Higher Relative Abundance Research Articles

Activation of Cryptic Donor Splice Sites within the UDP-Glucuronosyltransferase (UGT)1A First-Exon Region Generates Variant Transcripts That Encode UGT1A Proteins with Truncated Aglycone-Binding Domains.

The human UDP-glucuronosyltransferases (UGTs) have crucial roles in metabolizing and clearing numerous small lipophilic compounds. The UGT1A locus generates nine UGT1A mRNAs, 65 spliced transcripts, and 34 circular RNAs. In this study, our analysis of published UGT-RNA capture sequencing (CaptureSeq) datasets identified novel splice junctions that predict 24 variant UGT1A transcripts derived from ligation of exon 2 to unique sequences within the UGT1A first-exon region using cryptic donor splice sites. Of these variants, seven (1A1_n1, 1A3_n3, 1A4_n4, 1A5_n1, 1A8_n2, 1A9_n2, 1A10_n7) are predicted to encode UGT1A proteins with truncated aglycone-binding domains. We assessed their expression profiles and deregulation in cancer using four RNA sequencing (RNA-Seq) datasets of paired normal and cancerous drug-metabolizing tissues from large patient cohorts. Variants were generally coexpressed with their canonical counterparts with a higher relative abundance in tumor than in normal tissues. Variants showed tissue-specific expression with high interindividual variability but overall low abundance. However, 1A8_n2 showed high abundance in normal and cancerous colorectal tissues, with levels that approached or surpassed canonical 1A8 mRNA levels in many samples. We cloned 1A8_n2 and showed expression of the predicted protein (1A8_i3) in human embryonic kidney (HEK)293T cells. Glucuronidation assays with 4-methylumbelliferone (4MU) showed that 1A8_i3 had no activity and was unable to inhibit the activity of 1A8_i1 protein. In summary, the activation of cryptic donor splice sites within the UGT1A first-exon region expands the UGT1A transcriptome and proteome. The 1A8_n2 cryptic donor splice site is highly active in colorectal tissues, representing an important cis-regulatory element that negatively regulates the function of the UGT1A8 gene through pre-mRNA splicing. SIGNIFICANT STATEMENT: The UGT1A locus generates nine canonical mRNAs, 65 alternately spliced transcripts, and 34 different circular RNAs. The present study reports a series of novel UDP-glucuronosyltransferase (UGT)1A variants resulting from use of cryptic donor splice sites in both normal and cancerous tissues, several of which are predicted to encode variant UGT1A proteins with truncated aglycone-binding domains. Of these, 1A8_n2 shows exceptionally high abundance in colorectal tissues, highlighting its potential role in the first-pass metabolism in gut through the glucuronidation pathway.

Microbiome Analysis Revealed Acholeplasma as a Possible Factor Influencing the Susceptibility to Bacterial Leaf Blight Disease of Two Domestic Rice Cultivars in Vietnam.

The microbiomes of two important rice cultivars in Vietnam which differ by their susceptibility to the bacterial leaf blight (BLB) disease were analyzed through 16S rRNA amplicon technology. A higher number of operational taxonomic units and alpha-diversity indices were shown in the BLB-resistant LA cultivar than in the BLB-susceptible TB cultivar. The BLB pathogen Xanthomonas was scantly found (0.003%) in the LA cultivar, whereas was in a significantly higher ratio in the TB cultivar (1.82%), reflecting the susceptibility to BLB of these cultivars. Of special interest was the genus Acholeplasma presented in the BLB-resistant LA cultivar at a high relative abundance (22.32%), however, was minor in the BLB-sensitive TB cultivar (0.09%), raising a question about its roles in controlling the Xanthomonas low in the LA cultivar. It is proposed that Acholeplasma once entered the host plant would hamper other phytopathogens, i.e. Xanthomonas, by yet unknown mechanisms, of which the triggering of the host plants to produce secondary metabolites against pathogens could be a testable hypothesis.

