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Surveillance for genetic variation of microbial pathogens, both within and among species, plays an important role in informing research, diagnostic, prevention, and treatment activities for disease control. However, large-scale systematic screening for novel genotypes remains challenging in part due to technological limitations. Towards addressing this challenge, we present an advancement in universal microbial high resolution melting (HRM) analysis that is capable of accomplishing both known genotype identification and novel genotype detection. Specifically, this novel surveillance functionality is achieved through time-series modeling of sequence-defined HRM curves, which is uniquely enabled by the large-scale melt curve datasets generated using our high-throughput digital HRM platform. Taking the detection of bacterial genotypes as a model application, we demonstrate that our algorithms accomplish an overall classification accuracy over 99.7% and perform novelty detection with a sensitivity of 0.96, specificity of 0.96 and Youden index of 0.92. Since HRM-based DNA profiling is an inexpensive and rapid technique, our results add support for the feasibility of its use in surveillance applications.

Microbial community dynamics on sinking particles control the amount of carbon that reaches the deep ocean and the length of time that carbon is stored, with potentially profound impacts on Earths climate. A mechanistic understanding of the controls on sinking particle distributions has been hindered by limited depth- and time-resolved sampling and methods that cannot distinguish individual particles. Here, we analyze microbial communities on nearly 400 individual sinking particles in conjunction with more conventional composite particle samples to determine how particle colonization and community assembly might control carbon sequestration in the deep ocean. We observed community succession with corresponding changes in microbial metabolic potential on the larger sinking particles transporting a significant fraction of carbon to the deep sea. Microbial community richness decreased as particles aged and sank; however, richness increased with particle size and the attenuation of carbon export. This suggests that the theory of island biogeography applies to sinking marine particles. Changes in POC flux attenuation with time and microbial community composition with depth were reproduced in a mechanistic ecosystem model that reflected a range of POC labilities and microbial growth rates. Our results highlight microbial community dynamics and processes on individual sinking particles, the isolation of which is necessary to improve mechanistic models of ocean carbon uptake.

Discovering new deep hydrothermal vent systems is one of the biggest challenges in ocean exploration. They are a unique window to elucidate the physical, geochemical, and biological processes that occur on the seafloor and are involved in the evolution of life on Earth. In this study, we present a molecular analysis of the microbial composition within the newly discovered hydrothermal vent field, JaichMaa ja ag, situated in the Southern Pescadero Basin within the Gulf of California. During the cruise expedition FK181031 in 2018, 33 sediment cores were collected from various sites within the Pescadero vent fields and processed for 16S rRNA amplicon sequence variants (ASVs) and geochemical analysis. Correlative analysis of the chemical composition of hydrothermal pore fluids and microbial abundances identified several sediment-associated phyla, including Thermotogota, that appear to be enriched in sediment horizons impacted by hydrothermal fluid flow. Comparative analysis of Thermotogota with the previously explored Auka hydrothermal vent field situated 2 km away displayed broad similarity between the two locations, although at finer scales (e.g., ASV level), there were notable differences that point to core-to-core and site-level factors revealing distinct patterns of distribution and abundance within these two sediment-hosted hydrothermal vent fields. These patterns are intricately linked to the specific physical and geochemical conditions defining each vent, illuminating the complexity of this unique deep ocean chemosynthetic ecosystem.

Background: Antibiotic resistance of Enterobacterales poses a major challenge in the treatment of urinary tract infections (UTIs). In low- and middle-income countries (LMICs), standard microbiological (i.e. urine culture and simple disk diffusion test) methods are considered the "gold standard" for bacterial identification and drug susceptibility testing, while PCR and DNA sequencing are less commonly used. In this study, we aimed to re-identifying Enterobacterales as the primary bacterial agents responsible for urinary tract infections (UTIs) by comparing the sensitivity and specificity of traditional microbiological methods with advanced molecular techniques for the detection of uropathogens in indigenous women from Otavalo, Ecuador. Methods: A facility-based cross-sectional study was conducted from October 2021 to February 2022 among Kichwa-Otavalo women. Pathogens from urine samples were identified using culture and biochemical typing. Morphological identification was doble-checked through PCR and DNA sequencing of 16S, recA, and rpoB molecular barcodes. The isolates were subjected to antimicrobial susceptibility-testing using disk diffusion test. Results: This study highlighted a 32% misidentification rate between biochemical and molecular identification. Using traditional methods, E. coli was 26.19% underrepresented meanwhile Klebsiella oxytoca was overrepresented by 92.86%. Furthermore, the genera Pseudomonas, Proteus, and Serratia were confirmed to be E. coli and Klebsiella spp. by molecular method, and one Klebsiella spp. was reidentified as Enterobacter spp. The susceptibility profile showed that 59% of the isolates were multidrug resistant strains and 31% produced extended spectrum beta-lactamases (ESBLs). Co-trimoxazole was the least effective antibiotic with 61% of the isolates resistant. Compared to previous reports, resistance to nitrofurantoin and fosfomycin showed an increase in resistance by 25% and 15%, respectively. Conclusions: Community-acquired UTIs in indigenous women in Otavalo were primarily caused by E. coli and Klebsiella spp. Molecular identification (16S/rpoB/recA) revealed a high rate of misidentification by standard biochemical and microbiological techniques, which could lead to incorrect antibiotic prescriptions. UTI isolates in this population displayed higher levels of resistance to commonly used antibiotics compared with non-indigenous groups. Accurate identification of pathogens causing UTIs and their antibiotic susceptibility in local populations is important for local antibiotic prescribing guidelines. [ABSTRACT FROM AUTHOR]

The rumen microbiota--a symbiont to its host and consists of critical functional substances--plays a vital role in the animal body and represents a new perspective in the study of adaptive evolution in animals. This study used Slide Viewer slicing analysis system, gas chromatography, RT-qPCR and other technologies, as well as 16S and metabolomics determination methods, to measure and analyze the microstructure of rumen epithelium, rumen fermentation parameters, rumen transport genes, rumen microbiota and metabolites in Tibetan sheep and Hu sheep. The results indicate that the rumen nipple height and cuticle thickness of Tibetan sheep are significantly greater than those of Hu sheep (p < 0.01) and that the digestion and absorption of forage are greater. The levels of carbohydrate metabolism, lipid metabolism, and protein turnover were increased in Tibetan sheep, which enabled them to ferment efficiently, utilize forage, and absorb metabolic volatile fatty acids (VFAs). Tibetan sheep rumen metabolites are related to immune function and energy metabolism, which regulate rumen growth and development and gastrointestinal homeostasis. Thus, compared with Hu sheep, Tibetan sheep have more rumen papilla and cuticle corneum, and the synergistic effect of the microbiota and its metabolites is a characteristic and strategy for adapting to high-altitude environments. [ABSTRACT FROM AUTHOR]

Background: Microbial communities significantly influence the vector capacity of ticks, which, along with tick-borne diseases, pose an increasing global threat. Due to the substantial individual variability caused by various factors, it is essential to assess tick microbial communities and vectorial capacities under different environmental conditions. However, there is a relative scarcity of research on the microbial communities and pathogen transmission of ticks in different physiological states and environmental conditions, especially in Hainan Island, southern China. Methods: From 2021 to 2022, we collected 4,167 tick samples, grouping them by blood meal status, developmental stage, sex, time, geographical location, and tick species. We selected 128 samples for full-length 16S rRNA sequencing to describe microbial community characteristics and identify potential biomarkers. Seven hundred seventy-two samples were tested for seven tick-borne pathogens (Rickettsia, Borrelia burgdorferi, Ehrlichia, Anaplasma, Theileria, Babesia, and Hepatozoon), and sera from 208 residents of Hainan Island were tested for IgG antibodies against Rickettsia and B. burgdorferi. Results: Blood meal status, developmental stage, sex, time, geographical location, and tick species significantly influenced the microbial communities of ticks. We observed distinct microbial community characteristics across different states. We noted the non-random replacement of stable and transient species, with functional differences between parasitic and engorged ticks mainly driven by transient species. Functionally, we observed three distinct response patterns: driven by stable species, transient species, and both together in response to the six factors. We identified 273 potential biomarkers (200 robust core species and 73 robust differential species). Six genera and eight species of pathogens were detected in ticks, with an overall positivity rate of 12.44% (96/772). Among humans, 18.27% (38/208) of serum samples were positive for at least one tick-borne pathogen IgG. Conclusion: Our findings indicate that these six factors significantly influence both tick microbial communities and vectorial capacity, with varying effects on vector competence for different pathogens and inconsistent impacts on microbial communities under different conditions. This study supplemented the understanding of tick microbial communities on Hainan Island, assessed the relatively high risk of tick-borne pathogens in the region, and evaluated the impact of these factors on both microbial communities and vectorial capacity. [ABSTRACT FROM AUTHOR]

