16S rRNA Gene Sequence Research Articles

Targeting early tau pathology: probiotic diet enhances cognitive function and reduces inflammation in a preclinical Alzheimer’s model

BackgroundAlzheimer’s disease (AD) remains incurable, yet its long prodromal phase offers a crucial window for early intervention. Pretangle tau, a precursor to neurofibrillary tangles, plays a key role in early AD pathogenesis. Intervening in pretangle tau pathology could significantly delay the progression of AD. The gut-brain axis, increasingly recognized as a contributor to AD, represents a promising therapeutic target due to its role in regulating neuroinflammation and neurodegeneration. While probiotics have shown cognitive benefits in amyloid-centered AD models, their effect on pretangle tau pathology remains elusive.MethodsThis study evaluates the effects of probiotics in a rat model of preclinical AD, specifically targeting hyperphosphorylated pretangle tau in the locus coeruleus. TH-CRE rats (N = 47; 24 females and 23 males) received either AAV carrying pseudophosphorylated human tau (htauE14) or a control virus at 3 months of age. Probiotic or control diets were administered at 9–12 months, with blood and fecal samples collected for ELISA and 16S rRNA gene sequencing. Behavioral assessments were conducted at 13–14 months, followed by analysis of brain inflammation, blood-brain barrier integrity, and GSK-3β activation.ResultsRats expressing pseudophosphorylated tau displayed impairment in spatial Y-maze (F1,39 = 4.228, p = 0.046), spontaneous object location (F1,39 = 6.240, p = 0.017), and olfactory discrimination (F1,39 = 7.521, p = 0.009) tests. Phosphorylation of tau at S262 (t3 = -4.834) and S356 (t3 = -3.258) in the locus coeruleus was parallelled by GSK-3β activation in the hippocampus (F1,24 = 10.530, p = 0.003). Probiotic supplementation increased gut microbiome diversity (F1,31 = 8.065, p = 0.007) and improved bacterial composition (F1,31 = 3.4867, p = 0.001). The enhancement in gut microbiomes was associated with enhanced spatial learning (p < 0.05), reduced inflammation indexed by Iba-1 (F1,25 = 5.284, p = 0.030) and CD-68 (F1,26 = 8.441, p = 0.007) expression, and inhibited GSK-3β in female rats (p < 0.01 compared to control females).ConclusionsThis study underscores the potential of probiotics to modulate the gut-brain axis and mitigate pretangle tau-related pathology in preclinical AD. Probiotic supplementation could offer a novel early intervention strategy for AD, highlighting the pivotal role of gut health in neurodegeneration.

Kineococcus halophytocola sp. nov., Isolated from Leaves of Halophyte Sesuvium portulacastrum L.

An aerobic, Gram-stain-positive, motile, coccus-shaped actinomycete, designated strain LSe6-4T, was isolated from leaves of sea purslane (Sesuvium portulacastrum L.) in Thailand and subjected to a polyphasic taxonomic studies. Growth of the strain occurred at temperatures between 15 and 38°C, and with NaCl concentrations 0-13%. The 16S rRNA gene sequences analysis indicated that the strain was most closely related to Kineococcus endophyticus KLBMP 1274T (99.2%), and Kineococcus mangrovi L2-1-L1T (99.0%). The genome of strain LSe6-4T was estimated to be 4.22 Mbp in size, with DNA G+C content of 74.57%. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) relatedness values between strain LSe6-4T and the closely related species were less than the threshold values for identifying a novel species. Strain LSe6-4T showed morphological and chemotaxonomic characteristics of the genus Kineocoocus. The whole-cell hydrolysates contained meso-diaminopimelic acid as the diagnostic diamino acid, with arabinose, galactose, and ribose as whole-cell sugars. The predominant menaquinone was MK-9(H2). The polar lipid profile composed of phosphatidylglycerol, diphosphatidylglycerol, an unidentified phospholipid, three unidentified aminophospholipids, and an unidentified aminolipid. Major cellular fatty acids (> 10% of total fatty acids) were anteiso-C15:0 and iso-C14:0. It is evident from the combination of genotypic and phenotypic characteristics that strain LSe6-4T represents a novel species of the genus Kineococcus, for which the name Kineococcus halophytocola sp. nov. is proposed. The type strain is strain LSe6-4T (= TBRC 17798T = NBRC 116401T).