Mechanical excavation of wetland habitat failed to eradicate invasive American red swamp crayfish (Procambarus clarkii) in Malta

Abstract Invasive crayfish are an important ecological concern in many freshwater ecosystems. Many efforts have been made to eradicate them, but there is very little documentation of the effectiveness of these efforts. Between 2019 and 2020, a restoration project funded by the European Regional Development Fund tried to eradicate invasive American red swamp crayfish Procambarus clarkii from the Fiddien valley system in Malta by mechanically excavating the valley's stream bed and exporting contaminated debris securely off‐site to a dry quarry. Three years post‐intervention, we systematically surveyed the valley system to explore the distribution and relative abundance of the invasive crayfish population. We placed traps in a stratified random sample of stream segments (both those that were included in the original restoration project and those that were not) and recorded catch per unit effort (crayfish caught per trap night) and the size/frequency distribution of crayfish caught. The invasive crayfish were still abundant in the upper reaches of the valley system, and, despite the excavation effort, crayfish were present at the highest relative abundance (4.3–14.8 CPUE, median = 12.3) within the restored area. Despite substantial effort and spending of more than 700,000 €, mechanical excavation did not eradicate invasive crayfish populations. We urge caution for future projects planning to attempt crayfish eradication using this approach and call for much greater impact evaluation, and at the very least post‐project monitoring, to ensure lessons can be learnt from such failures in future.

Microbiological exploration of the Cueva del Viento lava tube system in Tenerife, Canary Islands.

Cueva del Viento, located in the Canary Islands, Spain, is the Earth's sixth-longest lava tube, spanning 18,500 m, and was formed approximately 27,000 years ago. This complex volcanic cave system is characterized by a unique geomorphology, featuring an intricate network of galleries. Despite its geological significance, the geomicrobiology of Cueva del Viento remains largely unexplored. This study employed a combination of culture-dependent techniques and metabarcoding data analysis to gain a comprehensive understanding of the cave's microbial diversity. The 16S rRNA gene metabarcoding approach revealed that the coloured microbial mats (yellow, red and white) coating the cave walls are dominated by the phyla Actinomycetota, Pseudomonadota and Acidobacteriota. Of particular interest is the high relative abundance of the genus Crossiella, which is involved in urease-mediated biomineralization processes, along with the presence of genera associated with nitrogen cycling, such as Nitrospira. Culture-dependent techniques provided insights into the morphological characteristics of the isolated species and their potential metabolic activities, particularly for the strains Streptomyces spp., Paenarthrobacter sp. and Pseudomonas spp. Our findings underscore the potential of Cueva del Viento as an ideal environment for studying microbial diversity and for the isolation and characterization of novel bacterial species of biotechnological interest.

The association between the gut microbiome and fatigue in individuals living with cancer: a systematic review.

Fatigue is the most distressing symptom for individuals with cancer. While numerous studies have investigated biological pathways that could underlie the mechanism of fatigue, the cause of fatigue remains unclear. This review aimed to investigate the association between gut microbial composition and fatigue in individuals with cancer. Medline (PubMed), Embase (Elsevier), and CINAHL Complete (Ebscohost) were systemically searched on March 30, 2023, for articles investigating gut microbial composition (relative abundance, alpha diversity, and beta diversity) and fatigue in individuals with cancer; no limitations were placed on dates, participant age, nor cancer type/treatment. Microbial composition in the form of relative abundance was correlated with fatigue in six of the seven articles. A high relative abundance of g_Ruminoccocus was observed in individuals with low fatigue. An elevated relative abundance of g_Escherichia and f_Enterobacteriaceae was associated with high fatigue. However, other associations between fatigue and relative abundance composition, such as with g_Bifidobacterium and g_Faecalibacterium, had conflicting results. For alpha diversity and fatigue, the findings were contradictory; the association between beta diversity and fatigue was unclear due to conflicting results. Pro-inflammatory bacteria, such as f_Enterobacteriaceae, were more commonly associated with higher fatigue scores, while anti-inflammatory or short-chain fatty acid producing bacteria, such as g_Ruminoccocus, were linked with lower fatigue scores in individuals with cancer. The relationship between alpha and beta diversity and fatigue was inconclusive. Further investigation is needed to clarify whether gut microbial changes play a correlative or causal role in the development of fatigue in individuals with cancer.

