Genus Level Research Articles

Abstract PO4-03-04: Characterization of Gut Microbiome of patients with early-stage breast cancer treated with neoadjuvant chemotherapy

Abstract Objective: The gut microbiome (GM) has been identified as one of the major environmental factors that can regulate the development and maintenance of the immune system. In oncology, while the importance of GM has been evaluated in more immunogenic tumors such as melanoma, lung carcinoma and clear cell carcinoma, its importance in early-stage breast cancer (eBC) is underexplored. The aim of this study was to characterize the GM of patients with eBC who underwent neoadjuvant chemotherapy (NACT) and to evaluate its association with clinicopathologic prognostic factors and outcomes. Methods: This was a prospective study conducted at two Brazilian institutions. Fecal samples were collected at baseline (time 1) and prior to surgery (time 2) from 55 patients who received NACT with anthracycline/taxane. Gut microbiome was analyzed by 16S rRNA amplicon sequencing to characterize the α (InvSimpson index) and β (weighted UniFrac distance metric) diversity, as well as taxonomic composition. Clinicopathologic prognostic factors were retrieved from medical records. Pathological complete response (pCR) was defined as the absence of invasive carcinoma in breast and axillary nodes (ypT0/Tis ypN0). Stromal tumor-infiltrating lymphocytes (sTIL) were reported according to the TIL working group criteria. Information about prior use (< 60 days before stating on NACT) of antibiotic (ATB) was obtained directly from patients. Statistical significance was set at P ≤ 0.05 and analysis of composition of microbiomes (ANCOM-BC2) was used to identify enriched genera with p-values adjusted using FDR correction ≤ 0.25. Results: Median age was 49 years (range 31-73). Eleven patients (20%) reported prior antibiotic use at baseline. About 34.5% of patients had HR+/HER2- tumors, 45.4% had triple negative breast cancer (TNBC), and 20% had HER2-positive breast cancer. Fourteen (25%) patients achieved a pCR. Out of 55, 47 (85.4%) had sTIL information. There was no significant difference in alpha diversity (p = 0.6) or beta-diversity (p = 0.8) between the pCR and residual disease group nor within clinical pathologic factors (age, staging, histological tumor grade, subtype of breast cancer based on IHC, sTIL). The most abundant taxon in both time 1 and time 2 were the same (Blautia at genus level, Lachnospiraceae at family level, and Lachnospirales at order level), and longitudinal samples collected during NACT showed no significant changes in GM composition. At baseline, we found an enrichment for Clostridia sp. among patients who did not use ATB (p < 0.05, pFDR ≤ 0.25). Additionally, we found enrichment for Bifidobacterium (p < 0.05, pFDR ≤ 0.25) among patients with HER2 subtype who presented residual disease. Conclusions: Gut microbiome analysis in early breast cancer is feasible and to our knowledge, this is the first study to evaluate the intestinal microbiota of Brazilian patients with breast cancer. We did not observe any significant association between GM diversity and taxonomic composition with clinical pathologic factors and pCR in this study, nor did we observe changes in the ecological balance of the GM following NACT in breast cancer. Further studies are needed to explore the potential influence of the gut microbial ecosystem on tumor biology and response to neoadjuvant chemo-immunotherapy. Citation Format: Ludmila Thommen, Vitor Heidrich, Rosângela Vieira de Andrade, Luiza Nardin Weis, Maria Sueli Soares Felipe, Melissa Lole Da Cas Vita, Thiago David Alves Pinto, Anamaria Camargo, Romualdo Barroso-Sousa. Characterization of Gut Microbiome of patients with early-stage breast cancer treated with neoadjuvant chemotherapy [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO4-03-04.

Phyto-parasitic nematodes of bell pepper plant and farm soil in Abua, Rivers State, Nigeria

Bell pepper farming significantly contributes to economic development in Abua. However, phyto-parasitic nematodes are endemic in the area and affect quality of crop yield. Hence, this study was undertaken to investigate the dynamics of occurrence of nematodes in bell pepper roots and soil samples of the farms in Abua. Roots and soil from the root rhizosphere were simultaneously collected at 0-20 cm depth using an improvised soil auger and knife. Modified sieve plate technique was employed for nematode detection and a pictorial key was used for nematode identification at the genera level. An overall nematode abundance of 746 nematodes in the soil around the root region and 216 nematodes in the root tissues of the bell peppers were recorded. Gracilachus species (10.6 %) was more prevalent in the soil, and Meloidogyne species (35.2 %) exhibited the highest population in roots. The study found that Abua's cultivated soil is susceptible to nematode infestation, limiting crop performance. The nematodes showcased root burrowing which is an inherent pattern for survival. The result on root nematodes across the five bell farms surveyed was not significant (p > 0.05). The result opined that farmers in Abua, Rivers State, should understand the role of the soil nematodes and implement soil improvement strategies for improved crop performance and rural economic development.