Spatial variations in the microbiota: comparative analysis of microbial composition and predicted functions across different intestinal segments and feces in donkeys

Donkeys, as single-stomach herbivores, have a complex and diverse microbial community in their digestive tracts. The intestinal bacterial community is crucial for maintaining intestinal homeostasis, as well as the host’s overall nutrition and health. However, research on donkey gut microbes is relatively limited, particularly regarding the microbial colonization patterns in different intestinal segments of adult donkeys. Therefore, this study examined the abundance and function of microbiota across various sites of the intestinal tract (duodenum, jejunum, ileum, cecum, colon) and feces of healthy adult Dezhou male donkeys using 16S rRNA gene sequencing and PICRUSt analysis. The results indicate that donkeys have a rich gut microbial diversity and a large microbial population. No significant differences in the indices of alpha diversity were observed among the donkey’s duodenum, jejunum, ileum, cecum, colon, and feces. A Venn diagram analysis revealed the presence of both unique (Duodenum: 4645; Jejunum: 3586; Ileum: 4904; Cecum: 4253; Colon: 6135; Feces: 4885) and shared (339) ASVs among the different sections. A principal coordinate analysis (PCoA) revealed significant differences (R2 = 0.2076, p &amp;lt; 0.007) across the six intestinal segments of the donkeys. At the phylum level, Firmicutes (63.64%), Bacteroidetes (20.72%), Verrucomicrobiota (9.16%), Patescibacteria (1.95%), Spirochaetota (1.87%), Actinobacteriota (1.13%), and Proteobacteria (0.42%) were the dominant bacteria in all samples. The Wilcoxon rank-sum test revealed significant differences in the proportions of genera among different intestinal segments. Specific genera were significantly enriched in various segments: Lachnospiraceae_UCG-008 and Sphaerochaeta in the duodenum; Christensenellaceae_R-7_group and Bacillus in the jejunum; NK4A214_group and Alloprevotella in the ileum; UCG-005 and Lactobacillus in the cecum; Clostridium_sensu_stricto_1 and Chlamydia in the colon; and Rikenellaceae_RC9_gut_group and Prevotellaceae_UCG-004 in the feces. A PICRUSt2 functional prediction analysis indicated that carbohydrate metabolism, prokaryotic cellular communities, antimicrobial drug resistance, immune diseases, membrane transport, signal transduction, and transcription exhibited significant differences among the different intestinal segments. This study provided critical primary data on the differences in donkey gut microbiota and the synergistic effects between gut microbiota and host functions. These findings can be used to assess donkey health status, improve breeding, and develop microbial additives.

Lactobacillus gasseri prevents ibrutinib-associated atrial fibrillation through butyrate.

Ibrutinib, a widely used anti-cancer drug, is known to significantly increase the susceptibility to atrial fibrillation (AF). While it is recognized that drugs can reshape the gut microbiota, influencing both therapeutic effectiveness and adverse events, the role of gut microbiota in ibrutinib-induced AF remains largely unexplored. Utilizing 16S rRNA gene sequencing, fecal microbiota transplantation, metabonomics, electrophysiological examination, and molecular biology methodologies, we sought to validate the hypothesis that gut microbiota dysbiosis promotes ibrutinib-associated AF and to elucidate the underlying mechanisms. We found that ibrutinib administration predisposes rats to AF. Interestingly, ibrutinib-associated microbial transplantation conferred increased susceptibility to AF in rats. Notably, ibrutinib induced a significantly decrease in the abundance of Lactobacillus gasseri (L. gasseri), and oral supplementation of L. gasseri or its metabolite, butyrate, effectively prevented rats from ibrutinib-induced AF. Mechanistically, butyrate inhibits the generation of reactive oxygen species (ROS), thereby ameliorating atrial structural remodeling. Furthermore, we demonstrated that ibrutinib inhibited the growth of L. gasseri by disrupting the intestinal barrier integrity. Collectively, our findings provide compelling experimental evidence supporting the potential efficacy of targeting gut microbes in preventing ibrutinib-associated AF, opening new avenues for therapeutic interventions.

