Abundance Of Taxa Research Articles

Impact of Fertilization and Seasonal Changes on Paddy Soil: Unveiling the Interplay between Agricultural Practices, Enzyme Activity, and Gene Diversity

Climate change and soil acidification are critical factors affecting crop production and soil quality. This study comprehensively analyzed the impact of fertilization practices, including conventional (CA), sustainable (SA), and unfertilized (BK), on soil properties, enzyme activities, and gene diversity in paddy fields across seasonal changes. Soil pH was significantly influenced by fertilization, with higher pH in BK and a decrease in pH with increased fertilization. Soil enzyme activities and Biolog EcoPlate™ analysis revealed the lowest activities in September, with the highest in December under different practices. Metagenomic analysis showed the highest genetic richness in CA soil, with seasonal variations influencing genetic diversity. From the perspective of genes in species taxonomy, Sorangium cellulosum and Anaeromyxobacter sp. were the most abundant taxa. Soil genes annotated by CAZy, COG, and GO databases revealed highly similar gene structures among different practices. Moreover, the genetic origins of soil enzymes were linked to specific bacterial contributors. While not all gene’s diversity and abundance were associated with soil enzyme activity, arylsulfatase showed an obvious correlation. Enzyme activities proved more sensitive indicators of microbial activity than gene abundance. This study emphasizes the need for rational fertilization strategies to maintain soil enzyme activities, considering agricultural practices and seasonal variations.

Perinatal Exposure to Phenols and Poly- and Perfluoroalkyl Substances and Gut Microbiota in One-Year-Old Children.

The role of the gut microbiota in human health calls for a better understanding of its determinants. In particular, the possible effects of chemicals with widespread exposure other than pharmaceuticals are little known. Our aim was to characterize the sensitivity of the early-life gut microbiota to specific chemicals with possible antimicrobial action. Within the SEPAGES French couple-child cohort, we assessed 12 phenols in repeated urine samples from 356 pregnant women and their offspring and 19 poly- and perfluoroalkyl substances (PFASs) in serum from the pregnant women. We collected stool samples from the children at one year of age, in which the V3-V4 region of the 16S rRNA gene was sequenced, allowing for gut bacterial profiling. Associations of each chemical with α- and β-diversity indices of the gut microbiota and with the relative abundance of the most abundant taxa were assessed using single-pollutant and mixture (BKMR) models. Perinatal exposure to certain parabens was associated with gut microbiota α- and β-diversity and with Firmicutes and Proteobacteria. Suggestive associations of certain phenols with genera of the Lachnospiraceae and Enterobacteriaceae families were observed, but these were not maintained after correction for multiple testing. Parabens, which have known antimicrobial properties, might disrupt the child gut microbiota, but larger studies are required to confirm these findings.

Calcareous nannofossil biostratigraphy, bioevents, and palaeoecological interpretation of the lower-middle Miocene outcrops in west central Sinai (Egypt)

The Burdigalian/Langhian (B/L) boundary has not yet been designated as a Global Stratotype Section and Point (GSSP), despite various proposed zonal schemes. In the Gulf of Suez region of Egypt, the Burdigalian-Langhian successions are notable for hosting significant hydrocarbon reservoirs within a tectonic rift setting. Therefore, biostatigraphy plays a crucial role in exploration endeavors in this area. The nannofossil biostratigraphy is investigated in two sections, Wadi Baba and Wadi Gharandel, of the lower-middle Miocene from west-central Sinai. Three biozones, NN3 (Sphenolithus belemnos) Zone, NN4 (Helicosphaera ampliaperta) Zone, and NN5 (Sphenolithus heteromorphus) Zone, are identified from the studied interval. The NN4 Zone could be divided into MNN4a/b and MNN4c. Important biovents are discussed, such as the S. heteromorphus paracme interval and the first occurrence and evolution of the Discoaster exilis and Discoaster variabilis groups. Based on the cluster analysis, the recorded taxa can be subdivided into four groups that reflect their palaeoclimatic preferences. The paleoecological interpretation of the studied Rudies Formation indicates prevailing cool and eutrophic nutrient conditions based on the dominance of taxa such as Coccolithus pelagicus, Reticulofenestra minuta, and Cyclicargolithus floridanus. The nannofossil taxa responses to sea level curve are interpreted. Fluctuations in taxa abundance and diversity indicate a slight rise in the sea level at the base of the Burdigalian followed by sudden drop in the sea level at the middle Burdigalian. High sea-level conditions prevailed again until the B/L boundary. During the Langhian period, many small-scale fluctuations in sea-level curve are detected.