Abstract PO3-09-03: Dysbiosis of gut microbiota in patients with breast cancer

Abstract [Background] The effects of gut microbiome on various diseases have become widely known, and many studies reported that there was a correlation between the change of gut microbiota, that is dysbiosis, and the progression of digestive tract cancer. In addition, it is well-known that gut microbiota was correlated to the efficacy of immune checkpoint inhibitors for multiple types of cancer. However, the significance of gut microbiota in patients with breast cancer still remains unclear. The aim of this study is to analyze the gut microbiota in patients with breast cancer, compared with healthy women. [Subjects and Methods] We used the pre-treatment feces of 79 patients with primary breast cancer who received treatment at our facility and performed metagenome analysis of the V3-4 region of 16S rDNA. We also analyzed the breast cancer patients' microbiota with QIIME2 analysis method, compared to randomly selected 100 women aged 30-77 years from NIBIOHN's public data . We also assessed the characteristics of the gut microbiota of breast cancer patients by subtypes and its relationship with clinical and pathological factors. [Results] In Japanese gut microbiota, the Firmicutes and Bacteroidetes phyla make up the majority, but Firmicutes was the most common bacterial phylum in 52% of the public cohort, whereas 96.2% (76/79) of the breast cancer patients’ group (BC) showed a significantly higher proportion (p< 0.0001). In addition, ANCOM analysis revealed that the relative bacterial amounts of the Firmicutes, Bacteroidetes, and Proteobacteria phyla were significantly decreased in BC compared to the public cohort (PC), and at the bacterial genus level, the Feacalibacterium genus was significantly decreased in BC. Furthermore, the percentage of Fusobacteria phylum, which is a well-known oral bacteria that exacerbates digestive tract cancer, was 49.3% in BC, compared to 35% in PC (p=0.04). Among BC, the relative frequency of Fusobacteria phylum was significantly higher in the HER2-negative group than in the HER2-positive group (p< 0.0001). In BC, both alpha diversity (p< 0.0001) and beta diversity (p=0.001) were significantly lower than in PC. [Conclusion] An increase in the Firmicutes phylum is known to be associated with obesity, and also likely to affect the incidence risk of breast cancer. The results suggest that the Fusobacteria phylum and Feacalibacterium genus may be risk or preventive factors for breast cancer. Dysbiosis of gut microbiota is suggested to be associated with various diseases, and in this study the decrease in bacterial amount and diversity was observed in BC compared to PC, which may affect the onset and progression of breast cancer. Citation Format: Mai Yamada, Takafumi Morisaki, Yo Sato, Kimihisa Mizoguchi, Yuka Takao, Yurina Ochiai, Yoshiki Ootubo, Saori Hayashi, Masafumi Nakamura, Makoto Kubo. Dysbiosis of gut microbiota in patients with breast cancer [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO3-09-03.

Fermented bile acids improved growth performance and intestinal health by altering metabolic profiles and intestinal microbiome in Micropterus salmoides

A type of fermented bile acids (FBAs) has been produced through a biological method, and its effects on growth performance, metabolism, and intestinal microbiota in largemouth bass were investigated. The results demonstrated that incorporating 0.03 %–0.05 % FBAs diet could improve the final weight, weight gain and specific growth rate, and decrease the feed conversion ratio. Dietary FBAs did not significantly affect the levels of high-density lipoprotein, low-density lipoprotein, and triglycerides, but decreased the activities of α-amylase in most groups. Adding FBAs to the diet significantly increased the integrity of the microscopic structure of the intestine, thickened the muscular layer of the intestine, and notably enhanced its intestinal barrier function. The addition of FBAs to the diet increased the diversity of the gut microbiota in largemouth bass. At the phylum level, there was an increase in the abundance of Proteobacteria, Firmicutes, Tenericutes and Cyanobacteria and a significant decrease in Actinobacteria and Bacteroidetes. At the genus level, the relative abundance of beneficial bacteria Mycoplasma in the GN6 group and Coprococcus in the GN4 group significantly increased, while the pathogenic Enhydrobacter was inhibited. Meanwhile, the highest levels of AKP and ACP were observed in the groups treated with 0.03 % FBAs, while the highest levels of TNF-α and IL-10 were detected in the group treated with 0.04 % FBAs. Additionally, the highest levels of IL-1β, IL-8T, GF-β, IGF-1, and IFN-γ were noted in the group treated with 0.06 % FBAs. These results suggested that dietary FBAs improved growth performance and intestinal wall health by altering lipid metabolic profiles and intestinal microbiota in largemouth bass.

