhibited this ability at pH 2.0. All isolates were resistant to 0.3% and 1% bile salts and survived at 1.5% (v/v) NaCl. However, the majority of isolates exhibited survival at 10% (v/v) NaCl (73 isolates), phenol (0.4%) (64 isolates), and pepsin (81 isolates) and pancreatin presence (78 isolates). The majority of the isolates demonstrated susceptibility to antibiotics and exhibited antimicrobial activities. Furthermore, some isolates demonstrated limited proteolytic and β-galactosidase activities, with the limited proteolytic activity being particularly beneficial for contributing to positive sensorial properties in this study. Following the evaluation of the probiotic test results, selected isolates were identified as Lactiplantibacillus plantarum, Lactiplantibacillus pentosus, Levilactobacillus brevis, Lentilactobacillus parabuchneri and Pediococcus parvulus based on 16S rRNA sequence analysis. Cucumber pickles were then produced with presumptive probiotics (L. brevis T7, L. parabuchneri T10, L. plantarum T12, and P. parvulus T13) in both single and mixed cell forms, fermented for 15 days and stored at 4 °C for 5 weeks. The results demonstrated that cucumber pickles contained > 6 log CFU/g of presumptive probiotics at the end of fermentation. Sensory analysis results showed that cucumber pickles enriched with presumptive probiotics were acceptable compared to the negative control sample (spontaneously fermented). The findings also highlight the functional potential of the samples, with PS3 offering benefits for lactose-intolerant individuals and PS2 demonstrating antimicrobial activity. It is possible to offer cucumber pickles to consumers as an alternative probiotic product; however, further research is required to ascertain the viability of probiotics over an extended period.

Isolation and Characterization of Lactic Acid Bacteria: A Strategy to Produce Inoculum for Forage Ensiling

Purpose: Sri Lankan dairy sector faces challenges due to seasonal variability and suboptimal quality of forage for dairy cattle feeding. While silage offers year-round availability of forage, concerns arise regarding potential quality degradation during forage ensiling. Microbial inoculants are utilized to expedite the ensiling and minimize quality deterioration. This study involves the isolation and characterization of lactic acid bacteria (LAB) from silage, with the aim of identifying potential candidates to be used as silage inoculants.Research Method: Lactobacillus were isolated from 10 silage samples of each forage type: sorghum, maize, and guinea grass. They were characterized using the 16S rRNA gene sequencing procedure. The anaerobic sugar fermentation ability of the isolated LAB was evaluated by inoculating them into sterilized sugar solutions, and measuring the titratable acidity (TA) and pH value over time.Findings: The isolates were identified to be non-motile, non-spore-forming and Gram-positive rods. Further, they tested negative for catalase, triple sugar iron, citrate, urease, indole, gelatine hydrolysis, motility, and oxidase tests. The LAB isolated from guinea grass, sorghum, and maize corresponded to Lactobacillus oris, Lactobacillus rhamnosus, and Lactobacillus plantarum, respectively. The TA in all inoculated solutions was higher compared to the control (0.55-0.66% vs. 0.48%), with L. plantarum showing the highest TA (0.66%) at 30 hours incubation. Additionally, all sugar solutions treated with LAB isolates exhibited a lower pH value at 30 hours compared to the control (4.70-5.07 vs. 5.75). Notably, L. plantarum demonstrated the most significant pH value reduction at 18 hours (5.85 vs. 6.29-6.64).Value: Lactobacillus oris, L. rhamnosus, and L. plantarum, isolated from guinea grass, sorghum, and maize silage, respectively, have the potential to be developed as inoculants for ensiling forage.

Host-microbe multi-omics and succinotype profiling have prognostic value for future relapse in patients with inflammatory bowel disease

ABSTRACT Crohn’s disease (CD) and ulcerative colitis (UC) are chronic relapsing inflammatory bowel disorders (IBD), the pathogenesis of which is uncertain but includes genetic susceptibility factors, immune-mediated tissue injury and environmental influences, most of which appear to act via the gut microbiome. We hypothesized that host-microbe alterations could be used to prognostically stratify patients experiencing relapses up to four years after endoscopy. We therefore examined multiple omics data, including published and new datasets, generated from paired inflamed and non-inflamed mucosal biopsies from 142 patients with IBD (54 CD; 88 UC) and from 34 control (non-diseased) biopsies. The relapse-predictive potential of 16S rRNA gene and transcript amplicons (standing and active microbiota) were investigated along with host transcriptomics, epigenomics and genetics. While standard single-omics analysis could not distinguish between patients who relapsed and those that remained in remission within four years of colonoscopy, we did find an association between the number of flares and a patient’s succinotype. Our multi-omics machine learning approach was also able to predict relapse when combining features from the microbiome and human host. Therefore multi-omics, rather than single omics, better predicts relapse within 4 years of colonoscopy, while a patient’s succinotype is associated with a higher frequency of relapses.