Infantile colic is associated with development of later constipation and atopic disorders.

Infantile colic is a common condition with limited knowledge about later clinical manifestations. We evaluated the role of the early life gut microbiome in infantile colic and later development of atopic and gastrointestinal disorders. Copenhagen Prospective Studies on Asthma in Childhood2010 cohort was followed with 6 years of extensive clinical phenotyping. The 1-month gut microbiome was analyzed by 16S rRNA sequencing. Infantile colic was evaluated at age 3 months by interviews. Clinical endpoints included constipation to age 3 years and prospectively diagnosed asthma and atopic dermatitis in the first 6 years of life, and allergic sensitization from skin prick tests, specific Immunoglobulin E, and component analyses. Of 695 children, 55 children (7.9%) had infantile colic. Several factors were associated with colic including race, breastfeeding, and pets. The 1-month gut microbiome composition and taxa abundances were not associated with colic, however a sparse Partial Least Squares model including combined abundances of nine species was moderately predictive of colic: median, cross-validated AUC = 0.627, p = .003. Children with infantile colic had an increased risk of developing constipation (aOR, 2.88 [1.51-5.35], p = .001) later in life, but also asthma (aHR, 1.69 [1.02-2.79], p = .040), atopic dermatitis (aHR, 1.84 [1.20-2.81], p = .005) and had a higher number of positive allergic components (adjusted difference, 116% [14%-280%], p = .012) in the first 6 years. These associations were not mediated by gut microbiome differences. We link infantile colic with risk of developing constipation and atopic disorders in the first 6 years of life, which was not mediated through an altered gut microbiome at age 1-month. These results suggest infantile colic to involve gastrointestinal and/or atopic mechanisms.

Rare rather than abundant taxa of soil bacteria and fungi regulate soil multifunctionality in Eucalyptus plantations

Soil multifunctionality not only contributes to the production of ecosystem services (e.g., nutrient cycling, boosts in plant production, and provision of biological processes), but also supports the survival of species (protecting biodiversity) in an ecosystem. Multi-generational planting (sprouting from logging stumps) of Eucalyptus is widely adopted for timber production in southern China, which distinctly induces the decline of soil properties and destroys soil microbial communities. However, research on various Eucalyptus management practices has predominantly concentrated on soil nutrients and microbial populations. The effects of these practices on soil multifunctionality remain unexplored. Furthermore, the underlying mechanisms influencing the abundant and rare microorganisms have not been fully understood. Here, an 18-year Eucalyptus plantation experiment, including single-generation continuous planting (Y18), multiple-generation felling of the same years (D4), and evergreen broadleaf forest control (CK), was designed. Twenty-three parameters associated with soil nutrient cycling were obtained to quantify soil multifunctionality, and partial least squares path modeling (PLS-PM) was used to reveal the main driving force regulating soil multifunctionality. Our results demonstrated that multi-generational Eucalyptus planting significantly reduced soil multifunctionality, microbial diversity, and network stability. Comparatively, single-generational planting showed slight effects on soil multifunctionality and microbial communities. Stochastic processes dominated the assembly of abundant taxa in Eucalyptus plantations, whereas deterministic processes dominated rare taxa. PLS-PM results revealed that soil organic carbon (SOC), dissolved organic carbon (DOC), total nitrogen (TN), and total phosphorus (TP) directly regulated soil multifunctionality or indirectly through modifying the diversity and networks of rare taxa. The total effect analysis showed that the diversity and network of rare taxa had a greater impact on soil multifunctionality than abundant taxa. SOC and DOC played a crucial role in driving changes in soil multifunctionality. Our findings highlight the need to decrease rotation intensity and conserve rare taxa to mitigate soil quality degradation in artificial Eucalyptus plantations.