In this study, the impact of culture media filtrate of QD3 actinobacterial isolate on two potato cultivars, Spunta and Diamond, infected with potato virus Y (PVY) was investigated. Various parameters, including infection percentage, PVY virus infectivity, disease severity scoring, PVY optical density, photosynthetic and defense-related biochemical markers, enzymatic profiling, phenolic compounds, proline content, salicylic acid levels, and growth and yield parameters, were assessed to elucidate the potential of the QD3 actinobacterial isolate culture filtrate in mitigating PVY-induced damage. The physiological and biochemical characteristics of the QD3 actinobacterial isolate, including its salinity tolerance, pH preferences, and metabolic traits, were investigated. Molecular identification via 16S rRNA gene sequencing confirmed its classification as Streptomyces fradiae QD3, and it was deposited in GenBank with the gene accession number MN160630. Distinct responses between Spunta and Diamond cultivars, with Spunta displaying greater resistance to PVY infection. Notably, pre-infection foliar application of the QD3 filtrate significantly reduced disease symptoms and virus infection in both cultivars. For post-PVY infection, the QD3 filtrate effectively mitigated disease severity and the PVY optical density. Furthermore, the QD3 filtrate positively influenced photosynthetic pigments, enzymatic antioxidant activities, and key biochemical components associated with plant defense mechanisms. Gas chromatography‒mass spectrometry (GC‒MS) analysis revealed palmitic acid (hexadecanoic acid, methyl ester) and oleic acid (9-octadecanoic acid, methyl ester) as the most prominent compounds, with retention times of 23.23 min and 26.41 min, representing 53.27% and 23.25%, respectively, of the total peak area as primary unsaturated fatty acids and demonstrating antiviral effects against plant viruses. Cytotoxicity assays on normal human skin fibroblasts (HSFs) revealed the safety of QD3 metabolites, with low discernible toxicity at high concentrations, reinforcing their potential as safe and effective interventions. The phytotoxicity results indicate that all the seeds presented high germination rates of approximately 95–98%, suggesting that the treatment conditions had no phytotoxic effect on the Brassica oleracea (broccoli) seeds, Lactuca sativa (lettuce) seeds, and Eruca sativa (arugula or rocket) seeds. Overall, the results of this study suggest that the S. fradiae filtrate has promising anti-PVY properties, influencing various physiological, biochemical, and molecular aspects in potato cultivars. These findings provide valuable insights into potential strategies for managing PVY infections in potato crops, emphasizing the importance of Streptomyces-derived interventions in enhancing plant health and crop protection. [ABSTRACT FROM AUTHOR]

Background: Although the etiology of aneurysms remains elusive, recent advances in high-throughput sequencing technology and ongoing human microbiome investigations suggest a potential link between microbiome composition and the onset of various human diseases. Objective: This study aimed to utilize high-throughput 16 S rRNA gene sequencing to analyze the oral flora bacterial profiles of individuals, comparing patients with intracranial aneurysms to a healthy control group. Importantly, we sought to identify differences in the oral microbiota and offer novel insights and methods for early diagnosis and identification of intracranial aneurysms. Method: Saliva samples were collected from 60 patients with cerebral aneurysms (case group) and 130 healthy individuals (control group). The V3-V4 region of the bacterial 16 S rRNA gene was amplified and sequenced using the HiSeq high-throughput sequencing platform to establish the bacterial profile. Sequencing data were analyzed using QIIME2 and Metastats software to compare composition differences and relative abundance at the phylum and genus levels in the oral microbiota of the two groups. Results: Significant differences in oral microbiota composition were observed between patients in the case and control groups (P < 0.05). Genus-level identification highlighted key positions occupied by Eubacterium, Saccharimonadaceae, Rothia, Gemella, Streptococcus, Lactobacillales, Phocaeicola, Bacteroides, Saccharimonadales, and Abiotrophia. Conclusion: This study revealed noteworthy distinctions in the composition, abundance, and diversity of oral microbiota between intracranial aneurysm patients and healthy controls. These disparities suggest a potential correlation between oral microbiota and the development of intracranial aneurysms, offering new avenues for early diagnosis and intervention. However, limitations such as a small sample size, lack of prospective design, and absence of causal inference warrant further validation and exploration. [ABSTRACT FROM AUTHOR]

Bioturbation plays an important role in structuring microbial communities in coastal sediments. This study investigates the bacterial community composition in sediment associated with the ghost shrimp Lepidophthalmus louisianensis at two locations in the Northern Gulf of Mexico (Bay St. Louis, MS, and Choctawhatchee Bay, FL). Bacteria were analysed for shrimp burrows and for three different depths of bioturbated intertidal sediment, using second-generation sequencing of the 16S rRNA gene. Burrow walls held a unique bacterial community, which was significantly different from those in the surrounding sediment communities. Communities in burrow walls and surrounding sediment communities also differed between the two geographic locations. The burrow wall communities from both locations were more similar to each other than to sediment communities from same location. Alpha- and Gammaproteobacteria were more abundant in burrows and surface sediment than in the subsurface, whereas Deltaproteobacteria were more abundant in burrows and subsurface sediment, suggesting sediment mixing by the bioturbator. However, abundance of individual ASVs was geographic location-specific for all samples. Therefore, it is suggested that the geographic location plays an important role in regional microbial communities distinctiveness. Bioturbation appears to be an important environmental driver in structuring the community around burrows. Sampling was conducted during times of the year and water salinity, tidal regime and temperature were variable, nevertheless the structure microbial communities appeared to remain realatively stable suggesting that these environmental variable played only a minor role. [ABSTRACT FROM AUTHOR]

High levels of social connectivity among group-living animals have been hypothesized to benefit individuals by creating opportunities to rapidly reseed the microbiome and maintain stability against disruption. We tested this hypothesis by perturbing the microbiome of a wild population of Grant's gazelles with an antibiotic and asking whether microbiome recovery differs between individuals with high versus low levels of social connectivity. We found that after treatment, individuals with high social connectivity experienced a faster increase in microbiome richness than less socially connected individuals. Unexpectedly, the rapid increase in microbiome richness of highly connected individuals that received treatment led to their microbiomes becoming more distinct relative to the background population. Our results suggest that the microbiome of individuals with high social connectivity can be rapidly recolonized after a perturbation event, but this leads to a microbiome that is more distinct from, rather than more similar to the unperturbed state. This work provides new insight into the role of social interactions in shaping the microbiome. [ABSTRACT FROM AUTHOR]

Background: Yersiniosis is one of the most significant intestinal disorders caused by Yersinia enterocolitica and affects both humans and animals. This study aimed to investigate the prevalence of Y. enterocolitica in New Valley Governorate, Egypt in animals, humans, fresh milk and dried milk. Additionally, this study analyzed the presence of virulence genes, including ail and Yst in tested isolates and conducted a phylogenetic analysis to determine the genetic similarity between human, and animal Y. enterocolitica isolates. Finally, the antimicrobial resistance patterns of the isolates were examined. Results: Among the 982 samples examined, the prevalence of Y. enterocolitica based on ISO10273-2017 was 11.7% in animal samples including 12.8% of animal faeces, and 10.4% in milk samples. Moreover, the prevalence of Y. enterocolitica was 13.2% in human stool, and 9.5% in dried milk samples. The molecular characterization of the six randomly selected isolates showed that the 16S rRNA, ail and Yst genes were found in 50, 33.3 and 100% of the examined Y. enterocolitica isolates, respectively. Phylogenetic analysis of animal and human isolates based on the 16S rRNA gene revealed a high degree of similarity between the isolates. All the tested animal and human Y. enterocolitica isolates (100%) were resistant to ampicillin and cefotaxime, but highly sensitive to norfloxacin. Conclusions: The high prevalence of Y. enterocolitica in animal and human samples with high degrees of genetic similarity poses a threat to public and animal health. Animal faeces, milk and milk powder represent the main sources of Y. enterocolitica infection in humans. Additionally, high levels of antibiotic resistance of Y. enterocolitica can cause public health hazards by leading to the failure of disease prevention and treatment programs in humans and animals. [ABSTRACT FROM AUTHOR]

Root-knot nematodes (RKNs) of the genus Meloidogyne are one of themost damaging genera to cultivated woody plants with a worldwide distribution. The knowledge of the soil and rhizosphere microbiota of almonds infested with Meloidogyne could help to establish new sustainable and efficient management strategies. However, the soil microbiota interaction in deciduous woody plants infected with RKNs is scarcely studied. This research was carried out in six commercial almond groves located in southern Spain and infested with different levels of Meloidogyne spp. within each grove. Several parameters were measured: nematode assemblages, levels and biocontrol agents in Meloidogyne's eggs, levels of specific biocontrol agents in rhizoplane and soil, levels of bacteria and fungi in rhizoplane and soil, fungal and bacterial communities by high-throughput sequencing of internal transcribed spacer (ITS), and 16S rRNA gene in soil and rhizosphere of the susceptible almond hybrid rootstock GF-677 infested with Meloidogyne spp. The studied almond groves showed soil degradation by nematode assemblies and fungi:bacterial ratio. Fungal parasites of Meloidogyne eggs were found in 56.25% of the samples. However, the percentage of parasitized eggs by fungi ranged from1% to 8%. Three fungal species were isolated fromMeloidogyne eggs, specifically Pochonia chlamydosporia, Purpureocillium lilacinum, and Trichoderma asperellum. The diversity and composition of themicrobial communities were more affected by the sample type (soil vs rhizosphere) and by the geographical location of the samples than by the Meloidogyne density, which could be explained by the vigorous hybrid rootstock GF-677 and a possible dilution effect. However, the saprotrophic function in the functional guilds of the fungal ASV was increased in the highly infected roots vs the low infected roots. These results indicate that the presence of biocontrol agents in almond fields and the development of new management strategies could increase their populations to control partially RKN infection levels. [ABSTRACT FROM AUTHOR]