Biotreatment of crude oil waste sludge using a novel bacterial formula

To address the challenges faced during the breakdown of crude oil waste sludge (COWS), this study developed an active bacterial formula (ABF) to enhance the breakdown of COWS. The formula used was a bacteria consortium (BC) with the desired characteristics immobilised on corncob powder (CCP). A mixture of soil-COWS (SSM) (w/w) was treated with ABF (w/w) in a laboratory trial for 90 days. The treated SSM was analysed for residual concentrations of hydrocarbon components of the COWS by solvent extraction and GC/MS. To elucidate the bacterial community composition, Illumina/MiSeq was used. Immobilised bacteria cells (IBC) on corncob powder (CCP) were confirmed and effectively shown by scanning electron microscopy (SEM) images. The formula on SSM caused a shift in microbial composition, ascribed to nutrients and carbon sources (CS) used in the treatment and other features such as symbiosis and competition to use the diverse carbon sources. The four phyla Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes identified were dominant and affiliated to 90 genera including Rhodococcus, Bacillus, Gordonia, Dietzia, Ochrobactrum, Clostridium, Pseudomonas, and Microbacterium at a high relative abundance of >1.0 to >10. Parameters such as bacterial diversity (BD) and composition, relative abundance (RA), and PAH-residual concentration were used to assess the effectiveness of ABF. The results obtained suggest that ABF alleviated issues of survival of degrading bacteria and nutrient deficiency, as some PAH were thoroughly degraded (100 %) and others almost wholly degraded (95 %) in 90 days in all the treatments, unlike the 10 months in preceding studies.

Spatiotemporal distribution of hematophagous flies (Diptera: Muscidae) on beef cattle farms in Bangkok, Thailand.

A spatiotemporal investigation of hematophagous fly prevalence was conducted over a 1-year period on 12 beef cattle farms located in major livestock areas of Bangkok, Thailand, using Vavoua traps. The survey revealed 5,018 hematophagous flies belonging to Muscidae and Tabanidae, with the 3 dominant species identified as Stomoxys calcitrans (Linnaeus) (2,354; 46.91%), Musca crassirostris Stein (1,528; 30.45%), and Haematobia exigua de Meijere (922; 18.37%). The abundance of S. calcitrans per trap per week was significantly higher during the rainy season (45.64 ± 14.10), followed by the cold and dry seasons (6.39 ± 2.16 and 3.04 ± 1.27, respectively). The relative abundance of S. calcitrans reached the highest apparent density per trap per day (ADT) index of 9.83 in August 2022 during the rainy season. Subsequently, there was a rapid decline, and the ADT index dropped to nearly zero in December 2022 during the cold season. This low abundance continued through the dry months from March to May 2023. The higher rainfall and relative humidity could significantly contribute to the high relative abundance of S. calcitrans. In contrast, M. crassirostris and H. exigua showed population fluctuations that were not significantly associated with seasonal changes and weather conditions. Remote sensing data and spatial regression analyses using ordinary least squares regression showed the high spatial density of S. calcitrans in the north direction of the Khlong Sam Wa district during the rainy season; it shifted toward the south in the cold and dry seasons, corresponding with rainfall.

Impact of Organic Carbons Addition on the Enrichment Culture of Nitrifying Biofloc from Aquaculture Water: Process, Efficiency, and Microbial Community.

In this study, we developed a rapid and effective method for enriching the culture of nitrifying bioflocs (NBF) from aquacultural brackish water. The self-designed mixotrophic mediums with a single or mixed addition of sodium acetate, sodium citrate, and sucrose were used to investigate the enrichment process and nitrification efficiency of NBF in small-scale reactors. The results showed that NBF with an MLVSSs from 1170.4 mg L-1 to 2588.0 mg L-1 were successfully enriched in a period of less than 16 days. The citrate group performed the fastest enrichment time of 10 days, while the sucrose group had the highest biomass of 2588.0 ± 384.7 mg L-1. In situ testing showed that the highest nitrification efficiency was achieved in the citrate group, with an ammonia oxidation rate of 1.45 ± 0.34 mg N L-1 h-1, a net nitrification rate of 2.02 ± 0.20 mg N L-1 h-1, and a specific nitrification rate of 0.72 ± 0.14 mg N g-1 h-1. Metagenomic sequencing revealed that Nitrosomonas (0.0~1.0%) and Nitrobacter (10.1~26.5%) were dominant genera for AOB and NOB, respectively, both of which had the highest relative abundances in the citrate group. Linear regression analysis further demonstrated significantly positive linear relations between nitrification efficiencies and nitrifying bacterial genera and gene abundance in NBF. The results of this study provide an efficient enrichment culture method of NBF for the operation of biofloc technology aquaculture systems, which will further promote its wide application in modern intensive aquaculture.

Metabolite Profiling of Colvillea racemosa via UPLC-ESI-QTOF-MS Analysis in Correlation to the In Vitro Antioxidant and Cytotoxic Potential against A549 Non-Small Cell Lung Cancer Cell Line.