Nasal microbial diversity is associated with survival in piglets infected by a highly virulent PRRSV-1 strain

BackgroundPorcine reproductive and respiratory syndrome virus (PRRSV) is a major threat to swine industry worldwide, especially virulent variants arising during the last years, such as Spanish PRRSV-1 Rosalia strain. The role of the nasal microbiota in respiratory viral infections is still to be unveiled but may be promisingly related with the health status of the animals and thus, their susceptibility. The goal of this project was to study the nasal microbiota composition of piglets during a highly virulent PRRSV-1 outbreak comparing animals that died due to the infection with animals that survived it. The microbiota composition was inferred by V3–V4 regions of the 16S rRNA gene sequencing and bioinformatics analysis. To deepen the analysis, we added samples taken from piglets before the outbreak as well as from the sows giving birth to piglets under study.ResultsPiglets that survived the PRRSV-1 outbreak reported a more diverse and different nasal microbiota at three weeks of age compared to piglets dying, which was highly related with the litter of origin and the sow of the piglets. In addition, a high abundance of classical swine nasal colonizers belonging to genera such as Bergeyella, Glaesserella, Neisseria and Moraxella (among others), was related with good outcome. On the other hand, a dysbiotic community dominated by Escherichia and a different clade of Moraxella was found in piglets with bad outcome. Moreover, samples taken before the outbreak showed similar dynamics prior to virulent PRRSV-1 arrival, suggesting that microbiota-related susceptibility was already occurring in the animals and that the increase in mortality seen was related to the new highly virulent strain.ConclusionOur study suggests that the susceptibility to an infection such as PRRSV could be related to the nasal microbiota composition at the moment of infection and may serve as starting point to explore animal resilience. Since the dysbiosis detected as an initial response to infection may be not specific for this virus, further investigations should explore this phenomenon in the context of other viral infections.

Pig nasal and rectal microbiotas are involved in the antibody response to Glaesserella parasuis

Vaccination stands as one of the most sustainable and promising strategies to control infectious diseases in animal production. Nevertheless, the causes for antibody response variation among individuals are poorly understood. The animal microbiota has been shown to be involved in the correct development and function of the host immunity, including the antibody response. Here, we studied the nasal and rectal microbiota composition in association with the antibody response against the pathobiont Glaesserella parasuis. The nasal and rectal microbiotas of 24 piglets were sampled in two farms before vaccination and in one unvaccinated farm (naturally exposed to the pathobiont) at similar time. Microbiota composition was inferred by V3V4 16S rRNA gene sequencing and bioinformatics analysis, and the antibody response was quantified using the variation between the levels before and after vaccination (normalized per farm). Piglets with higher antibody responses showed more diverse nasal and rectal microbial communities compared to piglets with lower responses. Moreover, swine nasal core microbiota colonizers were associated with higher antibody levels, such as several members from Bacteroidales and Clostridiales orders and genera including Moraxella, Staphylococcus, Fusobacterium and Neisseria. Regarding taxa found in the rectal microbiota, associations with antibody responses were detected only at order level, pointing towards a positive role for Clostridiales while negative for Enterobacteriales. Altogether, these results suggest that the microbiota is associated with the antibody response to G. parasuis (and probably to other pathogens) and serves as starting point to understand the factors that contribute to immunization in pigs.

Intrasporangium zincisolvens sp. nov., A Novel Actinobacterium Isolated from Rhizosphere Soil.

A novel phosphate-solubilizing and zinc-solubilizing actinobacterium strain YIM S08009T was isolated from rhizosphere soil collected from Pinus yunnanensis in Wuliangshan National Nature Reserve, Pu'er City, Yunnan Province, southwest PR China. Cells of strain YIM S08009T were Gram-stain-positive, non-motile, irregular rods to cocci, and formed yellow and white colonies on nutrient agar. Growth was observed at 10-40°C (optimum 25-35°C), pH 6.0-8.5 (optimum 7), and 0-4% (w/v) NaCl (optimum 1%). The cell wall peptidoglycan contained LL-diaminopimelic acid. The whole-cell sugars were mannose, ribose, glucose, and galactose. The predominant menaquinone was MK-8(H4). Major polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, unknown lipid, and 3 unknown phospholipids. The predominant fatty acids were iso-C14:0, iso-C15:0, and iso-C16:0. The DNA G + C content was 72.6%. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM S08009T belonged to genus Intrasporangium, and was most closely related to Intrasporangium flavum MUSC 78T, with 99.0% 16S rRNA gene sequence similarity. Strain YIM S08009T shared 90.1% orthologous average nucleotide identity (OrthoANI) and 39.8% digital DNA-DNA hybridization (dDDH) with I. flavum MUSC 78T. The genome of strain YIM S08009T contained phosphate-solubilizing genes (SenX3, RegX3, pstSCAB, ugpBAEC, phoA) and zinc-solubilizing genes (znuABC, zupT), and the strain had also demonstrated in vitro phosphorus and zinc solubilization. Based on the genotypic and phenotypic analyses, strain YIM S08009T (= CGMCC 1.60168T = NBRC 116604T = KCTC 59021T) represents a novel Intrasporangium species, for which the name Intrasporangium zincisolvens sp. nov. is proposed.