Background: The gut microbiota plays an important role in primates, which may be associated with their habitat. In Malaysia, pig‐tailed macaques (Macaca nemestrina) live in different habitat environments and have traditionally been used for coconut plucking for more than a century. There is currently no information regarding the gut microbiota of this macaque in Malaysia. To address this oversight, this study employed a fecal metabarcoding approach to determine the gut microbiota composition of pig‐tailed macaques and establish how these microbial communities correspond with the macaque external environments of residential area, forest edge, and fragmented forest. Methods: To determine this connection, 300 paired‐end sequences of 16S rRNA were amplified and sequenced using the MiSeq platform. Results: In the pig‐tailed macaque fecal samples, we identified 17 phyla, 40 orders, 52 families, 101 genera, and 139 species of bacteria. The most prevalent bacterial families in the gut of pig‐tailed macaques were Firmicutes (6.31%) and Proteobacteria (0.69%). Our analysis did not identify a significant difference between the type of environmental habitat and the gut microbiota composition of these macaques. Conclusions: There was great variation in the population richness and bacterial community structure. The abundance of Firmicutes and Proteobacteria helps this macaque digest food more easily while maintaining a healthy gut microbiota diversity. Exploring the gut microbiota provides an initial effort to support pig‐tailed macaque conservation in the future. [ABSTRACT FROM AUTHOR]

Background: The gut morphology of Symphalangus syndactylus exhibits an intermediate structure that aligns with its consumption of fruit and ability to supplement its diet with leaves. The Siamang relies on its gut microbiome for energy extraction, immune system development, and the synthesis of micronutrients. Gut microbiome composition may be structured based on several factors such as age, sex, and habitat. No study has yet been carried out on the gut microbiota of the Hylobatidae members in Malaysia especially S. syndactylus. Methods: This study aims to resolve the gut microbiome composition of S. syndactylus by using a fecal sample as DNA source, adapting high‐throughput sequencing, and 16S rRNA as the targeted region. Results: A total of 1 272 903 operational taxonomic units (OTUs) reads were assigned to 22 phyla, 139 families, and 210 genera of microbes. The {Unknown Phylum} Bacteria‐2 is the dominant phyla found across all samples. Meanwhile, {Unknown Phylum} Bacteria‐2 and Firmicutes are genera that have the highest relative abundance found in the Siamang gut. Conclusions: This study yields nonsignificance relationship between Siamang gut microbiome composition with these three factors: group, sex, and age. [ABSTRACT FROM AUTHOR]

The cross-species transmission of intestinal bacteria caused by mixed-group contact in animals is currently an issue of concern. Herring gulls (Larus argentatus) and common shelducks (Tadorna tadorna) often forage in mixed groups, a process which is known as sympatric mixed foraging. This study sought to explore how mixed foraging affects the gut bacteria structure in herring gulls and common shelducks on Binzhou Seashell Island, China. Illumina high-throughput sequencing was employed to analyze the intestinal bacteria of these birds during their wintering period, with the goal of understanding the impact of mixed-species interactions on gut microbiota diversity. The results showed that alpha diversity of intestinal flora in common shelducks was higher than that in herring gulls, and there was no significant difference in beta diversity between the two species. The similarity ratio of the top five abundances of bacteria at the phylum classification level reached 42.86%. Judging from the results, there is resemblance in the structure of the intestinal flora between the two species. The study not only enhances our understanding of the adaptive strategies and interactions of these two avian species within the ecosystem, but also establishes a crucial foundation for bird resource management and disease prevention and control in this region. It holds significant scientific and practical implications for fields such as ecological conservation and biodiversity. [ABSTRACT FROM AUTHOR]

1. Preventing disease is important in poultry production systems, but this has mainly been studied in chickens. The aim of this study is to explore the impact of microbial aerosols in intensive goose house environments. 2. To evaluate the environmental quality of geese housing, fine particulate matter (PM2.5) was collected using an ambient air particulate matter sampler. High-throughput sequencing was used to analyse bacterial diversity and relative abundance. Results showed that the number of general and operational taxonomic units (OTUs) were 1,578 and 19 112 in all PM2.5 samples. Firmicutes, Bacteroidota, Proteobacteria, Acidobacterota were the four most abundant phyla in PM2.5. 3. Compared with bacterial phyla in the PM2.5 from chicken houses, those in the genus Acidobacterota were increased in goose housing. There are various genera of bacteria present in PM2.5, and their composition was similar across different samples. No significant change was observed in the diversity of microbiota in the PM2.5, although multiple pathogenic bacteria were detected. 4. A prediction function showed that a variety of bacterial phyla correlated positively with the human diseases. 5. In summary, the microbial aerosols in the goose shed pose significant risks to the health of the geese. Regular monitoring of the composition of microbial aerosols is important for the healthy growth of geese and disease prevention and control. [ABSTRACT FROM AUTHOR]

In this study, we aimed to develop a species-level phylogeny for the Nannospalax genus, identify cryptic species that are difficult to differentiate using standard methods, and further evaluate the relationships across chromosomal forms of several species. 16S rRNA gene sequences from 81 Turkish regions were evaluated and statistical analyzes were conducted. Results are as follows; (i) Nannospalax cilicicus was found to be monophyletic and sister in relation to Nannospalax xanthodon; (ii) We suggested for the first time that the Central-Anatolian populations should be classified under the species name Nannospalax cilicicus (stat. n.); (iii) the unidentified 2n = 52 cytotypes from Bolu and Nannospalax leucodon cytotypes were reciprocally monophyletic, these data support the notion that the 2n = 52 cytotypes from Bolu belong to an unidentified taxon; (iv) study also offered evidence for the monophyly of N. tuncelicus for the first time; (v) Nannospalax xanthodon (2n = 36, 38, and 40) and Nannospalax nehringi composed several species-specific clades, which form polytomy structure, so relationships between these species are still unclear. [ABSTRACT FROM AUTHOR]

Objective: The objective of this study was to investigate the influence of yacon root extracts (YREs) on productive performance and health of laying hens. Methods: Six hundred 30-week-old Xiaoshan Chicken layers were divided into 5 groups, control group, antibiotic positive control group, and 3 YREs treatment groups. In a 9-wk feeding experiment, at the end of wk 3, 6, and 9, twenty eggs were collected from each replicate to measure egg qualities. At the end of wk 9, three hen serum samples, and 5 hen cecal content samples were collected from each replicate. Results: Compared to the control group, 0.8%, 1.6%, and 2.4% YREs treatments could increase hens’ daily feed intake, and YREs supplementation affected daily feed intake in linear manner. YREs did not change egg size, but 0.8% and 2.4% YREs changed egg shape by decreasing the egg shape index and sphericity, and 0.8% YREs tended to improve the eggshell breaking strength. Diet supplemented with 1.6% YREs might decrease yolk color grade but optimize the pH of thick egg white in fresh egg; moreover, 1.6% and 2.4% YREs might be helpful for eggs to inhibit water loss during storage, and YREs supplementation affected water loss rate in linear manner. 2.4% YREs could decrease the serum lactate dehydrogenases (LDH) level, and YREs supplemental levels linearly affected serum LDH content. Finally, YREs could enrich the diversity of intestinal microbiota of hens fed with 0.8% and be beneficial for the relative abundance of phylum Bacteroidota and Halobacterota; 2.4% YREs might increase the abundance of phylum Actinobacteriota and genus Bifidobacterium, while decrease genus Bacteroides; YREs supplemental levels affected the abundance of phylum Actinobacteriota, and genera Bifidobacterium and Bacteroides in linear manner. Conclusion: Dietary supplementation with YREs could affect egg quality, protect the health of organs and exhibit prebiotic activity. [ABSTRACT FROM AUTHOR]

Sterile insect technique (SIT) is a useful strategy for preventing and mitigative establishment of invasive insect species. SIT of the pest tephritid Mediterranean fruit fly, Ceratitis capitata (Wiedemann, 1824) WiedemannWiedemann , has been effective in preventing population establishment in vulnerable agricultural areas of the United States. However, irradiation-induced sterilization can have detrimental impacts resulting in reduced performance metrics. Mediterranean fruit fly males reared for SIT have been shown to have differences in their microbiomes relative to other population sources, which has been postulated to be a factor in how well flies compete with wild conspecifics. To identify baseline performance metrics on the effects of irradiation on the gut microbiome of mass-reared flies in Hawai'i, a study was performed to assess performance metrics and microbiome (bacterial 16S rRNA) variation across multiple timepoints. Mediterranean fruit fly pupae were selected from mass-reared trays intended for release, and paired samples were either irradiated or remained as controls and transported to the laboratory for evaluation. Irradiated flies exhibited fewer successful fliers, more rapid mortality rates, and were less active relative to control nonirradiated flies. Contrary to initial expectations, irradiation did not exert substantial impacts on the composition or diversity of bacterial reads. Samples were primarily comprised of sequences classified as Klebsiella and there were low levels of both read and taxonomic diversity relative to other 16S surveys of medfly. Although this study does not demonstrate a strong effect of irradiation alone on the Mediterranean fruit fly microbiome, there are several explanations for this discrepancy. [ABSTRACT FROM AUTHOR]