In this study, flower and leaf extracts of Colvillea racemosa were considered a source of bioactive compounds. In this context, the objective of the study focused on investigating the anticancer potential as well as the phytochemical composition of both extracts. The extracts were analyzed by UPLC-ESI-QTOF-MS, and the bioactivity was tested using in vitro antioxidant assays (FRAP, DPPH, and ABTS) in addition to cytotoxic assays on non-small cell lung cancer cell line (A549). Our results clearly indicated the potent radical scavenging capacity of both extracts. Importantly, the flower extract exhibited a greater antioxidant capacity than the leaf extract. In terms of cytotoxic activity, leaf and flower extracts significantly inhibited cell viability with IC50 values of 17.0 and 17.2 µg/mL, respectively. The phytochemical characterization enabled the putative annotation of 42 metabolites, such as saccharides, phenolic acids, flavonoids, amino acids, and fatty acids. Among them, the flavonoid C-glycosides stand out due to their high relative abundance and previous reports on their anticancer bioactivity. For a better understanding of the bioactive mechanisms, four flavonoids (vitexin, kaempferol-3-O-rutinoside, luteolin, and isoorientin) were selected for molecular docking on hallmark protein targets in lung cancer as represented by γ-PI3K, EGFR, and CDK2 through in-silico studies. In these models, kaempferol-3-O-rutinoside and vitexin had the highest binding scores on γ-PI3K and CDK2, followed by isoorientin, so they could be highly responsible for the bioactive properties of C. racemosa extracts.

Novel adaptive activated sludge process leverages flow fluctuations for simultaneous nitrification and denitrification in rural sewage treatment

The fluctuating characteristics of rural sewage flow pose a significant challenge for wastewater treatment plants, leading to poor effluent quality. This study establishes a novel adaptive activated sludge (AAS) process specifically designed to address this challenge. By dynamically adjusting to fluctuating water flow in situ, the AAS maintains system stability and promotes efficient pollutant removal. The core strategy of AAS leverages the inherent dissolved oxygen (DO) variations caused by flow fluctuations to establish an alternating anoxic-aerobic environment within the system. This alternating operation mode fosters the growth of aerobic denitrifiers, enabling the simultaneous nitrification and denitrification (SND) process. Over a 284-day operational period, the AAS achieved consistently high removal efficiencies, reaching 94 % for COD and 62.8 % for TN. Metagenomics sequencing revealed HN-AD bacteria as the dominant population, with the characteristic nap gene exhibiting a high relative abundance of 0.008 %, 0.010 %, 0.014 %, and 0.015 % in the anaerobic, anoxic, dynamic, and oxic zones, respectively. Overall, the AAS process demonstrates efficient pollutant removal and low-carbon treatment of rural sewage by transforming the disadvantage of flow fluctuation into an advantage for robust DO regulation. Thus, AAS offers a promising model for SND in rural sewage treatment.

Piped-slow-release calcium nitrate dosing: A new approach to in-situ sediment odor control in rural areas

Calcium nitrate addition is economically viable and highly efficient for the in-situ treatment of contaminated sediment and enhancement of surface water quality, particularly in rural areas. However, conventional nitrate addition technologies have disadvantages such as excessive nitrate release, sharp ammonium increase, and weakened sulfide oxidation efficiency owing to rapid nitrate injection into the sediment. To resolve these defects, we propose a piped-slow-release (PSR) calcium nitrate dosing method and investigate its treatment efficiency and underlying mechanisms. The results illustrated that PSR dosing had a longer half-life (t1/2 = 5.08 days) and a lower maximum apparent nitrate escape rate of 1.28 % than conventional nitrate injection and other dosing methods. In addition, the PSR managed the inorganic nitrogen release into the overlying water, and after the treatment, the nitrate, ammonium, and nitrite concentrations of 0 mg/L, 8.60 mg/L, and 0 mg/L on day 28 were close to those of the control group (0 mg/L, 8.76 mg/L, and 0 mg/L, respectively). Moreover, the PSR method maintained a moderate nitrate concentration of approximately 3000 mg/L in sediment interstitial water by its controlled-release design, thus greatly enhancing the sulfide oxidation efficiency by relieving the inhibitory effects of high nitrate concentrations, with 83.0 % sulfide being eradicated within 5 days. Sulfide-ferrous nitrate reduction (denitrification and dissimilatory nitrate reduction to ammonium) genera (e.g., Sulfurimonas, Thiobacillus, and Thioalkalispira) were successively enhanced and dominated the microbial community, and the related functional genes displayed high relative abundances. These results imply that the PSR dosing method for calcium nitrate, characterized by flexible operation, high efficiency, low cost, and controllable processes, is appropriate for remediating black-odorous sediment in rural areas.