Modulation effect of sulfated polysaccharide from Sargassum fusiforme on gut microbiota and their metabolites in vitro fermentation.

The present study demonstrated the digestion behavior and fermentation characteristics of a sulfated polysaccharide from Sargassum fusiforme (SFSP) in the simulated digestion tract environment. The results showed that the molecular weight of two components in SFSP could not be changed by simulated digestion, and no free monosaccharide was produced. This indicates that most of SFSP can reach the colon as prototypes. During the fermentation with human intestinal flora in vitro, the higher-molecular-weight component of SFSP was utilized, the total sugar content decreased by 16%, the reducing sugar content increased, and the galactose content in monosaccharide composition decreased relatively. This indicates that SFSP can be selectively utilized by human intestinal flora. At the same time, SFSP also changed the structure of intestinal flora. Compared with the blank group, SFSP significantly increased the abundance of Bacteroidetes and decreased the abundance of Firmicutes. At the genus level, the abundances of Bacteroides and Megamonas increased, while the abundances of Shigella, Klebsiella, and Collinsella decreased. Moreover, the concentrations of total short-chain fatty acids (SCFAs), acetic, propionic and n-butyric acids significantly increased compared to the blank group. SFSP could down-regulate the contents of trimethylamine, piperidone and secondary bile acid in fermentation broth. The contents of nicotinic acid, pantothenic acid and other organic acids were increased. Therefore, SFSP shows significant potential to regulate gut microbiota and promote human health.

Identifying and characterization of novel broad-spectrum bacteriocins from the Shanxi aged vinegar microbiome: Machine learning, molecular simulation, and activity validation

Shanxi aged vinegar microbiome encodes a wide variety of bacteriocins. The aim of this study was to mine, screen and characterize novel broad-spectrum bacteriocins from the large-scale microbiome data of Shanxi aged vinegar through machine learning, molecular simulation and activity validation. A total of 158 potential bacteriocins were innovatively mined from 117,552 representative genes based on metatranscriptomic information from the Shanxi aged vinegar microbiome using machine learning techniques and 12 microorganisms were identified to secrete bacteriocins at the genus level. Subsequently, employing AlphaFold2 structure prediction and molecular dynamics simulations, eight bacteriocins with high stability were further screened, and all of them were confirmed to have bacteriostatic activity by the Escherichia coli BL21 expression system. Then, gene_386319 (named LAB-3) and gene_403047 (named LAB-4) with the strongest antibacterial activities were purified by two-step methods and analyzed by mass spectrometry. The two bacteriocins have broad-spectrum antimicrobial activity with minimum inhibitory concentration values of 6.79 μg/mL-15.31 μg/mL against Staphylococcus aureus and Escherichia coli. Furthermore, molecular docking analysis indicated that LAB-3 and LAB-4 could interact with dihydrofolate reductase through hydrogen bonds, salt-bridge forces and hydrophobic forces. These findings suggested that the two bacteriocins could be considered as promising broad-spectrum antimicrobial agents.