Introduction: The gut bacteria of insects play an important role in regulating their metabolism, immune system and metabolizing pesticides. Our previous results indicate that carvacrol has certain gastric toxic activity on Lymantria dispar larvae and affects their detoxification metabolism at the mRNA level. However, the impact of carvacrol on the gut bacteria of L. dispar larvae has been unclear. Methods: In this study, the 16S rRNA sequencing technology was used to sequence and analyze the gut bacteria of the larvae which were exposed with sublethal concentration (0.297mg/mL) and median lethal concentration (1.120mg/mL), respectively. Results: A total of 10 phyla, 16 classes, 47 orders, 72 families, 103 genera, and 135 species were obtained by using a 97% similarity cutoff level. The dominant bacterial phyla in the gut of the L. dispar larvae are Firmicutes and Proteobacteria. The treatment with carvacrol can significantly affect the structure of gut bacteria in the larvae of the L. dispar. At both doses, carvacrol can shift the dominant gut bacteria of the larvae from Proteobacteria to Firmicutes. At the genus level, two doses of carvacrol can significantly enhance the relative abundance of probiotic Lactobacillus in the gut of L. dispar larvae (p = 0.01). Additionally, significant differences were observed among the five bacterial genera Burkholderia-Caballeronia-Paraburkholderia, Anoxybacillus, Pelomonas, Mesorhizobium (p = 0.05). The analysis of α-diversity and β-diversity indicates that the treatment with carvacrol at two doses significantly affect the bacterial richness and diversity in the larvae. However, the results of functional classification prediction (PICRUSt) indicate that carvacrol significantly down-regulate 7 functions, including Energy metabolism, Cell growth and death, and up-regulate 2 functions, including Carbohydrate metabolism and Membrane transport. The network analysis indicates that the correlation between gut bacteria also has been changed. In addition, the insecticidal activity results of carvacrol against L. dispar larvae with gut bacteria elimination showed that gut bacteria can reduce the insecticidal activity of carvacrol against L. dispar larvae. Discussion: This study provides a theoretical foundation for understanding the role of gut bacteria in detoxifying plant toxins and conferring pesticide resistance. [ABSTRACT FROM AUTHOR]

BACKGROUND AND OBJECTIVES: The utilization of disposable masks during and subsequent to the COVID-19 pandemic has led to the emergence of mask waste. The bacteria that thrive on mask waste have special characteristics. The objective of this research was to identify, choose, and analyze the bacteria present in discarded face masks at landfill sites (Piyungan, Yogyakarta and Jatibarang, Semarang), coastal areas (Tanjung Pasir, Tangerang, and Marina, Semarang), as well as mangrove forests (Teluk Naga, Tangerang, and Tirang, Semarang) situated in Java, Indonesia. METHODS: The bacterial isolation was performed using minimal salt medium. Bacterial isolates were screened in a minimal salt medium supplemented with three types of masks (black duckbill, blue medical, white Korean filter) as the sole carbon and energy source at the various potential of hydrogen levels (5, 7, 9), temperatures (10, 30, 50 degrees Celsius), and sodium chloride concentrations (2.5, 5.0, 7.5 percent). The bacterial strains with the highest optical density values across all treatments were determined through the sequencing of the 16S ribosomal ribonucleic acid gene. These selected bacteria were then evaluated for their ability to produce biofilms under different potential of hydrogen and salt concentrations. The resistance to heavy metals (lead, copper, iron) and antibiotics (penicillin, chloramphenicol, tetracycline, erythromycin, ciprofloxacin, kanamycin) was also investigated. FINDINGS: A grand total of 183 bacterial strains were obtained, comprising 80 isolates from landfills, 47 isolates from beaches, and 56 isolates from mangroves. The selected bacteria identified as Bacillus cereus, Pseudomonas aeruginosa, Proteus mirabilis, Staphylococcus sciuri, and Staphylococcus arlettae based on 16 svedberg ribosomal ribonucleic acid gene analysis. The chosen strains exhibited the capacity to generate biofilm across various potential of hydrogen and salinity conditions. Furthermore, these strains displayed resilience to heavy metals (such as lead, copper, and iron) as well as resistance to antibiotics (including penicillin, chloramphenicol, tetracycline, erythromycin, ciprofloxacin, and kanamycin). CONCLUSION: Mask waste discovered in landfills, beaches, and mangroves can promote bacterial growth. This study indicated that the selected bacteria are capable of flourishing through the utilization of various mask types as their exclusive carbon and energy source across a wide range of potential of hydrogen levels, temperatures, and salinity concentrations. The ability to produce biofilms, withstand antibiotics, and endure heavy metal ions provides a protective environment for bacteria, enhancing their resilience against environmental stresses, and antimicrobial agents. Analysis of bacterial profiles reveals the intricate connections between microorganisms and their surroundings. The results of this study have implications for public health, environmental pollution, and ecosystem dynamics. [ABSTRACT FROM AUTHOR]

This study identified the phenotypic and genotypic characteristics of the bacteria that nodulate wild Lathyrus and Vicia species natural distribution in the Gaziantep province of Turkey. Principle component analysis of phenotypic features revealed that rhizobial isolates were highly resistant to stress factors such as high salt, pH and temperature. They were found to be highly sensitive to the concentrations (mg/mL) of the antibiotics neomycin 10, kanamycin, and tetracycline 5, as well as the heavy metals Ni 10, and Cu 10, and 5. As a result of REP-PCR analysis, it was determined that the rhizobial isolates were quite diverse, and 5 main groups and many subgroups being found. All of the isolates nodulating wild Vicia species were found to be related to Rhizobium sp., and these isolates were found to be in Clades II, III, IV, and V of the phylogenetic tree based on 16S rRNA. The isolates that nodulated wild Lathyrus species were in Clades I, II, IV, V, VI, VII, and VIII, and they were closely related to Rhizobium leguminasorum, Rhizobium sp., Phyllobacterium sp., Serratia sp., and Pseudomonas sp. According to the genetic analyses, the isolates could not be classified at the species level, the similarity ratio was low, they formed a distinct group that was supported by strong bootstrap values in the phylogenetic tree, and the differences discovered in the network analysis revealed the diversity among the isolates and gave important findings that these isolates may be new species. [ABSTRACT FROM AUTHOR]

Irritable bowel syndrome (IBS) is a prevalent gut disorder linked to changes in the gut microbiota, including lactic acid bacteria (LAB). However, research on LAB biodiversity in IBS patients is limited. This study aimed to compare LAB microbiota in healthy individuals and those with IBS through biochemical and molecular techniques. Fecal samples from 15 IBS patients and 13 healthy individuals were collected, and LAB were isolated using biochemical methods. Fifty isolates were chosen based on Gram staining and catalase tests and identified through 16S rRNA gene sequencing. A phylogenetic tree was used to analyze strain diversity, and correlation diagrams and swarm plots were employed to explore variable relationships. The study revealed a significant difference in LAB numbers between IBS and healthy subjects, with average of 5.91 and 6.63, respectively. Most bacteria were Gram‐positive cocci or bacilli, with homofermentative characteristics, except for one heterofermentative sample from the healthy group. Both IBS and healthy groups exhibited strains from Lactobacillus and Enterococcus genera, with Enterococcus faecium being predominant in both. Demographic analysis showed higher IBS prevalence among individuals aged 20–40, with IBS‐C more common in women and IBS‐D in men. The study concluded that individuals with IBS had significantly lower LAB microbiota counts, potentially impacting intestinal defense function. Further exploration of LAB behavioral and immunomodulatory traits may enhance understanding of intestinal microbiota's role in IBS and aid in developing treatment strategies. [ABSTRACT FROM AUTHOR]

The olive fly, Bactrocera oleae (Rossi, 1790), is the major insect pest of olives attacking both cultivated and wild olive. Bactrocera oleae carries a primary and vertically transmitted symbiont, the bacterium Candidatus Erwinia dacicola. As any primary symbiont, it plays an important role in the reproduction and lifespan of the fly. The genetic 16S rRNA diversity of the primary symbiont and the mitochondrial haplotype variation of the insect host were simultaneously examined in 54 olive fly populations. The aim was to unravel the biogeographic patterns of this economically relevant host-bacteria interaction across a wide distribution area. Three symbiont haplotypes were identified. The primary symbiont showed a lower haplotype diversity than that of its host, a characteristic indicative of a long-term interaction. A significant genetic and geographic association between host and primary symbiont was observed, with an East-West genetic differentiation pattern in the Mediterranean basin, coinciding with the historical genetic distribution of the olive tree. The study shows promise, informing and aiding the development of future tools for the control of the olive fly. [ABSTRACT FROM AUTHOR]

Introduction: The Aotearoa New Zealand ghost shrimp of the infraorders Axiidea and Gebiidea have never been comprehensively reviewed, with recent work uncovering a diverse regional fauna representing eight of the 14 known families. Methods: Using standard morphological and DNA sequencing tools, the family Callianopsidae is, for the first time, recorded off New Zealand, represented by a new species of Vulcanocalliax. Results: The new species was found near hydrocarbon seeps on the Hikurangi Margin, on the eastern New Zealand continental slope, and is only the second species now known in this genus. The single congener, V. arutyunovi, is only known from a mud volcano in the Gulf of Cádiz, off the Iberian Peninsula. Vulcanocalliax sp. nov. was formerly reported as an unnamed host of a new endemic New Zealand rhizocephalan barnacle Parthenopea australis and is here formally described as Vulcanocalliax beervana sp. nov. Discussion: The new species differs, e.g., in the shape of the anterior carapace margin (convexly rounded and without elevated postantennal shoulder present in V. arutyunovi), the ocular peduncle having a convex anterolateral margin (compared to a straight margin), and the uropodal exopod has a dorsomedian ridge, lacking the elevated anterior portion that is distinct in V. arutyunovi. This brings the number of described New Zealand ghost shrimp species to 18. A key to all known Callianopsidae is provided. [ABSTRACT FROM AUTHOR]