Considering microplastic characteristics in ecological risk assessment: A case study for China

Microplastics (MPs) pose a significant global concern, requiring a multifaceted approach to their risk assessment procedures, especially concerning their characteristics in the environment. The Horqin Left Middle Banner in Northeast China was chosen for the research region to investigate the abundance, composition, distribution, and ecological impact of MPs in surface agricultural soils. The concentrations of MPs ranged from 300 to 12800 items/kg, with a median concentration of 1550 items/kg (average = 1994 items/kg). The normal-sized MPs (500–5000 µm) had a higher relative abundance than small MPs (<500 µm). MPs were mainly derived from textiles and packaging and were affected by atmospheric transportation. Rayon and PET fibers were the main polymers identified. Furthermore, the potential environmental risks posed by the fundamental characteristics (abundance, chemical composition, and size) of MPs were quantified using multiple risk assessment models. The conditional fragmentation model indicated a propensity for MPs to degrade into smaller particles. Ecological risk assessments using pollution load index, pollution hazard index, and potential ecological risk index models revealed varying levels of risk. This study conducted a comprehensive assessment of the ecological risks of MPs based on their environmental characteristics, emphasizing the importance of considering multiple factors in the risk assessment process. Environment implicationThis study investigates the occurrence, distribution, and ecological risk of microplastics (MPs) in agricultural soils of the Northeast Plain of China, a major food production area. MPs are persistent organic pollutants that can pose threats to soil health, crop quality, and food security. By analyzing the composition, size, and source of MPs, as well as their fragmentation and stability in soil, this study provides valuable data for assessing the environmental risk of MPs in agricultural regions. The study also suggests strategies for mitigating MPs pollution and protecting soil ecosystems.

Phytophthora Infection Reorients the Composition of Rhizospheric Microbial Assembly in Khasi Mandarin (Citrus reticulata Blanco)

Phytophthora gummosis, foot rot, and root rot are considered major challenges to the citrus industry worldwide. Little is known about the Phytophthora–microbiome interaction, despite several studies demonstrating changes in the microbial composition of the rhizosphere following challenges by a pathogen. In the present study, we studied the microbial diversity and community structure in healthy rhizospheres and Phytophthora-infected rhizospheres of Khasi mandarin (Citrus reticulata Blanco), a commercial cultivar extensively grown in the northeast of India. An exploratory study was conducted to identify Phytophthora-infected orchards of Khasi mandarin, and the isolated pathogen was confirmed as P. nicotianae based on its morpho-cultural and molecular characteristics coupled with pathogenicity tests. This study on culturable microbes established the dominance of Trichoderma spp. in the healthy rhizosphere, while the diseased rhizosphere showed the presence of Fusarium spp. A metagenomic study further revealed that the rhizospheres of Phytophthora-infected plants were dominated by species such as Bacteroidia spp., Patescibacteria spp., and Pythium spp., while the healthy Khasi mandarin rhizospheres had a more diverse community predominantly represented by Trichoderma, Penicillium, Linnemannia, Mortierella, Talaromyces, Saitozyma, Bacteroidetes, Pseudomonas, Cytophagia, Cyanobacteria, Bacteroidia, Sphingobacteriia, Burkholderia, Bacillus, and Bradyrhizobium. Terrabacteria and FCB (Fibrobacterota, Chlorobiota, and Bacteroidota groups) were found to exist in higher relative abundance in disease-free soils than in Phytophthora-infected soils, while phylum Proteobacteria showed identical relative abundance in all soil types. The phyla represented by Pseudomonas, Flavobacteriia, Candidatus, Mycobacterium, Rhizobium, Mesorhizobium, Sphingomonas, and Cytophagia were the most common bacterial phyla in all soil samples, but healthy soil exhibited a greater abundance of Bacteroidetes, Pseudomonas, Cytophagia, Cyanobacteria, Bacteroidia, Sphingobacteriia, Burkholderia, Bacillus, and Bradyrhizobium. Our study suggests that the presence of Phytophthora spp. in the rhizosphere alters microbial community structure, having potentially strong implications for plant health and productivity. These rhizosphere microbiome-derived citrus responses shed light on exploring effective management strategies for Phytophthora gummosis disease ailing Khasi mandarin.

The Relationship between the Edge Density of the Forest Fragments and the Tree Species Richness in the Detached Fragments of Kakamega Forest.