Seasonal Dynamics of the Bacterial Community in Lake Urmia, a Hypersaline Ecosystem

Lake Urmia is one of the world’s most unique and hypersaline aquatic ecosystems. The aim of this study was to investigate the diversity, abundance and frequency of these microorganisms in water samples from the eastern regions of the lake over four seasons. Amplicon sequencing for the 16S rRNA gene was performed to examine bacterial communities in the samples. The study revealed significant seasonal variations in water quality parameters and their influence on the microbial communities. Majority and rarity analyses showed that winter and spring had higher core abundance and higher Gini index values, indicating a greater dominance of certain genera, while autumn and summer had a more balanced distribution. Analysis of beta diversity using the Bray–Curtis dissimilarity index emphasized that bacterial communities diverge most strongly in summer and winter, reflecting the significant changes in the environment with the season. Overall, understanding the seasonal variation in water chemistry and bacterial communities is critical for effective ecosystem management and conservation efforts.

Jackfruit Bronzing Disease Surveillance Study in Selected Orchards of Peninsular Malaysia

Purpose: IIn Malaysia, jackfruit (variety Tekam Yellow) significantly contributes to the nation’s economy. The valuable fruit production is affected by jackfruit bronzing disease (JBD). Information on JBD occurrence in Peninsular Malaysia is necessary to develop effective disease control strategies. Hence, this study aimed to survey JBD occurrence and identify the corresponding causative pathogens in selected jackfruit orchards distributed in Peninsular Malaysia.Research Method: A total of eight jackfruit orchards from five states in Peninsular Malaysia were selected for JBD sampling. Fruit samples were described for characteristic symptoms and disease incidence was expressed in percentage. The causative pathogens were identified using morphological observation and molecular methods while the pathogenicity test was done using Koch’s Postulates.Findings: JBD incidence in Peninsular Malaysia ranged between 20.13-70.25%. JBD-causal pathogen isolation showed that the bacterium was gram-negative, oxidase-negative, and non-capsulated straight rod shape with an average size of 0.35 x 1.31 μm (facultative anaerobic). A DNA sequence analysis on the 16S rRNA gene indicated that 15 putative isolates were unique to P. stewartii and one to P. dispersal at a 99-100% similarity index. Pathogenicity test of the P. stewartii isolates showed JBD characteristic symptoms suggesting that JBD occurrence caused by P. stewartii is common in Peninsular Malaysia and the pathogen could co-exist with P. dispersa.Research Limitations: The number of orchards sampled in this study is low and therefore, the findings pose biases to a certain extent.Originality/Value: JBD occurrence is common in small jackfruit orchards in Peninsular Malaysia. JBD is primarily caused by P. stewartii while both P. stewartii and P. dispersa could co-exist in JBD pathosystem

Antimicrobial Resistance Gene Profiles in Communities Selected with Novel and Previously Encountered Antibiotics

Antibiotics are extensively employed worldwide for therapeutic purposes, often leading to overuse, which constitutes a contributing factor to the emergence of antibiotic resistance (ABR). This phenomenon arises from diminished effectiveness of antibiotics in treating bacterial infections due to resistance development. However, limitations in experimental conditions and equipment making it challenging to pinpoint the precise sources of antibiotic resistance, consequently constraining the breadth of research on ABR. Genomic analysis of antibiotic-resistant bacteria assists in unveiling the origins and pathways of resistance dissemination. This study employs Nanopore-based metagenomic sequencing, enabling direct sequencing of microbial DNA within macrogenomic samples, thereby yielding comprehensive sequence data. Coupled with qPCR and 16S rRNA gene datasets, this approach facilitates the exploration of antibiotic resistance gene distribution and prevalence within microbial communities across different environments Focusing on microbial communities within Scottish farmlands, isolated colonies were exposed to antibiotics (sulfamonomethoxine and erythromycin) for several weeks. By comparing them to untreated control group microorganisms, the identification of antibiotic resistance genes (ABRGs), along with their variations in prevalence and abundance, aims to analyse the impact of these two antibiotics on these species.

