Core Species Research Articles

Characterizing the oral and gastrointestinal microbiome associated with healthy aging: insights from long-lived populations in Northeastern China.

The oral and gastrointestinal (GI) tract microbiota in humans is susceptible to geographical influences and represents vital factors impacting healthy aging. The northeastern region of China, characterized by distinct dietary and climatic conditions, significantly influences the human microbiome composition. However, the microbial structure of the entire long-lived population in this area has not been evaluated. This study recruited a cohort of 142 individuals aged 55-102 residing in Northeast China, and their oral and gut microbiota were evaluated using full-length 16S rRNA gene amplicon sequencing. The results indicate that the oral and GI tract microbiota of long-lived individuals showed reduced microbial taxonomic richness and evenness compared to sub-longevity individuals. With aging, the core species experience a gradual decline in abundance, while subordinate species show an increase. The long-lived population exhibited a heightened ability to enrich beneficial bacteria including Akkermansia, Alistipes, Parabacteroides, and Eubacterium coprostanoligenes in the GI tract, which are associated with host metabolism and have the potential to act as probiotics, reducing the risks of unhealthy aging in the northeast population. Bifidobacterium sp. and Lactobacillus salivarius have been found to coexist in both the oral cavity and the GI tract of long-lived individuals. We hypothesize that beneficial bacterial taxa from the oral cavity colonize the GI tract more extensively in long-lived individuals compared to those with a shorter lifespan. These findings pave the way for identifying probiotic strains that can promote healthy aging in Northeast China.

Core-periphery structure of a medicinal botanical system in Uruguay

BackgroundHuman evolution has granted upon an individual’s cognitive mechanisms necessary for remembering experiences, vital for both survival and reproduction. These experiences manifest into cultural traits, influencing human culture, particularly in healthcare and maintenance. Studies regarding medicinal plants and treatments are integral to the study of the medical botanical system. Pharmacopeias highlight the prevalence of specific species widely used, aligning with the “consensus within diversity theory” in evolutionary ethnobiology. Within the framework of this theory, we reflect on the results we’ve achieved in a priority area recognized by UNESCO for its biocultural significance, both locally and regionally.MethodsThis study integrated network analysis and qualitative methods to examine the botanical medical system of “Parque Regional Quebradas del Norte” in Rivera, Uruguay.ResultsStudy results demonstrate a core-periphery structure, with a strongly interconnected core resistant to fragmentation, ensuring structural stability. Additionally, the presence of peripheral nodes throughout the system was identified, enhancing the resilience of the botanical medicinal system against potential disturbances.ConclusionThe core species renowned for their versatility and multiple medicinal uses, treating less severe ailments effectively. Additionally, core plants serve as prototypes for innovations. Their extinction poses a threat to the system’s resilience. Conversely, peripheral plants, though vulnerable, offer possibilities for therapeutic innovations. In the face of environmental change, conservation efforts should prioritize species that are vulnerable to extinction, particularly within the core. Simultaneously, preserving knowledge associated with peripheral plants presents a bicultural conservation strategy, ensuring the botanical system’s robustness among evolving ecological conditions.

Development of a flavor-oriented synthetic microbial community for pour-over rice wine: A comprehensive microbial community analysis

Huangjiu, a traditional Chinese alcoholic beverage, varies widely in quality and consistency when brewed using the traditional pour-over rice wine technique, largely due to the variability in its microbial community in an open fermentation environment. This study streamlined the microbial complexity using amplicon sequencing and culture-dependent methods, leading to the identification of a set of core microbial species instrumental in flavor development. A synthetic microbial community was crafted from these key species and employed in fermentation experiments. In this study, we demonstrated that the synthetic microbial community not only replicated the major flavor profiles of traditional pour-over rice wine but also it is further proved that the core species directly determines the main flavor of pour-over rice wine, these findings are supported by our quantitative analysis of volatile compounds and sensory evaluation data. This research underscores the potential of synthetic microbial communities in standardizing production processes and improving the sensory quality of traditional beverages like Huangjiu.