Accumulated temperature dictates the regional structural variation of prokaryotic periphyton at soil-water interface in paddy fields

As a pervasive microbial aggregate found at the water-soil interface in paddy fields, periphyton plays crucial roles in modulating nutrient biogeochemical cycling. Consequently, it effectively mitigates non-point source pollution due to its diverse composition. Despite its significance, the mechanisms governing periphyton diversity across different rice planting regions remain poorly understood. To bridge this gap, we investigated periphyton grown in 200 paddy fields spanning 25° of latitude. Initially, we analyzed local diversity and latitudinal variations in prokaryotic communities within paddy field periphyton, identifying 7 abundant taxa, 42 moderate taxa, and 39 rare taxa as the fundamental prokaryotic framework. Subsequently, to elucidate the mechanisms governing periphyton diversity across large scales, we constructed interaction models illustrating triangular relationships among local richness, assembly, and regional variation of prokaryotic subcommunities. Our findings suggest that accumulated temperature-driven environmental filtering partially influences the assembly process of prokaryotes, thereby impacting local species richness and ultimately governing regional structural variations in periphyton. Furthermore, we determined that a latitude of 39° represents the critical threshold maximizing local species richness of periphyton in paddy fields. This study advances our understanding of the factors shaping periphyton geo-imprints and provides valuable insights into predicting their responses to environmental changes, potentially influencing rice production outcomes.

Potassium persulfate enhances humification of chicken manure and straw composting: The perspective of rare and abundant microbial community structure and ecological interactions

Improper disposal of organic solid waste results in serious environmental pollution. Aerobic composting provides an environmentally friendly treatment method, but improving humification of raw materials remains a challenge. This study revealed the effect of different concentrations of potassium persulfate (PP) on humification of chicken manure and straw aerobic composting and the underlying microbial mechanisms. The results showed that when 0.6 % PP was added (PPH group), humus and the degree of polymerization were 80.77 mg/g and 2.52, respectively, which were significantly higher than those in 0.3 % PP (PPL group). As the concentration of PP was increased, the composition of rare taxa (RT) changed and improved in evenness, while abundant taxa (AT) was unaffected. Additionally, the density (0.037), edges (3278), and average degree (15.21) in the co-occurrence network decreased compared to PPL, while the average path (4.021) and modularity increased in PPH. This resulted in facilitating the turnover of matter, information, and energy among the microbes. Interestingly, cooperative behavior between microorganisms during the maturation period (24–60 d) occurred in PPH, but competitive relationships dominated in PPL. Cooperative behavior was positively correlated with humus (p < 0.05). Because the indices, such as higher degree, betweenness centrality, eigenvector centrality, and closeness centrality of the AT, were located in the microbial network center compared to RT, they were unaffected by the concentration of PP. The abundance of carbohydrate and amino acid metabolic pathways, which play an important role in humification, were higher in PPH. These findings contribute to understanding the relative importance of composition, interactions, and metabolic functionality of RT and AT on humification during chicken manure and straw aerobic composting under different concentrations of PP, as well as provide a basic reference for use of various conditioning agents to promote humification of organic solid waste.

Large scale exploration reveals rare taxa crucially shape microbial assembly in alkaline lake sediments

Alkaline lakes are extreme environments inhabited by diverse microbial extremophiles. However, large-scale distribution patterns, environmental adaptations, community assembly, and evolutionary dynamics of microbial communities remain largely underexplored. This study investigated the characteristics of microbial communities on rare and abundant taxa in alkaline lake sediments in west and northwest China. We observed that abundant taxa varied significantly with geographical distance, while rare taxa remained unaffected by regional differences. The assembly process of abundant taxa was influenced by dispersal limitation, whilst rare taxa were predominantly driven by heterogeneous selection. Network analysis indicated that rare taxa as core species for community interactions and community stability. Rare taxa exhibited higher speciation and transition rate than abundant taxa, serving as a genetic reservoir and potential candidates to become abundance taxa, highlighting their crucial role in maintaining microbial diversity. These insights underscore the significant influence of rare taxa on ecosystem biodiversity and stability in alkaline lakes.