Integrative RNA, miRNA, and 16S rRNA sequencing reveals immune-related regulation network for glycinin-induced enteritis in hybrid yellow catfish, Pelteobagrus fulvidraco ♀ × Pelteobagrus vachelli ♂

Glycinin-induced foodborne enteritis is a significant obstacle that hinders the healthy development of the aquatic industry. Glycinin causes growth retardation and intestinal damage in hybrid yellow catfish (Pelteobagrus fulvidraco ♀ × Pelteobagrus vachelli ♂), but its immune mechanisms are largely unknown. In the current study, five experimental diets containing 0% (CK), 1.74% (G2), 3.57% (G4), 5.45% (G6), and 7.27% (G8) immunological activity of glycinin were fed to juvenile hybrid yellow catfish to reveal the mechanism of the intestinal immune response to glycinin through RNA and microRNA (miRNA) sequencing and to explore the interrelation between immune molecules and intestinal microbiota. The results demonstrated that glycinin content in the posterior intestine increased significantly and linearly with the rise of dietary glycinin levels. More than 5.45% of dietary glycinin significantly reduced the nutritional digestion and absorption function of the posterior intestine. Notably, an obvious alteration in the expression levels of inflammatory genes (tnf-α, il-1β, il-15, and tgf-β1) of the posterior intestine was observed when dietary glycinin exceeded 3.57%. Sequencing results of RNA and miRNA deciphered 4,246 differentially expressed genes (DEGs) and 28 differentially expressed miRNAs (DEmiRNAs) between the CK and G6 groups. Furthermore, enrichment analysis of DEGs and DEmiRNA target genes exhibited significant responses of the MAPK, NF-κB, and WNT pathways following experimental fish exposure to 5.45% dietary glycinin. Additionally, at the level of 3.57% in the diet, glycinin obviously inhibited the increase of microbiota, especially potential probiotics such as Ruminococcus bromii, Bacteroides plebeius, Faecalibacterium prausnitzii, and Clostridium clostridioforme. In sum, 5.45% dietary glycinin through the MAPK/NF-κB/WNT pathway induces enteritis, and inflammatory conditions could disrupt micro-ecological equilibrium through miRNA secreted by the host in hybrid yellow catfish. This study constitutes a comprehensive transcriptional perspective of how intestinal immunity responds to excessive glycinin in fish intestines.

Digestive and absorptive capacity and digesta microbiota throughout the gastrointestinal tract of nursery pigs from parents with divergent estimated breeding value for feed conversion ratio

This study investigated digestive and absorptive function changes and microbiota adaptations during weaning in nursery pigs from parents with divergent estimated breeding values for feed conversion ratio (EBV_FCR). The research aimed to investigate whether these changes differed between two groups: pigs from high EBV_FCR (low efficiency, LE) parents and pigs from low EBV_FCR (high efficiency, HE) parents. Furthermore, digesta samples from duodenum, jejunum, ileum, colon, and cecum were collected from 56-day-old post-weaned pigs and subjected to microbiota analysis using 16S rRNA gene profiling. Enzyme activity kinetics and gene expression analyses of nutrient transporters in various segments of the digestive tract showed no significant differences between the two groups. Tight junction proteins gene expression also showed no significant differences in the jejunum between the two groups. Microbiota analysis revealed consistent dominance of Firmicutes in the jejunum and ileum, with Firmicutes and Bacteroidetes prevalent in the cecum and colon across both groups. However, significant differences were observed at the genus level. Lactobacillus was predominant in the small intestine of HE pigs, while the large intestine of LE pigs harbored higher levels of Prevotella, Streptococcus, and Blautia compared to HE pigs. These differences suggest potential functional differences that warrant further investigation.

Microbial Contamination and Food Safety Aspects of Cassava Roasted Flour (“Rale”) in Mozambique

Cassava is an important staple food that contributes to the food security of small-scale Mozambican farmers. In southern Mozambique, cassava roots are usually processed into cassava roasted flour, locally known as “rale”. The handling and processing practices connected to “rale” production may introduce microbial contamination. We assessed the microbial contamination of “rale” processed in local farmers’ associations and consumed either locally or sold in rural markets. Microbial sampling was carried out both during the warmer rainy and cooler dry seasons, and microorganisms of relevance for food safety and fermentation were enumerated. The results revealed variation in terms of microbial diversity in all stages of cassava root processing. In samples collected in the warmer rainy season, molds, lactic acid bacteria, general aerobic bacteria and Bacillus spp. were isolated, whereas in samples collected in the cooler dry season, other groups of microorganisms such as yeasts and Staphylococcus aureus were present. Wickerhamomyces anomalus, Rhodotorula mucilaginosa, Pichia exigua, Meyerozyma caribbica and Torulaspora delbrueckii were the most frequent yeast species found within the cassava processing stages. Aflatoxin-producing molds were observed infrequently in this study, and only at low counts, thus, the risk for aflatoxin contamination appears to be low. The results obtained from the Illumina 16S rRNA gene sequencing can be considered a complementary technique to the plating methods relied on in this study. From a food quality and safety point of view, this staple food does not appear to pose a high risk for foodborne disease.