Methylisothiazolinone modulates community assembly and improves syntrophic cooperation via adaptive evolution during sludge anaerobic digestion

Various antimicrobials could pose multifaced threats to anaerobic digestion (AD) of waste-activated sludge (WAS), yet it is still unclear how antimicrobials would affect the metabolic activity and assembly process of anaerobic microbiome. In this study, a typical antimicrobial, methylisothiazolinone (MIT), was introduced in AD and induced an initial lag effect on methane production that was eventually recovered. Although MIT disintegrated WAS to promote the release of bioavailable substrates from extracellular polymeric substances (EPS), it also caused adverse stress to the microbiome. The initial microbial metabolic activities and syntrophic relationships associated with methane generation were distinctly inhibited. Because the self-adaptive systems of two-component systems (e.g., ddpF, and ddpD) and quorum sensing (e.g., cheR, and cydB) were activated to restore the syntrophic interaction among functional anaerobes, metabolic activities were gradually recovered for methane generation. Ultimately, the methane-generation species (e.g., Methanobacterium, and Methanomassiliicoccus) were driven as core species by deterministic processes, while non-functional species (e.g., Nitrospirota) were marginalized by stochastic processes under MIT stress. Overall, this finding indicated the intrinsic drive of evolutionary adaptation, unraveled the community assembly process at phylogenetic level under antimicrobial stress, and gave direction on the assessment and mitigation of external contaminant-related ecological risks in WAS treatment.

Sympatric populations of crop and wild carrots (Daucus carota ssp.) have distinct viromes, with shared core species more prevalent in farm-grown populations

Viral exchanges between crops and wild plants are important considerations in virus ecology and epidemiology but remain poorly understood. To investigate such exchanges, we compared the viromes of wild and farmed carrots (Daucus carota ssp.) growing near each other in France. Farm populations included cultivated varieties and off-type carrots (resembling wild ones) growing among them. This crop - wild relative pathosystem offers notable opportunities for virus exchange due to the hosts’ genetic closeness and geographic proximity. High-throughput sequencing found that viral taxonomic richness was greatest in wild carrots. However, hierarchical clustering and bipartite network analyses revealed that wild and farm carrot viromes differed in their seed-borne and vector-borne components. While ~50% of viral taxa were shared among carrot population types, others were uniquely associated with either wild or farm carrots. Individual-plant RT-PCR testing of 16 aphid-borne agents from the shared core virome found their prevalence was generally greatest in farm populations, with some geographic variability in virus pressure. The viromes of off-type and cultivated carrots were most similar, suggesting that proximity and/or management practices influence virome properties. For some aphid-borne viruses, similar isolates were found in wild and cultivated carrots, suggesting exchanges between them or with a shared source. However, isolates of other aphid-borne viruses clustered by carrot type, indicating barriers to viral fluxes, that might involve differential susceptibility of populations, vector preferences, or unidentified factors. To improve virus management, we need better understanding of how specific facilitators and barriers of viral exchange can be manipulated to reduce negative viral impacts.

Comparative analysis of the intestinal microbiota diversity in wild and farmed Gryllus bimaculatus

Abstract This study aims to investigate the structure and diversity of the intestinal microbiome of Gryllus bimaculatus from wild and farmed environments. Additionally, we sought to identify the core microbes to get information on the microbial diversity of the gut microbiome to the farm condition. We analyzed the microbial community diversity in intestinal samples of both wild and farmed G. bimaculatus using high-throughput sequencing of 16S rRNA gene and ITS rRNA amplicons. Using the PICRUSt2 software, we predicted the functional capabilities of bacterial communities. The analysis indicated significant differences in the diversity of the microbial communities (bacteria) within the gut of crickets under farmed and wild conditions, with notably higher bacterial diversity observed in the gut of farmed crickets compared to those in the wild. The gut bacterial communities exhibited significant similarity across the two conditions, and the variations in diversity are primarily influenced by species with low abundance. Genus-level analysis revealed that the abundance of pathogens, including genera Listeria, Staphylococcus, and Candida, was significantly higher in the gut microbiota of farmed crickets than in the wild ones. By identifying core genera (present in over 80% of the samples), we discovered 19 bacterial genera and 1 fungal genus. The core bacterial genera constituted 60.35% and 87.10% of the cricket’s gut bacterial abundance in farmed and wild environments, respectively. The functional prediction analysis performed using PICRUSt2 identified a significant increase of pathways about “Terpenoids and polyketides metabolism”, and “Infectious disease: bacterial” in the farmed group; as well as a significant decrease in pathways about “Environmental adaptation”, “Development and regeneration”, and the “Nervous system”, compared to the wild group. In conclusion our results showed that the gut microbial community of the G. bimaculatus could be influenced by its environment and diet. However, this influence is primarily manifested in the variation of low-abundance genera, with the gut microbial community remains dominated by a few microbial groups. Therefore, it is speculated that the combination of core and edge species in the gut microbial community of the G. bimaculatus may constitute an effective strategy that not only maintains the core functions of the community but also adapts to environmental changes through the diversity of edge species. The high population density and excessive feeding in the farmed condition could have allowed for the creation of a more diverse gut microbiota for G. bimaculatus, including potential pathogens. Therefore, when breeding G. bimaculatus, the environmental hygiene management should be strengthened to reduce the carrying and transmission of pathogens.