Purpose: The theoretical approach guiding this study was based on the Island Biogeography Theory. The purpose of this study was to assess the influence of the edge density of the forest fragments on tree species richness.&#x0D; Methodology: The study adopted a cross-sectional correlational research design. Proportionate random sampling was used. A sample of 30 plots each measuring 2m by 2m was established randomly in the fragments (0-200m from the edge towards the interior);Malava: Kisere: Ikuywa in that order for field sampling and measurements. Data was collected using tools such as measuring tapes,metre rule,GPS 64s Garmain and suunto inclinometer. A total of 39 species of trees were recorded from the three fragments with Funtumia africana being recorded as the most abundant species.&#x0D; Findings: The findings show 83%, 85%, and 92% variation of tree species richness in. Malava (r2 = 0.83), Kisere (r2 = 0.85) and Ikuywa (r2 = 0.92) in that order can be explained by the edge density of the fragments. The edge density also explained 87%, 94% and 94% variation of tree species relative abundance in Malava (r2 = 0.87), Kisere (r2 = 0.94) and Ikuywa (r2 = 0.94) in that order.&#x0D; Unique Contributor to Theory, Policy and Practice: It was concluded that tree species richness and tree species abundance in the detached portions of Kakamega forest were dominantly influenced by forest fragment total edge length and fragment edge density. For us to conserve more tree species we recommend maintenance of the total edge length of the fragments above 15km with edge density (3.413.79m\m2) in order to maintain high tree species richness and tree species relative abundance.

Nasopharyngeal Dysbiosis Precedes the Development of Lower Respiratory Tract Infections in Young Infants, a Longitudinal Infant Cohort Study

Background Infants suffering from lower respiratory tract infections (LRTIs) have distinct nasopharyngeal (NP) microbiome profiles that correlate with severity of disease. Whether these profiles precede the infection or are a consequence of it, is unknown. In order to answer this question, longitudinal studies are needed. Methods We conducted a retrospective analysis of NP samples collected in a longitudinal birth cohort study of Zambian mother-infant pairs. Samples were collected every two weeks from 1-week through 14-weeks of age. Ten of the infants in the cohort who developed LRTI were matched 1:3 with healthy comparators. We completed 16S rRNA gene sequencing on the samples each of these infants contributed and compared the NP microbiome of the healthy infants to infants who developed LRTI. Results The infant NP microbiome maturation was characterized by transitioning from Staphylococcus dominant to respiratory-genera dominant profiles during the first three months of life, similar to what is described in the literature. Interestingly, infants who developed LRTI had distinct NP microbiome characteristics before infection, in most cases as early as the first week of life. Their NP microbiome was characterized by the presence of Novosphingobium, Delftia, high relative abundance of Anaerobacillus, Bacillus, and low relative abundance of Dolosigranulum, compared to the healthy controls. Mothers of infants with LRTI also had low relative abundance of Dolosigranulum in their baseline samples compared to mothers of infants that did not develop an LRTI. Conclusions Our results suggest that specific characteristics of the NP microbiome precede LRTI in young infants and may be present in their mothers as well. Early dysbiosis may play a role in the causal pathway leading to LRTI or could be a marker of underlying immunological, environmental, or genetic characteristics that predispose to LRTI.

Combining fecal microbiome and metabolomics reveals diagnostic biomarkers for esophageal squamous cell carcinoma.