Introduction: To investigate the presence of dysbiosis in patients with naive bladder cancer. Methods: Twelve male patients with non-invasive bladder cancer and twelve age-matched healthy males had midstream urine and tissue samples taken. A history of endourological interventions was determined as an exclusion criterion, ensuring that the study was designed solely with naïve participants. The bacterial 16s ribosomal RNA V3-V4 regions were used to examine urine and tissue samples. We compared the microbiota composition of the bladder cancer and control groups. Results: Escherichia Shigella (p < 0.001), Staphylococcus (p < 0.001), Delftia (p < 0.001), Acinetobacter (p < 0.001), Corynebacterium (p < 0.001), and Enhydrobacter (p < 0.001) were abundant in bladder cancer tissue samples. Escherichia Shigella (p < 0.001), Ureaplasma (p < 0.001), Lactobacillus (p = 0.005), Stenotrophomonas (p < 0.001), Streptococcus (p < 0.001), Corynebacterium (p < 0.001), and Prevotella (p = 0.039) were abundant in bladder cancer urine samples. Midstream urine has a sensitivity of 83% for detecting dysbiotic bacteria in cancer tissue. Conclusions: Our research is the first microbiota study of bladder cancer done with naive patients who have never had an endourological intervention. Escherichia Shigella, Staphylococcus, Acinetobacter, Enhydrobacter, Delftia, Corynebacterium, and Pseudomonas were detected as dysbiotic bacteria in bladder cancer. The sensitivity of the midstream urine sample in detecting dysbiosis in tissue is 83%. [ABSTRACT FROM AUTHOR]

Amplifying small subunit (SSU) rRNA genes with universal primers in assessing microbial populations diversity, but target microorganisms are sometimes omitted due to inadequate primer coverage. Adding degenerate bases to primers can help, but existing methods are complex and time-consuming. This study introduces a user-friendly tool called "Degenerate primer 111" for adding degenerate bases to existing universal primers. By aligning one universal primer with one uncovered target microorganism's SSU rRNA gene, this tool iteratively generates a new primer, maximizing coverage for the target microorganisms. The tool was used to modify eight pairs of universal primers (515F Parada-806R Apprill, S-D-Bact-0341-b-S-17/S-D-Bact-0785-a-A-21, OP_F114-KP_R013, 27F-1492R, 341F-806R, OP_F066-KP_R013, 515F Parada-926R Quince, 616*F-1132R), and generated 29 new universal primers with increased coverage of specific target microorganisms without increasing coverage of non-target microorganisms. To verify the effectiveness of the improved primers, one set of original and improved primers (BA-515F-806R and BA-515F-806R-M1) was used to amplify DNA from the same sample, and high-throughput sequencing of the amplicons confirmed that the improved primers detected more microbial species compared to the original primers. Future researchers can use this tool to develop more personalized primers to meet their diverse microorganism detection needs. [ABSTRACT FROM AUTHOR]

The manure–compost–soil process is the main avenue for using agricultural livestock waste. Biochar not only impacts the composting process but also enhances the soil's organic matter and nitrogen content when applied with compost. This paper explores the profound impact of biochar as an additive on the manure–compost–soil process, uncovering novel mechanisms driving enhanced soil health and bacterial succession. The basic physicochemical properties (organic matter, total nitrogen, etc.) and microbial structure of the composting and soil samples were analyzed. Biochar additive increased the C/N ratio and the total carbon content of the compost. Biochar, compost, and biochar-based compost improved the total carbon and organic matter of the soil. After high-temperature composting, Saccharomonospora (from 2.68% to 0.80%), Atopostipes (from 5.71% to 0.13%), and Lactobacillus (from 5.27% to 0.04%) were almost eliminated. Lysobacter, Glutamicibacter, and Streptomyces were the dominant genera in the soil samples, promoting plant growth. Nocardiopsis, Saccharomonospora, Bacillus, and Oceanobacillus dominated the genera in the whole manure–compost–soil process. Thus, composting could eliminate the toxic or negative bacteria directly deposited into soil by manure. Those genera arising from compost or biochar-based compost in the soil could contribute to organic matter's cycle. [ABSTRACT FROM AUTHOR]

Objective: The purpose of this systematic bioinformatics analysis was to describe the compositions and differences in submucosal microbial profiles of peri-implants’ diseases and healthy implant. Material and methods: PubMed, Embase, ETH Z, Scopus, CNKI, and Wanfang databases were searched to screen relevant literature on the analysis of peri-implant microflora based on the sequencing analysis technique of 16S ribosomal RNA (16S rRNA) gene. High-throughput sequencing of the 16S rRNA gene of microorganisms from healthy implants, peri-implant mucositis, and periimplantitis was downloaded from the screened articles. EasyAmplicon and Usearch global algorithm were used to match the reads from each dataset to a full length of 16S rRNA or ITS gene sequence. The microorganisms based on the Human Oral Microbiome Database (HOMD) were re-classified, and the microbial diversity, flora composition, and differential species of the samples were reanalyzed, including taxonomic classification and alpha and beta diversity calculations. The co-occurrence network was also re-analyzed. Results: A total of seven articles with 240 implants were included. Among them, 51 were healthy implants (HI), 43 were in the peri-implant mucositis (PM) group, and 146 were in the peri-implantitis (PI) group. A total of 26,483 OTUs were obtained, and 877 microorganisms were annotated. The alpha diversity including Chao1 (healthy implants, 121.04 ± 92.76; peri-implant mucositis, 128.21 ± 66.77; peri-implantitis, 131.15 ± 84.69) and Shannon (healthy implants, 3.25 ± 0.65; peri-implant mucositis, 3.73 ± 0.61; peri-implantitis, 3.53 ± 0.67) of the samples from the three groups showed a significant difference. The beta diversity of the three samples was statistically different among groups. The genera of Treponema and Fretibacterium were significantly more abundant in the PI group than in the other two groups, and the genus of Streptococcus was more abundant in the HI group. The relative abundance of Porphyromonas in the peri-implantitis group was 6.1%. The results of the co-occurrence network showed differences in the network topology among the three groups of samples. The most connected three genera in the healthy implants were Halomonas, Fusobacterium, and Fretibacterium. The most connected three genera in peri-implant mucositis were Alistipes, Clostridia UCG-014, and Candidatus Saccharimonas. The most connected three genera in the peri-implantitis group were Lachnoanaerobaculum, Fusobacterium, and Atopobium. The betweenness of Porphvromonas gingivalis (red complex) in the PI group (7,900) was higher than in the HI group (23). Conclusions: The community compositions of peri-implant submucosal microorganisms were significantly different in healthy implants, peri-implant mucositis, and peri-implantitis. The submucosal microbial communities in peri-implantitis were characterized by high species richness and diversity compared with the healthy implants; the relative abundance of red complex, some members of the yellow complex, and some novel periodontal pathogens was higher in the peri-implantitis and peri-implant mucositis groups than in the healthy implant group. The core flora of the co-occurrence network of healthy implants, peri-implant mucositis, and peri-implantitis varied considerably. The peri-implantitis site presented a relative disequilibrium microbial community, and Porphyromonas may play an important role in the co-occurrence network. [ABSTRACT FROM AUTHOR]

Microbial communities play a crucial role in the physiology of animal hosts; however, little is known about bacterial symbionts with the group cephalopods, specifically octopuses, and the function of these symbionts. The goal of this study was to determine if octopuses have a unique skin microbiome. The skin microbiome of two sympatric octopuses (Octopus vulgaris and Macrotritopus defilippi) was compared with the surrounding environment, sediment and seawater, to determine if octopus have a unique skin microbiome. High throughput sequencing of the bacterial 16S rRNA gene (V3-V4 region) amplicons was performed using an Illumina MiSeq. Sediment showed the greatest alpha diversity followed by octopus then seawater. Beta diversity revealed a difference in microbial composition between the octopus skin microbiome and sediment and seawater. While phylum Bacteroidetes appeared rare in environmental samples, it was most abundant for the octopus skin microbiome with the majority of the bacteria comprising the family Flavobacteriaceae. Proteobacteria, the largest group of bacteria, also constituted the octopus skin microbiome. Many of these groups occur on both octopus species; however, certain taxa differed in relative abundance between octopus species and may show species-specific host selection. Several bacteria that were identified for the octopus skin microbiome have been isolated from other marine animal hosts, identified as biodegraders and/ or produce pigments and squalene, or act as predators of other bacteria. These groups may play a role in defense against environmental stressors or pathogenic bacteria. This is the first study to characterize the skin microbiome in two wild sympatric octopuses. Due to the importance of bacterial symbionts, this can provide insight to the physiology, behavior, ecology, and ultimately the health of these important animals in marine environments as well as care in captive or laboratory settings. [ABSTRACT FROM AUTHOR]