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 Impact of Storage Conditions on Stool Smellprints as Assessed by an Electronic Nose.

Necrotizing enterocolitis (NEC) is a devastating disease of the neonatal gastrointestinal tract. Volatile organic compounds (VOCs), odoriferous compounds released as a byproduct of bacterial metabolism, can be used as a proxy for gut health. We hypothesized that patients with NEC would have different microbial profiles and elicit different VOC signatures as assessed by gas chromatography/mass spectrometry (GC/MS) or an electronic nose compared to controls. Furthermore, we hypothesized that the temperature of sample storage and the length of time in storage would impact the VOC signatures. Forty-five human stool samples were obtained from Neonatal Intensive Care Units. They were stored at -80 °C as part of the Necrotizing Enterocolitis Biorepository. The microbiome composition was determined by 16S-rRNA gene sequencing and VOC profiles were obtained with GC-MS and by analysis with the Cyranose 320 electronic nose. In separate experiments, fresh stool samples were collected from three different strains of mice. Samples were stored for different times and different temperatures, and VOC signals were compared. A p-value less than 0.05 was considered significant. 16S-rRNA sequencing found a difference in the microbiome composition (p = 0.025) between human NEC and control samples. There was also a difference observed between NEC and control samples identified by GC-MS (p = 0.001). However, there were no differences in VOC smellprints between NEC and controls when analyzed with an electronic nose. When mouse specimens were analyzed, principal component values changed significantly over time and with different storage temperatures. NEC is associated with a different gut microbiome and the VOC profile compared to age-matched controls. However, this difference was not appreciated when biobanked stool samples were compared via an electronic nose. Older samples may experience VOC decay, or the electronic nose may not be sensitive enough to detect NEC in stool samples. Further studies on fresh human stool samples are needed, but the findings herein may limit the use of electronic noses as diagnostic tools for NEC.

Gallibacterium faecale sp. nov., Isolated from Dairy Cow Feces.

A facultative anaerobic, Gram-stain-negative, non-motile, rod-shaped bacterial strain AGMB14963T was isolated from the feces of a dairy cow. A 16S rRNA gene sequence-based phylogenetic analysis revealed that strain AGMB14963T belongs to the genus Gallibacterium, with Gallibacterium salpingitidis F150T being the closest species (95.8% 16S rRNA gene sequence similarity). Whole-genome sequence analysis revealed that strain AGMB14963T had a 37.0% G + C genomic DNA content and a genome size of 2.58Mb. In addition, the strain contained 53 tRNA and 2 rRNA genes. The average nucleotide identity and digital DNA-DNA hybridization values between strains AGMB14963T and G. salpingitidis F150T were 82.3 and 24.9%, respectively. Further, strain AGMB14963T was positive for oxidase and catalase, but negative for urease. Optimal growth of strain AGMB14963T occurred at 37 ℃, pH 8, and in 0.5% NaCl-containing medium. The predominant cellular fatty acids (> 10%) in strain AGMB14963T were C14:0, C16:0, and summed feature 3. Strain AGMB14963T produced lactic acid and isobutyric acid as the major end products of glucose fermentation. Polar lipids consisted of one phospholipid and one phosphoaminolipid. According to the genomic, physiologic, and chemotaxonomic characteristics, strain AGMB14963T represents a novel species of the genus Gallibacterium, for which the name Gallibacterium faecale sp. nov. is proposed. The type strain is AGMB14963T (= KCTC 25487T = NBRC 116419T).

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.

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.

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.

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.

Pseudocitrobacter cyperus, a novel bacterial species recovered from Cyperus alternifolius in Egypt