Ecological processes of bacterial microbiome assembly in healthy and dysbiotic strawberry farms

The bacterial microbiome plays crucial role in plants’ resistance to diseases, nutrient uptake and productivity. We examined the microbiome characteristics of healthy and unhealthy strawberry farms, focusing on soil (bulk soil, rhizosphere soil) and plant (roots and shoots). The relative abundance of most abundant taxa were correlated with the chemical soil properties and shoot niche revealed the least amount of significant correlations between the two. While alpha and beta diversities did not show differences between health groups, we identified a number of core taxa (16–59) and marker bacterial taxa for each healthy (Unclassified Tepidisphaerales, Ohtaekwangia, Hydrocarboniphaga) and dysbiotic (Udaeobacter, Solibacter, Unclassified Chitinophagales, Unclassified Nitrosomonadaceae, Nitrospira, Nocardioides, Tardiphaga, Skermanella, Pseudomonas, Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Curtobacterium) niche. We also revealed selective pressure of strawberry rhizosphere soil and roots plants in unhealthy plantations increased stochastic ecological processes of bacterial microbiome assembly in shoots. Our findings contribute to understanding sustainable agriculture and plant-microbiome interactions.

Association of Microbiome Diversity with Disease Symptoms in Brassica oleracea Leaves

Cabbage (Brassica oleracea), a crop of major economic importance worldwide, is affected by numerous diseases, which are caused by a wide range of microorganisms, including fungi, oomycetes, bacteria, and viruses, which lead to important losses in yield and quality. The increasing availability of reference genomes of plant-associated microbes together with recent advances in metagenomic approaches provide new opportunities to identify microbes linked to distinct symptomatology in Brassica leaves. In this study, shotgun metagenomics was used to investigate the microbial community in leaves of B. oleracea plants from agricultural farmlands. Compared with conventional techniques based on culture-based methods, whole-genome shotgun sequencing allows the reliable identification of the microbial population inhabiting a plant tissue at the species level. Asymptomatic and symptomatic leaves showing different disease symptoms were examined. In the asymptomatic leaves, Xanthomonas species were the most abundant taxa. The relative abundance of bacterial and fungal communities varied depending on disease symptoms on the leaf. The microbiome of the leaves showing mild to severe levels of disease was enriched in bacterial populations (Sphingomonas, Methylobacterium, Paracoccus) and to a lesser degree in some fungal taxa, such as Alternaria and Colletotrichum (e.g., in leaves with high levels of necrotic lesions). Sclerotinia species were highly abundant in severely damaged leaves (S. sclerotium, S. trifolium, S. bolearis), followed by Botrytis species. The common and specific bacterial and fungal species associated to disease symptoms were identified. Finally, the analysis of the gene functions in the metagenomic data revealed enrichment in carbohydrate-active enzymes potentially involved in pathogenicity, whose distribution also varied among disease severity groups. Understanding the B. oleracea leaf microbiome in agricultural ecosystems will pave the way for the efficient management of diseases in this crop.

Gut microbiota profiling reflects the renal dysfunction and psychological distress in patients with diabetic kidney disease.

The gut microbiota plays a pivotal role in the development of diabetes and kidney disease. However, it is not clear how the intestinal microecological imbalance is involved in the context of diabetic kidney disease (DKD), the leading cause of renal failure. To elucidate the gut microbial signatures associated with DKD progression towards end-stage renal disease (ESRD) and explore whether they could reflect renal dysfunction and psychological distress. A cross-sectional study was conducted to explore the gut microbial signatures of 29 DKD non-ESRD patients and 19 DKD ESRD patients compared to 20 healthy controls. Differential analysis was performed to detect distinct gut microbial alterations in diversities and taxon abundance of DKD with and without ESRD. Renal dysfunction was estimated by urea, creatinine, and estimated glomerular filtration rate. Psychological distress was assessed using the Self-Rating Anxiety Scale, Self-Rating Depression Scale, Hamilton Anxiety Rating Scale, and Hamilton Depression Rating Scale. Alpha diversity indexes were reduced in DKD patients, particularly those with ESRD. Beta diversity analysis revealed that the gut microbial compositions of DKD patients were different with healthy individuals whereas similar compositions were observed in DKD patients. Taxon differential analysis showed that when compared with the controls, DKD patients exhibit distinct microbial profiles including reduced abundances of butyrate-produced, anti-inflammatory bacteria Faecalibacterium, Lachnospira, Roseburia Lachnoclostridium, and increased abundances of pro-inflammatory bacteria Collinsella, Streptococcus etc. These distinctive genera presented consistent associations with renal dysfunction, as well as psychological distress, especially in DKD patients. DKD patients, especially those who have progressed to ESRD, exhibit unique characteristics in their gut microbiota that are associated with both renal dysfunction and psychological distress. The gut microbiota may be a significant factor in the deterioration of DKD and its eventual progression to ESRD.