This study aimed to evaluate the impact of long-term liquid dairy manure (LDM) application on the activity and structure of soil bacterial and archaea communities in two cropping seasons over 1 year of a no-till crop rotation system. The experiment was run in a sandy clay loam texture Oxisol, in Brazil, including LDM doses of 60, 120, and 180 m3 ha−1 year−1, installed in 2005. Soil sampling was conducted during spring 2018 and autumn 2019 at 0–10-cm depth. Microbial biomass carbon and nitrogen, 16S rRNA gene sequencing, microbial respiration and quotient were performed. Over the 14-year period, LDM application increased soil microbial community activity. Analysis of 16S rRNA gene sequencing revealed dominance by Proteobacteria, Acidobacteria, and Actinobacteria phyla (67% in spring and 70% in autumn). Genera Pirulla and Nitrososphaera showed enrichment at LDM doses of 120 and 180 m3 ha−1 year−1 doses, respectively. During spring, following black oat cropping, shifts in the relative abundance of Bacteroidetes, Proteobacteria, Firmicutes, Gemmatimonadetes, Verrucomicrobia, Chloroflexi, Actinobacteria, and AD3 phyla were observed due to LDM application, correlating with soil chemical indicators such as pH, K, Ca, Mn, and Zn. Our findings indicate that plant development strongly influences microbial community composition, potentially outweighing the impact of LDM. Our findings indicate that the application of liquid dairy manure alters the soil bacterial activity and community; however, this effect depends on the developing plant. [ABSTRACT FROM AUTHOR]

Background: With the widespread use of antibiotics, more attention has been paid to their side effects. We paid extra attention to the impact of antibiotics on children's bodies. Therefore, we analyzed the characteristic changes in the gut microbiota of children after antibiotic treatment to explore the pathogenesis of antibiotic-associated diseases in more depth and to provide a basis for diagnosis and treatment. Methods: We recruited 28 children with bronchopneumonia in the western district of Zhuhai, China, and divided them into three treatment groups based on antibiotic type. We took stool samples from children before and 3–5 days after antibiotic treatment. 16S rRNA gene sequencing was used to analyze the effects of antibiotic therapy on the gut microbiota of children. Continuous nonparametric data are represented as median values and analyzed using the Wilcoxon rank-sum test. Results: While alpha diversity analysis found no significant changes in the mean abundance of the gut microbiota of children after a short course of antibiotic treatment, beta diversity analysis demonstrated significant changes in the composition and diversity of the gut microbiota of children even after a short course of antibiotic therapy. We also found that meloxicillin sulbactam can inhibit the growth of Proteobacteria, Bacteroidetes, and Verrucomicrobia, ceftriaxone inhibits Verrucomicrobia and Bacteroides, and azithromycin inhibits Fusobacteria, Actinobacteria, Proteobacteria, and Verrucomicrobia. We further performed a comparative analysis at the genus level and found significantly different clusters in each group. Finally, we found that azithromycin had the greatest effect on the metabolic function of intestinal microbiota, followed by ceftriaxone, and no significant change in the metabolic process of intestinal microbiota after meloxicillin sulbactam treatment. Conclusions: Antibiotic treatment significantly affects the diversity of intestinal microbiota in children, even after a short course of antibiotic treatment. Different classes of antibiotics affect diverse microbiota primarily, leading to varying alterations in metabolic function. Meanwhile, we identified a series of intestinal microbiota that differed significantly after antibiotic treatment. These groups of microbiota could be used as biomarkers to provide an additional basis for diagnosing and treating antibiotic-associated diseases. [ABSTRACT FROM AUTHOR]

Background: Klebsiella pneumoniae is a major cause of hospital-acquired infections (HAIs), primarily spread through environmental contamination in hospitals. The effectiveness of current chemical disinfectants is waning due to emerging resistance, which poses environmental hazards and fosters new resistance in pathogens. Developing environmentally friendly and effective disinfectants against multidrug-resistant organisms is increasingly important. Methods: This study developed a bacteriophage cocktail targeting two common carbapenem-resistant Klebsiella pneumoniae (CRKP) strains, ST11 KL47 and ST11 KL64. The cocktail was used as an adjunctive disinfectant in a hospital's respiratory intensive care unit (RICU) via ultrasonic nebulization. Digital PCR was used to quantify CRKP levels post-intervention. The microbial community composition was analyzed via 16S rRNA sequencing to assess the intervention's impact on overall diversity. Results: The phage cocktail significantly reduced CRKP levels within the first 24 hours post-treatment. While a slight increase in pathogen levels was observed after 24 hours, they remained significantly lower than those treated with conventional disinfectants. 16S rRNA sequencing showed a decrease in the target pathogens' relative abundance, while overall species diversity remained stable, confirming that phages selectively target CRKP without disrupting ecological balance. Discussion: The findings highlight the efficacy and safety of phage-based biocleaners as a sustainable alternative to conventional disinfectants. Phages selectively reduce multidrug-resistant pathogens while preserving microbial diversity, making them a promising tool for infection control. [ABSTRACT FROM AUTHOR]

Honeybees harbor a distinct core microbiota that plays a crucial role in stress tolerance and disease resistance. However, infections can significantly alter the composition and diversity of their gut microbiota, impacting overall bee health. This study investigates the effects of Deformed Wing Virus (DWV) infection on the gut microbiota of Apis cerana honeybee. The samples were collected from six colonies in Hanoi, Vietnam, and analyzed using high-throughput sequencing of the 16S rRNA gene. Our results show that while the overall diversity of gut microbiota in DWV-infected and uninfected bees did not significantly differ, notable changes were observed in the relative abundances of specific bacterial taxa. In DWV-infected bees, the relative abundance of Proteobacteria significantly decreased, whereas Firmicutes increased compared to uninfected bees. At the genus level, a significant decrease in Gilliamella and an increase in Lactobacillus were observed in infected bees. Functional gene predictions indicated that pathways related to carbohydrate, fatty acid, and lipid metabolism, as well as the biosynthesis of cofactors, vitamins, and amino acids, were upregulated in DWV-infected bees. These findings highlight the impact of DWV infection on the gut microbiota of A. cerana and suggest potential avenues for using probiotics to restore gut microbial balance and improve honeybee health. This research provides a foundation for developing strategies to enhance the resilience of honeybee colonies against viral infections. [ABSTRACT FROM AUTHOR]

Colibacillosis is an intestinal tract infection in poultry caused by Escherichia coli. It is one of the leading causes of mortality and results in significant economic losses for the poultry farming sector due to its high incidence rate. Recently, E. coli has been considered a predominant bacterial pathogen that is responsible for diarrhea and bloodstream infections in chickens and ducks in Vietnam. In this study, E. coli strains associated with diarrhea were isolated from chicken and duck feces and intestines collected from poultry farms in Hai Phong province using a Macconkey selective medium. The obtained isolates were initially identified by the MALDITOF MS method, screened for hemolytic activity, and finally identified by 16S rRNA gene sequencing. As a result, eight E. coli strains exhibiting hemolytic activity were identified. Among them, E. coli_5, E. coli_6, and E. coli_8 strains were clustered with E. coli O78:H51, whereas E. coli_3 was grouped with E. coli O78:H4; E. coli_4 and E. coli_7 were clusterd with E. coli O25b: H4; and E. coli_9 and E. coli_16 were grouped with E. coli O26:H11. Our results provide insights into the genetic diversity of E. coli strains associated with diarrhea in poultry farms in Hai Phong province. The isolated strains will be further characterized for the development of effective strategies to control colibacillosis in poultry. [ABSTRACT FROM AUTHOR]

Haemotropic mycoplasmas (haemoplasmas) are obligate epierythrocytic bacteria that infect a wide range of vertebrate hosts. The molecular characterisation of Mycoplasma organisms in dogs has not previously been attempted from India. Hence, in the present study, the molecular characterisation of Mycoplasma spp. in dogs of different zones of Kerala was attempted using 16S rRNA gene. An overall prevalence of 18% for M. haemocanis was detected. The NCBI-BLAST analysis of all the selected sequences revealed > 99% identity with the sequences of M. haemocanis. The phylogenetic analysis revealed clustering of M. haemocanis and M. haemofelis in a single clade indicating low genetic variability. It was further supported by the genetic distance data and haplotype analysis. [ABSTRACT FROM AUTHOR]

The utilisation of enzymes in the industry has brought numerous benefits and advantages to production processes. Enzymes serve as biocatalysts, efficiently catalyzing reactions and hydrolysis in biochemical processes. However, there are challenges in applying enzymes in the industry, particularly concerning enzyme stability. The obstacle encountered in the production processes involving industrial enzyme applications is the low stability of enzymes when used at high temperatures. Heat-sensitive enzymes undergo damage or denaturation. Thermophilic microorganisms are chosen because they hold the potential to produce thermophilic enzymes. The thermophilic enzymes exhibit better heat stability compared to other enzymes, making them an effective alternative for future industrial production processes. This study aims to isolate thermotolerant bacteria from Nglimut Hot Spring sediment, screen for cellulase- and amylase-producing isolates, and molecularly identify the best isolate using 16S rRNA barcode. The results show that 22 bacterial isolates were found in the sediment of a hot spring; TS-14 was the best isolate in producing amylase, with the highest average amylolytic index of 2.38, whereas TS-15 had the highest cellulolytic index of 2.11. Based on 16S rRNA identification, TS-14 showed an homological identity of 79% with Bacillus amyloliquefaciens, while TS-15 had a 100% homological identity with Bacillus licheniformis. These results were important as the first step of screening bacterial potential to produce thermophilic enzymes that could be applied in the downstream processing in future industrial and biotechnology companies. [ABSTRACT FROM AUTHOR]