Microbial diversity and metabolic pathways linked to benzene degradation in petrochemical-polluted groundwater

The rapid advance in shotgun metagenome sequencing has enabled us to identify uncultivated functional microorganisms in polluted environments. While aerobic petrochemical-degrading pathways have been extensively studied, the anaerobic mechanisms remain less explored. Here, we conducted a study at a petrochemical-polluted groundwater site in Henan Province, Central China. A total of twelve groundwater monitoring wells were installed to collect groundwater samples. Benzene appeared to be the predominant pollutant, detected in 10 out of 12 samples, with concentrations ranging from 1.4 μg/L to 5,280 μg/L. Due to the low aquifer permeability, pollutant migration occurred slowly, resulting in relatively low benzene concentrations downstream within the heavily polluted area. Deep metagenome sequencing revealed Proteobacteria as the dominant phylum, accounting for over 63 % of total abundances. Microbial α-diversity was low in heavily polluted samples, with community compositions substantially differing from those in lightly polluted samples. dmpK encoding the phenol/toluene 2-monooxygenase was detected across all samples, while the dioxygenase bedC1 was not detected, suggesting that aerobic benzene degradation might occur through monooxygenation. Sequence assembly and binning yielded 350 high-quality metagenome-assembled genomes (MAGs), with 30 MAGs harboring functional genes associated with aerobic or anaerobic benzene degradation. About 80 % of MAGs harboring functional genes associated with anaerobic benzene degradation remained taxonomically unclassified at the genus level, suggesting that our current database coverage of anaerobic benzene-degrading microorganisms is very limited. Furthermore, two genes integral to anaerobic benzene metabolism, i.e, benzoyl-CoA reductase (bamB) and glutaryl-CoA dehydrogenase (acd), were not annotated by metagenome functional analyses but were identified within the MAGs, signifying the importance of integrating both contig-based and MAG-based approaches. Together, our efforts of functional annotation and metagenome binning generate a robust blueprint of microbial functional potentials in petrochemical-polluted groundwater, which is crucial for designing proficient bioremediation strategies.

High-Throughput Sequencing Technology Assisted Investigation of the Correlation between Intestinal Flora, Serum Biochemistry, Blood Lipids, and Tumour Markers in Patients with Gastric Cancer and Healthy Plateau Residents.

Aim The goal is to use high-throughput sequencing technology to compare and study the structure and variety of intestinal flora in people with gastric cancer and healthy people in the Qinghai-Tibet Plateau. Background Recent research has connected gut flora structure to numerous disorders. Metabolites, endotoxins, and immunomodulatory modulation might cause gastrointestinal or other systemic diseases and affect gastric cancer treatment and prognosis. We used the correlation study to uncover biomarkers associated with good intestinal flora and gastric cancer groups on the plateau to investigate their involvement in gastric cancer development. Objectives To investigate the possible links between intestinal flora and gastric cancer in the Qinghai Plateau region using a variety of clinical phenotypic data and to investigate the flora that may be linked to gastric cancer. Methods The 22 Qinghai Province tertiary hospital gastric cancer patients and 30 healthy people had their fresh faeces collected. To examine intestinal flora diversity and composition, 52 patients underwent 16S rDNA high-throughput gene sequencing of intestinal bacteria. The correlation between clinical phenotypes and the top 15 dominant intestinal flora at the phylum level was analyzed. Results The difference in total protein TP between the healthy group and the gastric cancer group was statistically significant (P<0.001). Globulin was significantly different (P<0.05), TC of total cholesterol was significantly different (P<0.05). High-density lipoprotein showed statistical significance (P<0.05).The difference in low-density lipoprotein was statistically significant (P<0.001). Alpha-fetoprotein was significantly different (P<0.05). CA72-4 carbohydrate antigen (P<0.05). Conclusion There were significant differences in total protein, globulin, total cholesterol, high density lipoprotein, low-density lipoprotein, alpha-fetoprotein and carbohydrate antigen CA72-4 in patients with gastric cancer in the plateau area compared with the healthy group, and the different clinical variables were correlated with intestinal flora at some phylum and genus levels.

Effects of metformin, saxagliptin and repaglinide on gut microbiota in high-fat diet/streptozocin-induced type 2 diabetic mice

IntroductionThere has been increasing evidence that the gut microbiota is closely related to type 2 diabetes (T2D). Metformin (Met) is often used in combination with saxagliptin (Sax) and repaglinide (Rep)...