Intratumor microbiome-derived butyrate promotes chemo-resistance in colorectal cancer

IntroductionColorectal cancer (CRC) is a leading cause of cancer-related mortality globally. Although tumor immunotherapy is widely recognized for treating unresectable CRC, challenges such as ineffective immunotherapy and drug resistance remain prevalent. While intratumor microbiome-derived butyrate has been implicated in promoting lung cancer metastasis, its role in CRC chemoresistance is not well understood. This study aimed to explore the relationship between intratumor butyrate and chemoresistance in CRC.MethodsWe performed a comprehensive analysis of the microbiome composition in CRC patients with varying resistance-free survival (RFS) durations, utilizing 16S rRNA sequencing. Furthermore, we assessed the prognostic significance of circulating microbiome DNA (cmDNA) and examined the effects of exogenous butyrate supplementation on the chemosensitivity of CRC cell lines.ResultsOur 16S sequencing analysis revealed a reduction in microbial diversity within tumor samples of patients with resistance, as indicated by metrics such as observed taxonomic units, Shannon, and Simpson indices. Notably, Roseburia and Fusobacteria emerged as prominent biomarkers for the resistance group, whereas Bifidobacterium, Helicobacter, and Akkermansia were identified as biomarkers for the non-resistant group. Utilizing a Lasso regression model, we identified six genera-Roseburia, Helicobacter, Gardnerella, Flavonifractor, Coprococcus, and Anaerostipes-that significantly correlated with recurrence-free survival. Furthermore, both the intratumor microbiome signature and circulating microbiome DNA were effective in accurately predicting CRC resistance. Experimental assays, including CCK8 and wound-healing, demonstrated that intratumor microbiome-derived butyrate enhances the proliferation and migration of HCT15 cells in a time- and concentration-dependent manner. Cell survival analysis further indicated that butyrate treatment significantly increased the IC50 value, suggesting heightened drug resistance in HCT15 cells. Mechanistically, this resistance was attributed to butyrate’s activation of the PI3K-AKT signaling pathway.ConclusionOur results suggest that intratumor microbiome-derived butyrate contributes to chemoresistance in colorectal cancer, highlighting the potential prognostic and therapeutic significance of the intratumor microbiome.

Antimicrobial and Cytotoxic Potential of Endophytic Aspergillus versicolor Isolate from the Medicinal Plant Plectranthus amboinicus.

Endophytic fungi are non-pathogenic organisms that colonise healthy plant tissues asymptomatically. Endophytes derived from medicinal plants are sources for identifying natural products and bioactive compounds with potential uses for industry, medicine, agriculture, and related sectors. In the present study, ethyl acetate crude extracts of four endophytic fungal isolates (CALF1, CALF4, and CASF1) from the medicinal plant Plectranthus amboinicus showed potent antimicrobial activity against the test pathogenic bacteria Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa, and Bacillus subtilis using disc diffusion assays. A colorimetric microdilution assay to detect the minimum inhibitory concentration (MIC) revealed that the extracellular extract (ECE) of CASF1 isolate had the lowest MIC values against the test pathogenic bacteria (0.19-6.25 mg/ml) compared to other CALF1 and CALF4.Cytotoxic activity of CASF1-ECE against the drug-resistant KB.CHR.8-5 cancer cell line tested by the MTT assay showed complete cell death at a concentration of 220 μg/mL and the half-maximum inhibitory concentration (IC50) was determined to be 77.9 ± 09 μg/mL.GC-MS analysis showed hexadecanoic acid, 2-hydroxy-1-(hydroxymethyl) ethyl ester, as the dominant compound among the bioactive compounds identified in the EXE of CASF1 isolate, with the highest peak in the GC chromatogram, indicating its role in the antimicrobial and cytotoxic activity of CASF1. Molecular identification of CASF1 using 18S rRNA sequencing and BLAST analysis detected CASF1 as an isolate of Aspergillus versicolor with 100% sequence identity.