BackgroundStrain Cyp38ST was isolated as an endophyte from the plant Cyperus alternifolius, collected along the banks of the River Nile in 2019. Preliminary analysis tentatively identified Cyp38ST as belonging to the genus Pseudocitrobacter.MethodsThe preliminary identification of Cyp38ST was performed using the VITEK®2 identification system, MALDI-TOF-MS, and 16S rRNA gene sequencing. To confirm its taxonomic classification, the draft genome of Cyp38ST was generated using DNBseq, and the genome-based taxonomic evaluation was conducted by calculating the overall genome-relatedness indices (OGRIs) such as Average Nucleotide Identity (ANI), digital DNA-DNA hybridization (dDDH), and the tetra-nucleotide signatures (Tetra). Additionally, the biochemical features, antimicrobial susceptibility profiles, and fatty acid methyl ester content of Cyp38ST were characterized.ResultsVITEK®2 misidentified Cyp38ST as Citrobacter werkmanii, MALDI-TOF-MS identified it as Pseudocitrobacter faecalis. While the 16S rRNA gene showed more than 99.0% similarity to other Pseudocitrobacter species, the calculated OGRIs were lower than the thresholds recommended for species assignment to all currently known Pseudocitrobacter species. Furthermore, the phylogenomic analysis revealed that Cyp38ST forms a distinct species cluster within the genus Pseudocitrobacter. Cyp38ST was predicted as a potential human pathogen and carried a unique ß-lactamase-coding gene.ConclusionHere we present Cyp38ST (= CCASU-2024-73T) as the type strain of a novel species within the genus Pseudocitrobacter to which we propose the name Pseudocitrobacter cyperus sp. nov. We provide a full description of the novel species and present its genome sequence and annotation. The discovery of this novel species highlights the potential of endophytic bacteria associated with unique plant hosts to harbor previously uncharacterized microbial diversity.

Phylotypr: an R package for classifying DNA sequences.

The phylotypr R package implements the popular naive Bayesian classification algorithm that is frequently used to classify 16S rRNA and other gene sequences to taxonomic lineages. A companion data package, phylotyprrefdata, also provides numerous versions of taxonomic databases from the Ribosomal Database Project, SILVA, and greengenes.

Whole Genome Sequence-Based Classification of Nonomuraea marmarensis sp. nov., Isolated from Island Soil

Actinomycetes are known to produce a vast array of bioactive secondary metabolites with potential therapeutic applications, including antimicrobials, anticancer agents, and enzyme inhibitors. Among these, members of the genus Nonomuraea have received much attention due to their broad ecological importance in nutrient cycling in soil and their ability to produce new bioactive compounds. A novel actinomycetes, designated strain M3C6T, was isolated from soil samples collected on Marmara Island, located in the Istanbul province, aiming to explore the microbial diversity of unexplored habitats, and characterized using a polyphasic approach. The isolate showed chemotaxonomic and morphological features consistent with members of the genus Nonomuraea. The 16S rRNA gene sequence analysis revealed that strain M3C6T shared the highest similarity, at 98.7% sequence identity, to Nonomuraea basaltis 160415T and Nonomuraea turkmeniaca DSM 43926T. However, the ANI and dDDH values between strain M3C6T and these reference strains were fairly low, ranging from 84.0 to 84.6% and 31.8 to 33.7%, respectively, below the generally accepted cutoffs for ANI and DDH that delineate different prokaryotic species. Genomic analysis of strain M3C6T showed that it had a genome size of 10.38 Mbp and a DNA G+C content of 69.5 mol%. Based on these chemotaxonomic, phenotypic, and genomic data, strain M3C6T is classified as a novel species within the genus Nonomuraea, for which the name Nonomuraea marmarensis sp. nov. is proposed. The type strain is M3C6T (= KCTC 49983T = CGMCC 4.8035T). Genomic analyses confirmed the high potential of M3C6T to produce specialized secondary metabolites.

Improving natural red pigment production by Streptomyces phaeolivaceus strain GH27 for functionalization of textiles with in silico ADME prediction

The red pigment was recovered from the S. phaeolivaceus GH27 isolate, which was molecularly identified using 16S rRNA gene sequencing and submitted to GenBank as OQ145635.1. The ideal growth conditions included 1% (w/v) starch, diammonium citrate, dibasic sodium phosphate, 5% (v/v) inoculum, pH 8, a rotation speed of 150 rpm, a temperature of 37 °C, and an incubation period of 9 days. Using ethanol as a solvent, the red pigment was effectively recovered. Data indicates that pigment content remained steady at 40 and 50 °C. Heating the pigment extract to 60, 70, 80, 90, and 100 °C for one hour results in pigment retention of 98%, 96.5%, 95.5%, 94.6%, and 92.6% of its pigment density, respectively. Studies indicate that the pigment extracts exhibited optimal stability at alkaline pH levels. The findings demonstrate that the red pigment extract has a peak absorbance range of 280–340 nm, with a λmax of 300 nm. GC/MS analysis revealed that the primary components of the pigment extract were linolenic acid methyl ester and oleic acid methyl ester, constituting 26.41% and 25.25%, respectively. Fabrics dyed with extracted red pigment exhibit excellent fastness when using the comprehensive green method. In comparison to conventional and nanotechnological attributes, printed samples exhibit significant color strength without environmental repercussions. The treatment of cotton, wool, and polyester samples suppressed pathogen growth to differing extents. Polyester had the most important inhibitory effects on Staphylococcus aureus (50.03%) and Bacillus cereus (39.49%). The ADME physicochemical properties of the predominant medication were assessed, together with its bioavailability. The radar plot demonstrated ideal parameters for size, polarity, lipophilicity, solubility, and saturation, excluding flexibility. It exhibited intermediate synthetic accessibility, exceptional permeability and absorption, elevated gastrointestinal absorption, and blood–brain barrier penetration; nonetheless, it did not adhere to the medicinal chemistry rule of three.Graphical