Phytoparasitic and free-living nematodes associated with the cultivation of Passiflora ligularis Juss. in the Sandia Valley, Puno Region, Peru

The identification of phytoparasitic nematodes, which is essential for the implementation of management strategies, is required for further study. The objective of this work was to identify, at the genus level, the phytoparasites and free-living nematodes associated with the cultivation of sweet granadilla (Passiflora ligularis Juss.) in the valley of Sandia, region Puno, Peru. For the study, 165 soil samples were evaluated, coming from eight communities from the district of Sandia, during the agricultural season 2018–2019. The samples were processed by the method of centrifugal fluctuation in sucrose solution, later identified on the basis of morphological characteristics. The results showed the presence of seven genera of phytoparasitic nematodes, Meloidogyne, Pratylenchus, Helicotylenchus, Mesocriconema, Xiphinema, Tylenchus, and Hemicycliophora, and two genera of free-living nematodes, Aphelenchus and Dorylaimus. The most harmful genera were Meloidogyne and Pratylenchus because they cause damage to other crops. In the nematode community, there was variability in the density and frequency of phytoparasitic and free-living nematodes in the evaluated localities.

Da-Jian-Zhong decoction alleviates diarrhea-predominant irritable bowel syndrome via modulation of gut microbiota and Th17/Treg balance

Ethnopharmacological relevanceDa-Jian-Zhong decoction (DJZD) is a herbal formula clinically used for abdominal pain and diarrhea induced by spleen-Yang deficiency syndrome. Recently, treatment of diarrhea-predominant irritable bowel syndrome (IBS-D) with DJZD has received increasing attention, but the underlying mechanism of action remains elusive. Aim of the studyWe aimed to evaluate the therapeutic effect of DJZD on IBS-D rats and to elucidate the underlying mechanisms. Materials and methodsAn IBS-D rats model was constructed using a two-factor superposition method of neonatal maternal separation and Senna folium aqueous extract lavage. Moreover, the effect of DJZD was evaluated based on the body weight, rectal temperature, abdominal withdrawal reflex (AWR), and Bristol stool scale score (BSS). The factors that regulate the DJZD effects on IBS-D were estimated using whole microbial genome, transcriptome sequencing (RNA-Seq), flow cytometry, and quantitative reverse transcription polymerase chain reaction (RT-qPCR) analyses. ResultsWe found that DJZD alleviated the symptoms of IBS-D rats, with the low-dose (2.4 g/kg) as the better ones, as shown by the higher body mass and lower AWR score and BSS. At the phylum level, the relative abundance of Bacteroidetes was obviously increased, and at the genus level, Bacteroides was increased, while that of Firmicutes_bacterium_424 and Ruminococcus gnavus was decreased in DJZD group. The significantly enriched GO terms after treatment with DJZD mainly included the immune response, positive regulation of activated T cell proliferation, and positive regulation of interleukin-17 (IL-17) production. Importantly, flow cytometry analysis further revealed that the T helper cell type 17/regulatory T cell (Th17/Treg) balance contributed to the DJZD-induced alleviation of IBS-D symptoms, as DJZD downregulated Th17/Treg ratio and Th17 cell-related cytokines IL-17 and IL-6 levels in the colon. ConclusionsThese results demonstrate that DJZD has a good therapeutic effect on IBS-D rats, probably by maintaining the homeostasis of gut microbiota and regulating Th17/Treg balance and its related inflammatory factors.

A novel endolysin from an Enterococcus faecalis phage and application

Enterococcus faecalis is the primary species detected in cases of secondary persistent infection resulting from root canal therapy failure. Due to the overuse of antibacterial agents, E. faecalis has developed resistance to these drugs, making it challenging to treat clinical diseases caused by E. faecalis infection. Therefore, there is an urgent need to explore new alternative drugs for treating E. faecalis infections. We aimed to clone and express the genes of phage endolysins, purify the recombinant proteins, and analyze their antibacterial activity, lysis profile, and ability to remove biofilm. The crude enzyme of phage endolysin pEF51 (0.715 mg/mL), derived from phage PEf771 infecting E. faecalis, exhibited superior bacterial inhibitory activity and a broader bactericidal spectrum than its parental phagePEf771. Furthermore, pEF51 demonstrated high efficacy in eliminating E. faecalis biofilm. Therapeutic results of the infected Sprague-Dawley (SD) rat model indicated that among 10 SD rats, only one developed a thoracic peritoneal abscess and splenic peritoneal abscess after 72 hours of treatment with pEF51. This suggests that pEF51 could provide protection against E. faecalis infection in SD rats. Based on the 16S rDNA metagenomic data of the intestinal microbial community of SD rats, endolysin pEF51 exerted a certain influence on the diversity of intestinal microorganisms at the genus level. Thus, pEF51 may serve as a promising alternative to antibiotics in the management of E. faecalis infection.