Esophageal squamous cell carcinoma (ESCC) is one of the most predominant subtypes of esophageal cancer. The characteristics of the gut microbiome and its metabolites from patients with ESCC have not been adequately studied and discussed. In this study, 40 fecal samples (20 from ESCC patients and 20 from healthy controls) were analyzed by 16S rRNA gene sequencing and untargeted metabolomics. The data sets were analyzed individually and synthesized using various bioinformatics methods. Alpha and beta diversity indicated significant differences in microbial diversity and abundance between ESCC and healthy control feces. At the genus level, the abundance of Phascolarctobacterium, Sutterella, and Streptococcus was significantly increased in ESCC. At the genus level, linear discriminant analysis effect size identified two biomarkers: Bacteroides_stercoris and Prevotella_copri. Untargeted metabolomics analysis revealed 307 differential metabolites between ESCC and healthy control feces, with indoles and derivatives, tropane alkaloids, lipids, and lipid-like molecules in higher relative abundance in ESCC feces than in healthy control feces. Kyoto Encyclopedia of Genes and Genomes enrichment analysis revealed that unsaturated fatty acids (FAs), ascorbate and aldarate metabolism, and hypoxia-inducible factor 1 signaling pathway were significantly associated with differential metabolite. Phenylethanolamine and despropionyl p-fluoro fentanyl could be used as reliable biomarkers to differentiate ESCC from healthy control. The correlation analysis showed that Prevotella may be involved in the synthesis of fatty acyl, carboxylic acids and derivatives, benzenes and substituted derivatives, organic oxygenates, and indoles and derivatives as metabolites. Fusicatenibacter and Lachnospira may be involved in the degradation of indoles and derivatives. Alistipes, Agathobacter, and Parabacteroides may be involved in the synthesis of indoles and derivatives with strong contributions. There is an intricate relationship between the gut microbiome and the levels of several metabolites (e.g., fatty acyls, carboxylic acids and derivatives, indoles, and derivatives). Microbial-associated metabolites can be used as diagnostic biomarkers in therapeutic exploration. Further analysis revealed that Prevotella, Alistipes, Agathobacter, and Parabacteroides might promote ESCC by regulating the synthesis of indoles and their derivatives. The results of this study provide favorable evidence for the early diagnosis of ESCC and subsequent individualized treatment and targeted interventions.IMPORTANCEWe describe for the first time the differences in fecal microbiome composition and metabolites between patients with esophageal squamous cell carcinoma (ESCC) and healthy controls by 16S rRNA gene sequencing and untargeted metabolomics. The results of this study provide a favorable basis for the early diagnosis of ESCC and subsequent targeted interventional therapy.

Long-term push–pull cropping system shifts soil and maize-root microbiome diversity paving way to resilient farming system

BackgroundThe soil biota consists of a complex assembly of microbial communities and other organisms that vary significantly across farming systems, impacting soil health and plant productivity. Despite its importance, there has been limited exploration of how different cropping systems influence soil and plant root microbiomes. In this study, we investigated soil physicochemical properties, along with soil and maize-root microbiomes, in an agroecological cereal-legume companion cropping system known as push–pull technology (PPT). This system has been used in agriculture for over two decades for insect-pest management, soil health improvement, and weed control in sub-Saharan Africa. We compared the results with those obtained from maize-monoculture (Mono) cropping system.ResultsThe PPT cropping system changed the composition and diversity of soil and maize-root microbial communities, and led to notable improvements in soil physicochemical characteristics compared to that of the Mono cropping system. Distinct bacterial and fungal genera played a crucial role in influencing the variation in microbial diversity within these cropping systems. The relative abundance of fungal genera Trichoderma, Mortierella, and Bionectria and bacterial genera Streptomyces, RB41, and Nitrospira were more enriched in PPT. These microbial communities are associated with essential ecosystem services such as plant protection, decomposition, carbon utilization, bioinsecticides production, nitrogen fixation, nematode suppression, phytohormone production, and bioremediation. Conversely, pathogenic associated bacterial genus including Bryobacter were more enriched in Mono-root. Additionally, the Mono system exhibited a high relative abundance of fungal genera such as Gibberella, Neocosmospora, and Aspergillus, which are linked to plant diseases and food contamination. Significant differences were observed in the relative abundance of the inferred metabiome functional protein pathways including syringate degradation, L-methionine biosynthesis I, and inosine 5'-phosphate degradation.ConclusionPush–pull cropping system positively influences soil and maize-root microbiomes and enhances soil physicochemical properties. This highlights its potential for agricultural and environmental sustainability. These findings contribute to our understanding of the diverse ecosystem services offered by this cropping system where it is practiced regarding the system's resilience and functional redundancy. Future research should focus on whether PPT affects the soil and maize-root microbial communities through the release of plant metabolites from the intercrop root exudates or through the alteration of the soil's nutritional status, which affects microbial enzymatic activities.

The bacteriome-coupled phage communities continuously contract and shift to orchestrate the traditional rice vinegar fermentation

Amounts of microbiome studies have uncovered the microbial communities of traditional food fermentations, while in which the phageome development with time is poorly understood. Here, we conducted a study to decipher both phageome and bacteriome of the traditional rice vinegar fermentation. The vinegar phageomes showed significant differences in the alpha diversity, network density and clustering coefficient over time. Peduoviridae had the highest relative abundance. Moreover, the phageome negatively correlated to the cognate bacteriome in alpha diversity, and undergone constantly contracting and shifting across the temporal scale. Nevertheless, 257 core virial clusters (VCs) persistently occurred with time whatever the significant impacts imposed by the varied physiochemical properties. Glycoside hydrolase (GH) and glycosyltransferase (GT) families genes displayed the higher abundances across all samples. Intriguingly, diversely structuring of toxin-antitoxin systems (TAs) and CRISPR-Cas arrays were frequently harbored by phage genomes. Their divergent organization and encoding attributes underlie the multiple biological roles in modulation of network and/or contest of phage community as well as bacterial host community. This phageome-wide mapping will fuel the current insights of phage community ecology in other traditional fermented ecosystems that are challenging to decipher.