Blind mole rats (Nannospalax) in Turkey, adapted to low-oxygen subterranean habitats, demonstrate considerable diploid chromosome number diversity, including species like Nannospalax xanthodon, Nannospalax leucodon, and Nannospalax ehrenbergi. However, uncertainties persist regarding the taxonomic status and nomenclature of populations with varying diploid chromosome numbers. Resolving these uncertainties is essential for effective biodiversity management and strategic conservation planning within the ecosystem. This study focuses on elucidating the phylogenetic relationships within the blind mole rat genus Nannospalax, particularly among individuals exhibiting the 2n = 54 cytotype across diverse Turkish geographical regions. Utilizing nuclear (IRBP gene region) and mitochondrial DNA (D-loop control region and 16S rRNA gene regions), the study addresses key questions regarding the phylogenetic relationships between allopatric cytotypes sharing the same diploid chromosome number. The analyses, employing Maximum Likelihood, Neighbor Joining, and Network phylogenetic methods, reveal a preliminary differentiation level suggesting the potential existence of at least three cryptic species within the 2n = 54 cytotypes in Anatolia. It is emphasized that these conclusions are preliminary due to the limited sample size, necessitating further investigation. Additionally, the research validates the morphologically based species Nannospalax tuncelicus among Turkish blind mole rats. Genetic distance values from sequence analyses indicate significant divergence, establishing Nannospalax tuncelicus as a distinct species from other recognized species in Turkey. The study underscores the importance of resolving uncertainties in taxonomic status for effective biodiversity management and conservation planning. Future studies should expand sample sizes and comprehensively address the phylogenetic background of cytotypes, especially the İmamoğlu-Adana (2n = 54) population within the Nannospalax ehrenbergi species, to enhance our understanding of the evolutionary dynamics within this genus. [ABSTRACT FROM AUTHOR]

Simple Summary: Oysters are sessile, filter-feeding bivalves that are vital to fisheries and ecology but are poorly understood in terms of genetic diversity and distribution. This study examines small flat oysters in the Mediterranean regions of Liguria and Sardinia (Italy) using 16S rRNA sequencing to identify species. The findings reveal new insights into the Ostrea stentina complex and introduce a new species, O. neostentina, improving knowledge of Ostrea species diversity and distribution. Oysters are sessile, filter-feeding bivalve molluscs widely distributed in estuarine and coastal habitats worldwide. They constitute a valuable resource for fisheries and extensive aquaculture and provide essential ecological services. Yet, their genetic diversity and distribution remain understudied. The variability in shell morphology complicates species classification, which is influenced by environmental and genetic factors. Although molecular phylogenetics research has refined oyster taxonomy and identified approximately 100 extant species, numerous taxonomic uncertainties persist. In the present study, we aimed to document the occurrence of small flat oysters of the genus Ostrea along the Mediterranean coastal areas of Liguria and Sardinia (Italy). Specifically, 16S rRNA sequence data were used to identify Ostrea species. Our findings offer novel insights into the O. stentina species complex and O. neostentina, a new species in the Mediterranean coastal areas of Italy. The study data further our understanding of Ostrea species diversity, distribution, and evolutionary patterns. [ABSTRACT FROM AUTHOR]

Helicobacter pylori is a human pathogen bacterium associated with gastritis, peptic ulcer, and gastric cancer. It can be identified through the 16S rRNA gene and characterized through cagA and vacA virulence genes. Clinical cultures of H. pylori were isolated and identified from human stomach biopsies. The isolates were characterized according to their colonial and microscopic morphology, and molecular genotyping was conducted to determine the bacterial virulence. A phylogenetic analysis of the 16S rRNA gene sequencing was performed. In addition, multilocus sequence typing analysis was performed to determine the phylogeographic nature of the isolated strains. Three bacterial isolates were selected from 22 gastric biopsies, identified as H. pylori through colonial morphology, Gram staining, urease, catalase, and oxidase tests and identification of the ureC gene through end-point PCR. Amplification of 16S rRNA, urea, and tonB genes was performed, as well. Differences between the cagA and vacA genotypes were determined among the isolates. The phylogenetic analysis confirmed the identity of the three isolates as the specie Helicobacter pylori. Different genotypes were obtained for each H. pylori strain, and all the clinical isolates showed the vacA s2/m2 genotype, indicating an absence of the VacA cytotoxin. Only HCGDL-MR01 is a cagA gene carrier with a greater risk to develop a serious disease, such as stomach cancer and peptic ulcer. The multilocus sequence typing placed all the strains within the hpEurope population structure. [ABSTRACT FROM AUTHOR]

The Fabaceae genus Trifolium comprises around 250 species widely distributed worldwide, with the temperate Northern Hemisphere exhibiting the highest variety. The plants in this genus are widely used as livestock fodder crops and are particularly significant economically. This study's objective included isolating bacteria from the root nodules of the Trifolium repens plant and diagnosing it at the molecular and microbiological levels. T. repens root nodules were used as the source of an endophytic bacteria isolated on Yeast Extract Mannitol (YEM) media that had solidified and diagnosed at the molecular level by DNA Sequencing technique for analysis of the sequence of the nitrogenous bases of 16S rRNA gene with the global database. The isolated bacteria were characteristic of greyish-white color after 48 hours of growth and appeared as a circular shape, slightly convex and gram-negative. The bacteria were resistant to the antibiotics 20µg/ml Aztreonam. The DNA sequencing technique for analysis of the sequence of the nitrogenous bases of 16S rRNA gene with the global database of the National Center for Biotechnology Information (NCBI) showed that the isolated bacteria was at least 96.22% similar to the species Acinetobacter baumannii As a result, it was recorded for the first time as Acinetobacter sp. AZS1 strain in NCBI. [ABSTRACT FROM AUTHOR]

Microbial pathogenesis contributes a significant proportion to the global human mortality rate. Further, the outbreak of antimicrobial-resistant strains represents an alarming threat to human and animal healthcare, which drives scientific research on searching for novel antimicrobials. The present study is one such initiative to isolate new classes of antibiotics from the marine actinomycetes to combat the perpetual increase of multidrug-resistant strains. The soil samples from Tamil Nadu, India's coastal regions, were collected, and eight isolates of the actinomycete species (S1, S1b, S2, S3, S4b, S4W, S4R, S5) were recovered. From their 16S rRNA sequencing, the isolates belonged to Streptomyces sp.; the phylogenetic tree was constructed through the neighbour-joining method. Further, the secondary metabolites of all the isolates were screened against ATCC strains, Staphylococcus aureus (ATCC 25923), Enterococcus faecalis (ATCC 29212), Escherichia coli (ATCC 25927) and Acinetobacter baumanni (ATCC 19606) and multidrug-resistant (MDR) strains, methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant Enterococcus faecalis (VRE), carbapenem-resistant Klebsiella pneumonia (OXA) and colistin-cephalosporin resistant Escherichia coli (MCR). Of the eight isolates, S1b and S3 showed good inhibition for all the strains tested and their genomic sequences were sequenced and submitted to Genbank, MK641472 (S1b) & MK641473 (S3). Conclusively, their metabolites were purified using LC-MS and no resemblances were found with standard classes of antimicrobials such as nitrofurans, sulfonamides, fluoroquinolones, tetracyclines, chloramphenicols or ivermectins, which suggests that these metabolites are novel and could be exploited for the prospective antimicrobial research. [ABSTRACT FROM AUTHOR]

The aim of this study was to investigate the characteristics of fructophilic lactic acid bacteria isolated from fructose-rich niches (bee digestive tract, yam fruit, hazelnut leaf, grape, tomato, white mulberry, pear, kiwi) for their use as probiotics. Among a large number of isolates from these sources, 10 catalase-negative and Gram-positive bacterial strains were initially selected. Cell morphology and genotypic characteristics (RAPD-PZR, 16S rRNA sequencing) of the selected strains were determined in the first stage. The fructophilic isolates included in the study were identified as Enterococcus faecalis. Phylogenetic analyses of the related isolates were performed and isolates isolated from the bee gastrointestinal tract and isolates isolated from different plant sources were grouped into separate clades. Isolates whose phenotypic and genotypic characteristics were defined were then tested for their potential probiotic properties. In this context, acid, pepsin and pancreatin resistance profiles of the isolates were determined. In addition, isolates coded A6, 7, 9 and 10 were proven to be potential bacteriocin producers. In this study, it was shown that fructophilic lactic acid bacteria can be isolated from different plant sources and may have probiotic potential. [ABSTRACT FROM AUTHOR]

• The composition of gut microbiota was evaluated in adults with and without CF. • Gut microbiota samples were analyzed using full-length 16S rRNA gene sequencing. • CF is associated with alterations of gut microbiota in adult CF patients. • Body Mass Index is related to gut microbiota dysbiosis in adults with CF. Microbial dysbiosis has been linked to cystic fibrosis (CF); however, the composition of gut microbiota in adult CF patients in relation to severity of CF transmembrane conductance regulator (CFTR) gene mutation and nutritional status have not yet been explored. Study aimed to assess the gut microbiota composition in adults with CF, and its relationship with the severity of CFTR mutations, and BMI. Gut microbiota of 41 adults with CF, and 26 non-CF controls were compared using whole 16S rRNA gene sequencing. Differences in the microbial community between groups of patients classified according to the severity of CFTR mutations, and BMI were assessed. The alpha diversity, beta diversity, and taxa abundance were identified to reflect gut microbiota composition. Results showed a significant decrease in alpha diversity of bacterial communities in CF compared to non-CF group, but no significant difference between the CF groups distinguished by the severity of CFTR mutations. However, more severe mutations were associated with the higher relative abundance of Bacteroides and Streptococcus and the lower relative abundance of Faecalibacterium and Blautia. Undernourished CF patients showed significantly lower alpha diversity compared to non-CF group and CF patients with BMI within the norm. Significant differences in the structure of the gut microbiota between CF and non-CF groups, as well as between BMI groups were also found. Our research indicates that CF is associated with alterations in gut microbiota in adults. Additionally, in adult CF patients, the composition of the gut microbiota is also related to BMI. [ABSTRACT FROM AUTHOR]