Effects of fermented and unfermented aging corn on ruminal fermentation, bacterial communities, lactation performance and plasma metabolites in Holstein cows

Aging reduces the nutritional value of corn grain, which may be improved by fermentation prior to use. This study investigated the effects of replacing conventional corn (CC) with aging corn (AC) and fermented aging corn (FAC) in the diets of lactating Holstein cows. Six healthy third-parity Holstein cows were used in a replicated 3 × 3 Latin square experiment with 21-day periods. Cows were fed twice and milked twice daily. The cows were randomly divided into three treatment groups: (1) CC diet: a diet with 23.6% starch in diet DM containing 24.0% conventional corn; (2) AC diet: a diet with 23.5% starch in diet DM containing 24.0% aging corn replacing conventional corn; and (3) FAC diet: a diet with 23.2% starch in diet DM containing 24.6% fermented aging corn replacing conventional corn. The diets were formulated to be isonitrogenous and contained identical roughage. The FAC treatment increased the starch digestibility compared with AC. Feeding FAC increased the concentrations of total VFA compared with CC and AC and decreased the molar proportion of acetate compared with AC. At the family level, the relative abundance of Prevotellaceae was higher on FAC than CC. The relative abundance of Succinivibrionaceae was lower on FAC than on CC and AC. Besides, at the genera level, the relative abundance of Succinivibrionaceae_UCG_002 in the rumen was higher on AC than CC and FAC. The relative abundance of Prevotella and Ruminococcus was higher on FAC than CC and AC. The relative abundance of Succinivibrionaceae_UCG_001 was lower on FAC than CC. The Simpson index was lower on FAC than CC and AC. The FAC treatment increased the milk yield (34.0, 33.7, and 35.2 kg/d for CC, AC, and FAC group, respectively) and protein yield, and thus, energy-corrected milk production was increased, and at the same time, decreased the somatic cell score (SCS) compared with CC and AC. The AC treatment increased the malondialdehyde concentration in plasma compared with CC and FAC. The concentrations in plasma of triglyceride and malondialdehyde were lower on FAC than AC. The immunoglobulin G concentration in plasma was higher on FAC than CC and AC. Overall, feeding AC resulted in decreased plasma antioxidant capacity compared with CC, whereas feeding FAC altered the relative abundance of bacteria in the rumen and improved starch digestibility, ruminal bacterial diversity, lactation performance, plasma antioxidant capacity and immune competence compared with AC in dairy cows.

Control of phosphorus release from sediment by the combined use of Elodea nuttallii, hydrous ferric oxide, zeolite and calcite: Efficiency, mechanism and response of bacterial communities

The effectiveness of Elodea nuttallii combined with a mixture of hydrous ferric oxide, zeolite and calcite (HZC) to reduce the internal loading of phosphorus (P) from sediment and its mechanism were studied, and the effect of Elodea nuttallii combined with HZC on the composition and function of the microbial communities in the surface sediment was also investigated. The results showed that the combination utilization of Elodea nuttallii and HZC can decrease the risk of phosphorus liberation from sediment to the overlying water, and the controlling efficiency of Elodea nuttallii combined with HZC was higher than that of Elodea nuttallii or HZC alone. The passivation of labile P measured by diffusive gradient in thin film device and mobile P played a crucial role in the control of internal P loading from sediment by the combined Elodea nuttallii + HZC treatment. HZC capping had a promoting effect on the growth of Elodea nuttallii. This was beneficial to the absorption of phosphorus from sediment by Elodea nuttallii. The combined application of Elodea nuttallii and HZC not only had a certain negative effect on the diversity of bacteria in the surface sediment, but also changed the microbial compositions of the surface sediment at the levels of phylum and genus. However, the microbial communities in the surface sediment still can perform good ecological function. The above results suggest that the combined application of Elodea nuttallii and HZC has a high potential in the management of internal P loading from sediment.