METASEED: a novel approach to full-length 16S rRNA gene reconstruction from short read data

BackgroundWith the emergence of Oxford Nanopore technology, now the on-site sequencing of 16S rRNA from environments is available. Due to the error level and structure, the analysis of such data demands some database of reference sequences. However, many taxa from complex and diverse environments, have poor representation in publicly available databases. In this paper, we propose the METASEED pipeline for the reconstruction of full-length 16S sequences from such environments, in order to improve the reference for the subsequent use of on-site sequencing.ResultsWe show that combining high-precision short-read sequencing of both 16S and full metagenome from the same samples allow us to reconstruct high-quality 16S sequences from the more abundant taxa. A significant novelty is the carefully designed collection of metagenome reads that matches the 16S amplicons, based on a combination of uniqueness and abundance. Compared to alternative approaches this produces superior results.ConclusionOur pipeline will facilitate numerous studies associated with various unknown microorganisms, thus allowing the comprehension of the diverse environments. The pipeline is a potential tool in generating a full length 16S rRNA gene database for any environment.

Diversity, distribution and knowledge gaps of Polychaeta on the continental shelf of southern Namibia

This study investigated the diversity, composition and distribution patterns of polychaete macrofauna inhabiting unconsolidated sediments on the continental shelf of southern Namibia. During the austral summer of 2021, 910 Van Veen grab samples were collected from 91 sites in water depths ranging between 43 and 146 m. All benthic macrofauna (> 1 mm) were extracted, identified, enumerated and weighed. Polychaetes were the most abundant taxon, equating to 66% of total abundance and 37% of total biomass. A total of 83 712 polychaete specimens comprising 112 species, 80 genera and 33 families were collected. Several taxa identified were listed as putative cosmopolitans (19 taxa) or have known wide local distributions (10 taxa). Voucher specimens were collected for DNA barcoding to improve reference sequence libraries for the region. Hierarchical cluster analyses using both abundance and biomass data were undertaken to determine spatial distribution patterns in polychaete communities. Both datasets yielded similar results with polychaete assemblages divided into inshore and offshore communities, that were further subdivided at a local scale. Investigation of physical and chemical drivers suggested that polychaete communities in southern Namibia are structured to varying degrees by water depth, latitude, sediment composition, redox potential and organic content. Deeper stations comprised the highest diversity of polychaeta fauna. Species adapted to hypoxic conditions (e.g. Sigambra parva, Pararionospio pinnata, Diopatra cf. monroi and Nepthys cf. hombergii) dominated an area known as the mudbelt, where organically enriched silts and clays originating from the Orange River are deposited on the mid-shelf between the 40 and 120 m isobaths.

Polymetallic contamination drives indigenous microbial community assembly dominated by stochastic processes at Pb-Zn smelting sites

Indigenous microbial communities in smelting areas are crucial for maintaining fragile ecosystem functions. However, the community assembly process and their responses to polymetallic pollution are poorly understood, especially the taxa in each bin from the amplicons that contributed to the assembly process. Herein, microbial diversity, co-occurrence patterns, assembly process and the intrinsic mechanisms across contamination gradients at a typical PbZn smelting site were systematically unravelled by high-throughput sequencing. The results showed a consistent compositional profile among the indigenous communities across sampling sites, wherein genera KD4–96 from Chloroflexi and Sphingomonas from Proteobacteria emerged as the most abundant taxa. Network modularity of the high- and middle-contaminated communities at Pb and Zn smelting sites was >0.44, indicating that community populations were clustered into modules to resist high heavy metal stress. Stochastic processes dominated the community assembly, with the greatest contribution from drift (DR), which was significantly correlated with Pb, Zn, Cr and Cu contents. What's particular was that the DR-controlled bins were dominated by Proteobacteria (typical r-strategists), while the HoS-controlled bins were by Chloroflexi (typical K-strategists). Furthermore, the proportion of DR in the bins dominated by Sphingomonadaceae (phylum Proteobacteria) increased gradually with the increase of heavy metal contents. These discoveries provide essential insights for community control in restoring and mitigating soil degradation at PbZn smelting sites.