Bacteriocins are proteins secreted by many species of bacteria to inhibit other bacteria, thus eliminating competitors to gain resources. Bacteria from the Lactobacillus group are known for their applications as probiotics and food preservatives. They have earned a reputation for producing substances that inhibit the growth of other microorganisms, which include organic acids, diacetyl, and bacteriocins. Produced by the ribosomes, bacteriocins are cationic proteins that inhibit other bacteria coexisting within a shared ecological habitat. Due to their potential uses in a variety of applications large-scale production of Bacteriocins would be necessary. The study aimed to identify and characterize Lactobacillus bacteria that produce potent bacteriocins and to analyze the antimicrobial activity and stability of the isolated bacteriocin under various physical and biochemical conditions. A total of 50 samples including buffalo dung, cheese, and rhizospheric region of plants were screened to isolate 8 Lactobacillus Li-1, Li-2, Li-3, Li-4, Li-5, Li-6, Li-7, and Li-8, confirmed by gram staining and other biochemical tests. The cell free supernatant from the Li-3 strain showed higher inhibition of Escherichia coli and Staphylococcus aureus, as compared to the other isolated strains. Li-3 strain was further identified as Levilactobacillus brevis strain ABRIINW-K by 16S rRNA gene sequencing. The bacteriocin isolated from this strain is a thermostable peptide (~6kDa), which is characteristic of class II bacteriocins, with potent antibacterial activity against Lactobacillus rhamnosus, Escherichia coli, and Salmonella enterica. [ABSTRACT FROM AUTHOR]

Objective(s): This study aimed to explore the therapeutic effect of fecal microbiota transplantation (FMT) on liver cirrhosis-induced rat models by studying changes in intestinal flora distribution and liver pathology. Materials and Methods: Cirrhosis was induced in adult male Sprague-Dawley rats using carbon tetrachloride; successful establishment of the cirrhosis model was verified using hematoxylin and eosin (HE) staining. Rats were divided into normal control, cirrhosis model+normal saline, and cirrhosis model+FMT groups. Fecal intestinal flora was analyzed using 16S rRNA high-throughput sequencing for each group. Alpha diversity, beta diversity, and functional prediction analyses were performed. Additionally, rat liver tissue was subjected to HE staining to compare the degree of fibrosis and liver damage between the groups. Results: FMT significantly improved the diversity, richness, and uniformity of the intestinal flora in rats with liver cirrhosis. Notably, post-FMT, the abundance of lactobacillaceae, bacilli, and bacteroidia increased, while the abundance of clostridia decreased. Moreover, hepatic fibrosis improved after FMT. Conclusion: The dysbiosis of intestinal flora in rats with liver cirrhosis improved after FMT. Thus, FMT can regulate intestinal flora, reduce liver inflammation, and improve hepatic fibrosis and cirrhosis. [ABSTRACT FROM AUTHOR]

The aim of the study was to develop a molecular diagnosis protocol of monocytic ehrlichiosis and granulocytic anaplasmosis in dogs by conventional polymerase chain reaction (PCR) and to compare the results from PCR and a rapid serological test. One hundred and six blood samples from dogs were tested by the rapid serological test SNAP 4Dx Plus (IDEXX Laboratories, Westbrook, ME) and by conventional PCR. Sixty-two of them (58.49%) were positive for antibodies to Ehrlichia canis/Ehrlichia ewingii and 14 (13.21%) for antibodies to Anaplasma phagocytophilum/Anaplasma platys. In 24 (22.64%) blood samples, antibodies against both pathogens were simultaneously detected. Six (5.66%) samples were seronegative. Fourty-six of the 106 tested samples (43.4%) were positive for a 345 bp segment of the ribosomal gene of family Anaplasmataceae. In 28 of them the presence of a 444 bp fragment of the ankA gene of A. phagocytophilum was detected, and in 26: a 409 bp fragment of the gene of E. canis. Nine samples were simultaneously positive for genetic sequences of E. canis and A. phagocytophilum. The target DNA fragments specific for the two studied pathogens were not detected in one of the Anaplasmataceae-positive samples. In the remaining 60 cases (56.6%), the presence of a 345 bp segment of the ribosomal gene was not detected. In the present study, the DNA of E. canis and of A. phagocytophilum was detected for the first time in Bulgarian dogs by the conventional PCR. [ABSTRACT FROM AUTHOR]

Biological invasions are among the major stressors on aquatic ecosystems. It can significantly affect species distribution and native biodiversity. Penaeus monodon invasions are frequently reported worldwide, leading to the establishment of several breeding populations. P. monodon was first recorded and morphologically identified in the Mediterranean Sea in Egypt in 2016. The current investigation aimed to assess the genetic diversity and origin of a P. monodon population from the Mediterranean Sea, Egypt, and to evaluate the genetic diversity of P. monodon populations worldwide using two different mitochondrial barcode regions, cytochrome c oxidase subunit I (COI) and 16S rRNA. Different P. monodon populations with Indo-Pacific and Atlantic origins were included for these purposes. Based on the COI, 16 haplotypes were recorded in nine P. monodon populations, with 45 polymorphic sites. High haplotype diversity (Hd = 0.7575) and high nucleotide diversity (π = 0.0261) were also recorded. Based on 16S rRNA, 37 haplotypes were recorded in seven P. monodon populations, with 72 polymorphic sites, high haplotype diversity (Hd = 0.9838), and high nucleotide diversity (π = 0.0985). The populations of P. monodon within its species range (of Indo-Pacific and Atlantic origins) shared many haplotypes, indicating shared lineages. Barrier analysis has divided the studied populations into groups in which Egypt was grouped with populations of Atlantic origin (based on COI and 16S rRNA) and supported with evidence of the Atlantic origin of the Egyptian population. This study showed that the Suez Canal is not the inevitable route for this species to invade the Mediterranean; therefore, precision must be exercised when determining the route of entry of any species into the Mediterranean Sea. The frequent introductions/invasions of the P. monodon population significantly contributed to the observed patterns of genetic diversity and favored its ability to adapt, colonize, and expand. [ABSTRACT FROM AUTHOR]

Globally, there is growing concern over the environmental contamination of coastal ecosystems caused by anthropogenic activities. Here,we performed a study to evaluate the degree of heavy metal contamination in 5 different sediment samples collected from five sites along the Southeastern coast of India. Additionally, the research aims to explore the potential ecological implications of heavy metal contamination on the bacterial diversity, a crucial factor in upholding a sustainable ecosystem. A total of seven heavy metals, i.e., chromium (Cr), copper (Cu), nickel (Ni), lead (Pb), mercury (Hg), cadmium (Cd) and arsenic (As), were assessed and quantified using inductively coupled plasma mass spectrometry. Targeted amplicon sequencing revealed that phylum Proteobacteria (36.9%) was the most dominating followed by Halobacterota (25.5%), Actinobacteriota (15%), Firmicutes (6.7%), Bacteroidota (4.0%), Thermoplasmatota (2.3%), Acidobacteriota (2.0%), Chloroflexi (1.6%), Planctomycetota (1.2%) and Crenarchaeota (1.1%). According to the alpha diversity estimate, lesser bacterial diversity was observed in areas with high pollution levels. Moreover, the physicochemical parameters of the sediments were analyzed. The contamination levels of the sediments were evaluated using the geo-accumulation index (Igeo), contamination factor (CF) and pollution loading index (PLI) to ascertain the comprehensive toxicity status of the sediments. The Igeo values revealed sediment pollution with metals such as Hg and Cd. The sediments obtained from the sampling site PU-01 showed the highest concentration of Hg pollution. Considering the ecotoxicological aspect, the estimated risk index (RI) values indicated a range from low to significant ecological risk. [ABSTRACT FROM AUTHOR]

During the last few decades, the main focus of numerous studies has been on the human breast milk microbiota and its influence on the infant intestinal microbiota and overall health. The presence of lactic acid bacteria in breast milk affects both the quantitative and qualitative composition of the infant gut microbiota. The aim of this study was to assess the most frequently detected cultivable rod-shaped lactobacilli, specific for breast milk of healthy Bulgarian women and fecal samples of their infants over the first month of life, in 14 mother–infant tandem pairs. Additionally, we evaluated the strain diversity among the most common isolated species. A total of 68 Gram-positive and catalase-negative strains were subjected to identification using the MALDI-TOF technique. Predominant cultivable populations belonging to the rod-shaped lactic acid bacteria have been identified as Lacticaseibacillus rhamnosus, Limosilactobacillus fermentum, Lacticaseibacillus paracasei, and Limosilactobacillus reuteri. Also, we confirmed the presence of Lactiplantibacillus plantarum and Lactobacillus gasseri. Up to 26 isolates were selected as representatives and analyzed by 16S rRNA sequencing for strain identity confirmation and a phylogenetic tree based on 16S rRNA gene sequence was constructed. Comparative analysis by four RAPD primers revealed genetic differences between newly isolated predominant L. rhamnosus strains. This pilot study provides data for the current first report concerning the investigation of the characteristic cultivable lactobacilli isolated from human breast milk and infant feces in Bulgaria. [ABSTRACT FROM AUTHOR]