Molecular taxonomy of fish larvae in the Northwestern Arabian gulf: A baseline study from Kuwait's first marine protected area

Sulaibikhat Bay, a shallow embayment dominated by tides and extensive mud flats along the northern coast of Kuwait Bay, serves as a crucial nursery ground for various commercially important species of finfish and shellfish in the Northwestern Arabian Gulf (NWAG). As the location of Kuwait's inaugural marine protected area (MPA), Sulaibikhat Bay plays a vital role in fostering numerous fish and marine invertebrate species of commercial importance in the Arabian/Persian Gulf. Accurate identification of larval specimens from this habitat is essential for understanding their spawning dynamics and recruitment process. However, limitations in taxonomic identification hinder scientific understanding of fish larval recruitment. To address this, our baseline study employed an integrated taxonomic approach, combining conventional morphology with molecular techniques. Fish larvae collected from the MPA and surrounding waters in Spring (2022) were identified up to the genus and species levels using partial gene sequencing of 16 S rRNA and mitochondrial cytochrome oxidase (COI) genes. Morphological analysis indicated the prevalence of Sparidae, Sillaginidae, and Dorosomatidae families. Molecular analysis confirmed the presence of these families and identified two species, Crenidens crenidens (Sparidae) and Nematalosa nasus (Dorosomatidae), along with two genera, Diplodus sp. (Sparidae) and Sillago sp. (Sillaginidae), which exhibited maximum similarity to available COI sequences of Diplodus sargus, and Sillago maculata, respectively. This represents the first baseline molecular study on fish larvae from NWAG, laying the groundwork for future in-depth analyses with more larval specimens and spatiotemporal samplings from the entire exclusive economic zone (EEZ) of Kuwait in the Arabian/Persian Gulf.

Automated identification of aquatic insects: A case study using deep learning and computer vision techniques

Despite huge attention in other domains, deep learning is only very slowly beginning to be applied in biodiversity research. Mayflies (Ephemeroptera), stoneflies (Plecoptera) and caddisflies (Trichoptera), often abbreviated as EPT, are frequently used for freshwater biomonitoring due to their large numbers and sensitivity to environmental changes. However, the unambiguous morphological identification of EPT species is a challenging, but fundamental task. Morphological identification of these freshwater insects is therefore not only extremely time-consuming and costly, but also often leads to misjudgments or generates datasets with low taxonomic resolution. Here, we investigated the application of deep learning to increase the efficiency and taxonomic resolution of biomonitoring programs. Our database contains 90 EPT taxa (genus or species level), with the number of images per category ranging from 21 to 300 (16,650 in total). Upon completion of training, a CNN (Convolutional Neural Network) model was created, capable of automatically classifying these taxa into their appropriate taxonomic categories with an accuracy of 98.7 %. For the extensive set of 68 tested taxa, our model achieved a perfect classification rate of 100 %. We achieved noteworthy classification accuracy with morphologically closely related taxa within the training data (e.g., species of the genus Baetis, Hydropsyche, Perla). Gradient-weighted Class Activation Mapping (Grad-CAM) visualized the morphological features responsible for the classification of the treated species in the CNN models. In the Ephemeroptera, the head was the most important feature, while the thorax and abdomen were equally important for the classification of Plecoptera taxa. For the order Trichoptera, the head and thorax were almost equally important. Our database is recognized as the most extensive aquatic insect database, notably distinguished by its wealth of included categories (taxa). Our approach can help solve long-standing challenges in biodiversity research and address pressing issues in monitoring programs by saving time in sample and data processing.

The Effects of Fermented Rice Drink With Lactiplantibacillus plantarum JSA22 in Overweight Irritable Bowel Syndrome Patients: A Randomized, Double-blind, Placebo-controlled Study.

This study aims to investigate the effect of a fermented rice drink with Lactiplantibacillus plantarum JSA22 on symptoms, blood tests, microbiomes, and fecal metabolites in patients with irritable bowel syndrome (IBS) who were overweight. Sixty overweight (body mass index ≥ 23 kg/m2) patients aged between 20 and 65 with IBS were enrolled. Patients were divided into 2 groups and administered either a fermented rice drink or an nonfermented rice drink for a month. The symptom questionnaire, blood samples, and stool samples for microbiome and metabolite were collected before and after the month of rice drink administration. The primary efficacy variable was the subject's global assessment of IBS symptoms. In both groups, global IBS symptoms, including abdominal pain, bowel habit, urgency, and abdominal distension, improved significantly (P < 0.01). The abdominal bloating was more significantly improved in the fermented rice drink group than in the nonfermented rice drink group (P < 0.05). Significant changes were not observed in metabolic syndrome-related blood tests or fecal metabolites in either group. However, microbiome analysis showed significant differences in genus levels before and after consuming fermented rice drink, such as in Blautia in stool (P = 0.020) and Prevotella (P = 0.017) and Oribacterium (P = 0.018) in saliva. The fermented rice drink with L. plantarum JSA22 showed a beneficial effect in reducing abdominal distension in IBS patients. Bacteria that reduce visceral fat accumulation increased in the stool and saliva of patients who consumed fermented rice drinks.