Distribution patterns of soil bacteria, fungi, and protists emerge from distinct assembly processes across subcommunities.

Environmental change exerts a profound effect on soil microbial domains-including bacteria, fungi, and protists-that each perform vital ecological processes. While these microbial domains are ubiquitous and extremely diverse, little is known about how they respond to environmental changes in urban soil ecosystems and what ecological processes shape them. Here we investigated the community assembly processes governing bacteria, fungi, and protists through the lens of four distinct subcommunities: abundant, conditionally rare, conditionally abundant, and rare taxa. We show that transient taxa, including the conditionally rare and conditionally rare or abundant taxa, were the predominant subcommunities. Deterministic processes (e.g., environmental filtering) had major roles in structuring all subcommunities of fungi, as well as conditionally rare and abundant protists. Stochastic processes had strong effects in structuring all subcommunities of bacteria (except rare taxa) and conditionally rare protists. Overall, our study underscores the importance of complementing the traditional taxonomy of microbial domains with the subcommunity approach when investigating microbial communities in urban soil ecosystems.

Gut microbiota in adults with cystic fibrosis: Implications for the severity of the CFTR gene mutation and nutritional status

BackgroundMicrobial 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. MethodsGut 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. ResultsResults 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. ConclusionsOur 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.

Differential responses of the phyllosphere abundant and rare microbes of Eucommia ulmoides to phytohormones

Phyllosphere microbiota play a crucial role in plant productivity and adaptation, and the abundant and rare microbial taxa often possess distinct characteristics and ecological functions. However, it is unclear whether the different subcommunities of phyllosphere microbiota respond variably to the factors that influence their formation, which limits the understanding of community assembly. The effects of two phytohormones, namely, indole-3-acetic acid (IAA) and N6-(delta 2-isopentenyl)-adenine (IP), on the phyllosphere microbial subcommunities of Eucommia ulmoides were investigated using potted experiments. The results demonstrated that the phytohormones induced significant variations in the composition, diversity, and function of the abundant microbial subcommunity in the phyllosphere of E. ulmoides, however, their effects on the rare subcommunity were negligible, and their effects on the moderate subcommunity were between those of the abundant and rare taxa. The phytohormones also induced significant alterations in the phenotypic and physiological properties of E. ulmoides, which indirectly affected the phyllosphere microbial community. Leaf thickness and average leaf area were the main phenotypic variables that affected the composition of the phyllosphere microbial community. The total alkaloid content and activity of superoxide dismutase (SOD) were the main physiological variables that affected the composition of the phyllosphere microbial community. The phenotypic and physiological indices of E. ulmoides explained the variations in the phyllosphere microbial subcommunities in descending order: abundant > moderate > rare taxa. These variables explained a significant proportion of the variations in the abundant taxa, and an insignificant proportion of the variations in the rare taxa. This study improves our understanding of the assembly of the phyllosphere microbiota, which provides important theoretical knowledge for future sustainable agriculture and forestry management based on the precise regulation of phyllosphere microbiota.

Prebiotic fibre mixtures counteract the manifestation of gut microbial dysbiosis induced by the chemotherapeutic 5-Fluorouracil (5-FU) in a validated in vitro model of the colon