Oral Microbiota Associated with Clinical Efficacy of Ustekinumab in Crohn's Disease.

Crohn's Disease (CD) is a chronic inflammatory gastrointestinal disease. Ustekinumab (UST) has been utilized as a therapeutic option for CD patients. However, approximately 40-60% of patients exhibit an inadequate response to UST. Accumulating evidence has confirmed the involvement of oral bacteria in the development of CD. Nevertheless, the relationship between oral microbiota and the efficacy of UST therapy in CD patients has remained unexplored. We recruited 28 healthy individuals and 53 CD patients, 47 of whom completed the entire UST therapy. Oral samples and clinical data were collected. The clinical response and clinical remission were defined based on the CDAI score. Oral samples were analyzed by 16S rRNA gene sequencing. The analysis of sequence data was performed by QIIME and R. We revealed the oral microbial difference between the Healthy Control (HC) group and the CD group. The enrichment of Fusobacteria, Leptotrichia, Capnocytophaga, and Campylobacter, and the diminution of Haemophilus and Rothia were observed in the CD group. Differences in oral microbiota were also identified among patients with different efficacy of UST. Compared to the response and remission groups, both the non-response and non-remission groups showed significantly higher levels of Fusobacteria and Leptotrichia. Predictive models for clinical response and clinical remission in UST were developed based on oral microbiota, with the Area Under the Curve (AUC) value of 0.944 and 0.930, respectively. Oral microbiota was relevant to the UST efficacy in patients with CD based on the predictive model. These findings suggest that oral microbiota could serve as a non-invasive prognostic biomarker for UST treatment in CD patients.

Landscapes of gut microbiome and blood metabolomic signatures in relapsing remitting multiple sclerosis.

Although disturbances in the gut microbiome have been implicated in multiple sclerosis (MS), little is known about the changes and interactions between the gut microbiome and blood metabolome, and how these changes affect disease-modifying therapy (DMT) in preventing the progression of MS. In this study, the structure and composition of the gut microbiota were evaluated using 16S rRNA gene sequencing and an untargeted metabolomics approach was used to compare the serum metabolite profiles from patients with relapsing-remitting MS (RRMS) and healthy controls (HCs). Results indicated that RRMS was characterized by phase-dependent α-phylogenetic diversity and significant disturbances in serum glycerophospholipid metabolism. Notably, α-phylogenetic diversity was significantly decreased in RRMS patients during the chronic phase (CMS) compared with those in the acute phase (AMS). A distinctive combination of two elevated genera (Slackia, Lactobacillus) and five glycerophospholipid metabolism-associated metabolites (four increased: GPCho(22:5/20:3), PC(18:2(9Z,12Z)/16:0), PE(16:0/18:2(9Z,12Z)), PE(18:1(11Z)/18:2(9Z,12Z)); one decreased: PS(15:0/22:1(13Z))) in RRMS patients when comparing to HCs. Moreover, a biomarker panel consisting of four microbial genera (three decreased: Lysinibacillus, Parabacteroides, UBA1819; one increased: Lachnoanaerobaculum) and two glycerophospholipid metabolism-associated metabolites (one increased: PE(P-16:0/22:6); one decreased: CL(i-12:0/i-16:0/i-17:0/i-12:0)) effectively discriminated CMS patients from AMS patients, which indicate correlation with higher disability. Additionally, DMTs appeared to attenuate MS progression by reducing UBA1819 and upregulating CL(i-12:0/i-16:0/i-17:0/i-12:0). These findings expand our understanding of the microbiome and metabolome roles in RRMS and may contribute to identifying novel diagnostic biomarkers and promising therapeutic targets.