The effects of Bacillus subtilis on the immunity, mucosal tissue morphology, immune-related gene transcriptions, and intestinal microbiota in flounder (Paralichthys olivaceus) with two feeding methods: Continuous versus discontinuous feeding

Probiotics as dietary additives can improve weight gain, feed efficiency, and disease resistance in cultured fish. In this research, we evaluated and compared the effects of Bacillus subtilis on immunity, mucosal tissue morphology, immune-related gene transcriptions, and intestinal microbiota in flounder (Paralichthys olivaceus) by a 30-day feeding experiment based on a continuous feeding schedule (E1) and a discontinuous feeding schedule (E2). As a result, the use of B. subtilis exerted the best positive effects on survival rate, enzyme activity, mucosal tissue morphology, immune-related gene transcriptions, and intestinal microbiota in flounders. Alkaline phosphatase (AKP), lysozyme (LZM), and superoxide dismutase (SOD) activities in the liver of E2 were higher than those of E1 (P < 0.05). Furthermore, the villi length in the intestinal tract and the fold length in the stomach of E2 were also higher than in E1 (P < 0.05). The il-1 expression levels in the spleen were significantly increased in E2 (P < 0.05) compared to E1. We performed 16 S rRNA sequencing analysis to find that Bacillus in E1 (1.06%) and E2 (1.01%) had higher relative abundances than in E0 (0.053%) at the end of the experiments, indicating that short-term application of B. subtilis with the continuous or discontinuous feeding method can allow both the adaptation of the ecosystem to the presence of probiotics by the establishment of new species in the gut microbiota and the ability these new probiotic species to perform corresponding functions. No significant differences in the ability of probiotic establishment were observed between E1 and E2. Our findings provided a unique perspective to explore the mechanism of immune enhancement with probiotics and to screen the optimal administration strategy in aquaculture application for probiotic use. Together, these results point to some level of enhancement in immune status by continuous and discontinuous feeding after a short-term feeding period, which could be used as a prophylactic strategy for flounder health management.

Soil microbial diversity and composition response to degradation of the alpine meadow in the southeastern Qinghai-Tibet Plateau.

With the interaction between global climate change and unreasonable human utilization, the alpine meadows on the Qinghai-Tibet Plateau have suffered various weathering degrees. Uncovering the degradation mechanism and restoration strategies can be facilitated by gaining insights into the diversity of soil microflora during meadow degradation. Therefore, we used Illumina sequencing technology to investigate the patterns of soil microbial diversity, microbial community composition, and the driving factors of microbial change in all non-degraded (ND), lightly degraded (LD), moderately degraded (MD), and severely degraded (SD) alpine meadows in the southeastern Qinghai-Tibet Plateau. Our results pointed out that with the intensification of degradation, vegetation characteristics were significantly reduced, and soil parameters significantly varied among all degraded meadows. The contents of soil organic carbon (SOC), total nitrogen (TN), available phosphorus (AN), and total phosphorous (AK) in soils decreased with the increase of degradation. The dominant bacterial phyla were the same regardless of the meadow degradation level with Actinobacteria (37.67%) and Proteobacteria (20.62%) having the highest relative abundance. Meanwhile, the dominant fungi were Ascomycota (49.9%). Based on the linear discriminant analysis (LDA) and effect size (LEfSe) method, 38 bacterial and 49 fungal species were found to be affected in the degraded alpine meadow, most of which belonged to Actinobacteria and Ascomycota, respectively. Mantel test analysis illustrated that the bacterial community was mainly significantly dependent on below-ground biomass, pH, soil organic carbon, and total nitrogen, while the fungal community was significantly dependent on soil organic carbon, total nitrogen, available nitrogen, and available potassium. These results suggest that the degeneration of alpine meadows contributes to the variability of the diversity and composition of microflora on the Tibetan plateau. Yet this effect is mainly dependent on soil factors.