Interfacial effects of perfluorooctanoic acid and its alternative hexafluoropropylene oxide dimer acid with polystyrene nanoplastics on oxidative stress, histopathology and gut microbiota in Crassostrea hongkongensis oysters

The increasing interfacial impacts of polystyrene nanoplastics (PS) and per- and polyfluoroalkyl substances (PFAS) complex aquatic environments are becoming more evident, drawing attention to the potential risks to aquatic animal health and human seafood safety. This study aims to investigate the relative impacts following exposure (7 days) of Crassostrea hongkongensis oysters to the traditional PFAS congener, perfluorooctanoic acid (PFOA) at 50 μg/L, and its novel alternative, hexafluoropropylene oxide dimer acid (HFPO-DA), also known as GenX at 50 μg/L, in conjunction with fluorescent polystyrene nanoplastics (PS, 80 nm) at 1 mg/L. The research focuses on assessing the effects of combined exposure on oxidative stress responses and gut microbiota in the C. hongkongensis. Comparing the final results of PS + GenX (PG) and PS + PFOA (PF) groups, we observed bioaccumulation of PS in both groups, with the former causing more pronounced histopathological damage to the gills and intestines. Furthermore, the content of antioxidant enzymes induced by PG was higher than that of PF, including Superoxide Dismutase (SOD), Catalase (CAT), Glutathione Reductase (GR) and Glutathione Peroxidase (GSH). Additionally, in both PG and PF groups, the expression levels of several immune-related genes were significantly upregulated, including tnfα, cat, stat, tlr-4, sod, and β-gbp, with no significant difference between these two groups (p > 0.05). Combined exposure induced significant changes in the gut microbiota of C. hongkongensis at its genus level, with a significant increase in Legionella and a notable decrease in Endozoicomonas and Lactococcus caused by PG. These shifts led to beneficial bacteria declining and pathogenic microbes increasing. Consequently, the microbial community structure might be disrupted. In summary, our findings contribute to a deeper understanding of the comparative toxicities of marine bivalves under combined exposure of traditional and alternative PFAS.

Research on a Biofilter for a Typical Application Scenario in China: Treatment of Pesticide Residue Wastewater in Orchards

To reduce pesticide pollution and promote sustainable agricultural development in China, we designed a pilot-scale biofilter system to treat residual imidacloprid wastewater in an orchard. The biofilter system demonstrated a high rate of removal of imidacloprid from the biodegradation wastewater, with removal rates from the outlet exceeding 99% at different concentrations of pesticides. Among environmental factors, imidacloprid concentration at the inlet and biomixture significantly affected the activity of imidacloprid-degrading bacteria. The dominant microbial communities during the stable operation of the biofilter system included Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidetes at the phylum level and Bacillus, Methylobacter, and unclassified_f__Microbacteriaceae at the genus level. In future initiatives to improve biofilter performance and applicability, increasing attention should be paid to the dominant microbial communities, the number of biofilter units, and important environmental factors. Orchard workers in China should improve the existing treatment of residual pesticide wastewater to mitigate agricultural non-point source pollution.

Late Miocene mollusks from the Dar Pahn Unit, Makran, SE Iran

Diverse, abundant and well-preserved mollusk fauna are here reported for the first time from the eastern coast Makram area, where Upper Miocene (Tortonian) sediments of the Dar Pahn Unit crop out, representing shoreface tidal influenced deposits composed mainly of ligh-gray marls. Multiple articulated bivalves and completely preserved the gastropod and bivalve shells indicate little or no transport at all from the original habitat of the mollusk assemblage. A total of 313 specimens, from which 271 correspond to gastropods, were identified only at generic level, since the purpose of this contribution is to offer an introduction to this exceptionally well-preserved mollusk assemblage. Previous studies of the area include detailed nannoplankton biostratigraphy and the report of a balaenopterid cetacean. Future studies include the detailed identification of the specimens, along with sediment analysis in order to find protoconchs and offer an extended version of this introductory report.