Background5-Fluorouracil (5-FU) is used as an antineoplastic agent in distinct cancer types. Increasing evidence suggests that the gut microbiota might modulate 5-FU efficacy and toxicity, potentially affecting the patient’s prognosis. The current experimental study investigated 5-FU-induced microbiota alterations, as well as the potential of prebiotic fibre mixtures (M1-M4) to counteract these shifts.MethodsA pooled microbial consortium was derived from ten healthy donors, inoculated in an in vitro model of the colon, and treated with 5-FU, with or without prebiotic fibre mixtures for 72 h. Four different prebiotic fibre mixtures were tested: M1 containing short-chain galacto-oligosaccharides (sc GOS), long-chain fructo-oligosaccharides (lcFOS), and low viscosity pectin (lvPect), M2 consisting of arabinoxylan, beta-glucan, pectin, and resistant starch, M3 which was a mixture of scGOS and lcFOS, and M4 containing arabinoxylan, beta-glucan, pectin, resistant starch, and inulin.ResultsWe identified 5-FU-induced changes in gut microbiota composition, but not in microbial diversity. Administration of prebiotic fibre mixtures during 5-FU influenced gut microbiota composition and taxa abundance. Amongst others, prebiotic fibre mixtures successfully stimulated potentially beneficial bacteria (Bifidobacterium, Lactobacillus, Anaerostipes, Weissella, Olsenella, Senegalimassilia) and suppressed the growth of potentially pathogenic bacteria (Klebsiella, Enterobacter) in the presence of 5-FU. The short-chain fatty acid (SCFA) acetate increased slightly during 5-FU, but even more during 5-FU with prebiotic fibre mixtures, while propionate was lower due to 5-FU with or without prebiotic fibre mixtures, compared to control. The SCFA butyrate and valerate did not show differences among all conditions. The branched-chain fatty acids (BCFA) iso-butyrate and iso-valerate were higher in 5-FU, but lower in 5-FU + prebiotics, compared to control.ConclusionsThese data suggest that prebiotic fibre mixtures represent a promising strategy to modulate 5-FU-induced microbial dysbiosis towards a more favourable microbiota, thereby possibly improving 5-FU efficacy and reducing toxicity, which should be evaluated further in clinical studies.

MiDAS 5: Global diversity of bacteria and archaea in anaerobic digesters

Anaerobic digestion of organic waste into methane and carbon dioxide (biogas) is carried out by complex microbial communities. Here, we use full-length 16S rRNA gene sequencing of 285 full-scale anaerobic digesters (ADs) to expand our knowledge about diversity and function of the bacteria and archaea in ADs worldwide. The sequences are processed into full-length 16S rRNA amplicon sequence variants (FL-ASVs) and are used to expand the MiDAS 4 database for bacteria and archaea in wastewater treatment systems, creating MiDAS 5. The expansion of the MiDAS database increases the coverage for bacteria and archaea in ADs worldwide, leading to improved genus- and species-level classification. Using MiDAS 5, we carry out an amplicon-based, global-scale microbial community profiling of the sampled ADs using three common sets of primers targeting different regions of the 16S rRNA gene in bacteria and/or archaea. We reveal how environmental conditions and biogeography shape the AD microbiota. We also identify core and conditionally rare or abundant taxa, encompassing 692 genera and 1013 species. These represent 84–99% and 18–61% of the accumulated read abundance, respectively, across samples depending on the amplicon primers used. Finally, we examine the global diversity of functional groups with known importance for the anaerobic digestion process.

Environmental DNA metabarcoding reveals diverse phytoplankton assemblages and potentially harmful algal distribution along the urban coasts of Türkiye

Marine phytoplankton are widely used to monitor the state of the water column due to their rapid changes in response to environmental conditions. In this study, we aimed to investigate the coastal phytoplankton assemblages, including bloom-forming species using high-throughput sequencing of 18S rRNA genes targeting the V4 region and their relationship with environmental variables along the Istanbul coasts of the Sea of Marmara. A total of 118 genera belonging to six phyla were detected. Among them, Dinoflagellata (36) and Bacillariophyta (26) were represented with the highest number of genera. According to the relative abundance of DNA reads, the most abundant taxa were Dinoflagellata_phylum (18.1%), Emiliania (8.4%), Biecheleria (8.4), and Noctiluca (8.1%). The ANOSIM test showed that there was a significant temporal difference in the assemblages, while the driving environmental factors were pH, water temperature, and salinity. According to the TRIX index, the trophic state of the coasts was highly mesotrophic and eutrophic. In addition, 45 bloom-forming and HAB taxa were detected and two species of Noctiluca and Emiliania, which frequently cause blooms in the area, were recorded in high abundance. Our results provide insight into the phytoplankton assemblages along the urbanized coastlines by analysing the V4 region of 18S rRNA. This data can support future studies that use both traditional methods and metabarcoding, employing various primers and targeting different genes and regions.