Gut Microbiota and Parkinson’s disease - a prospective analysis of the FINRISK 2002 Study

Abstract Background Parkinson’s disease (PD) is a neurodegenerative movement disorder with mainly unknown etiology. Constipation is a common symptom, and changes in gut microbiota may play role in PD pathogenesis. Previous studies exploring microbial associations to PD have been mostly cross-sectional, and the role of microorganisms in PD etiology remains unclear. Thus, we examined the association between microbiota features and incident PD in a prospective cohort design. Methods In the FINRISK 2002 Study, 7231 participants gave a stool sample that underwent shotgun metagenomic sequencing. Participants with missing stool sample, incomplete covariate data, pregnancy, antibiotic use, and prevalent cases were excluded (final n = 5562). Cox regression models, adjusted for age, sex, education, smoking, coffee consumption, diabetes, cardiovascular events, and constipation, were used to assess associations between incident PD and microbiota features, ie. alpha diversity (the number of different species present in a sample), beta diversity (the differences in microbial composition between individuals), and abundance of 381 core taxa (compositional detection rate of at least 0.1% and a prevalence of 1%). 120 incident cases of PD, identified through register linkage, occurred during a median follow-up of 17.8 years. Results In the multivariate models, PD incidence was not associated with the Shannon index, a measure on alpha diversity, (p-value 0.81), or with the ten first principal component axes in beta diversity analysis (p-values ranging between 0.49-0.91). In permutational analysis, PD did not explain differences in the composition of the gut microbiota (R2 <0.001, p-value 0.46)). None of the core species were associated with PD incidence (all FDR-corrected p-values > 0.05). Conclusions This prospective study showed no support for an association between gut microbiota features and incident PD. Key messages • Previous findings associating gut microbiota with PD may be due to the cross-sectional design, ie. PD affecting the gut microbiota. • Suggestions to screen gut bacteria to identify people at high risk of Parkinson’s disease are vastly premature as the scientific evidence is inconclusive.

Self-assembled nanostructured membranes with tunable pore size and shape from plant-derived materials.

Nanostructured materials derived from sustainable sources are of interest as viable alternatives to traditional petroleum-derived sources in membrane applications due to environmental concerns. Here, we present the development of pore size-tunable nanostructured polymer membranes based on a plant-derived material. The membranes were fabricated using a tri-functional amine as the templating core species and a cross-linkable ligand synthesized from rose oil-derived citronellol. The self-assembly of a supramolecular complex between the template core and the ligand forms a hexagonally packed columnar (Colh) mesophase, the dimensions of which can be precisely controlled by changing the stoichiometric ratio between these constituents. Within the hexagonal mesophase stoichiometric range, the pore size of the nanostructured membranes can be tuned from 1.0 to 1.3 nm, with a step size of approximately 0.1 nm. The membranes exhibited a clear distinction in molecular size selectivity, as demonstrated by dye adsorption experiments. The membrane fabricated with a ligand-to-core ratio of 3 to 1 demonstrated shape-based selectivity, exhibiting a higher permeability for propeller-shaped penetrants and highlighting its potential for shape-selective transport. We anticipate that this straightforward approach, using plant-derived materials, can contribute to important sustainability aspects while enhancing the performance of current state-of-the-art nanostructured membranes by enabling precise control over pore size.

Deciphering the acidophilia and acid resistance in Acetilactobacillus jinshanensis dominating baijiu fermentation through multi-omics analysis

Lactic acid bacteria (LAB) are pivotal in constructing the intricate bio-catalytic networks underlying traditional fermented foods such as Baijiu. However, LAB and their metabolic mechanisms are partially understood in Moutai flavor Baijiu fermentation. Here, we found that Acetilactobacillus jinshanensis became the· dominant species with relative abundance reaching 92%, where the acid accumulated rapidly and peaked at almost 30 g/kg in Moutai flavor Baijiu. After separation, purification, and cultivation, A. jinshanensis exhibited pronounced acidophilia and higher acid resistance compared to other LAB. Further integrated multi-omics analysis revealed that fatty acid synthesis, cell membrane integrity, pHi and redox homeostasis maintenance, protein and amide syntheses were possibly crucial acid-resistant mechanisms in A. jinshanensis. Structural proteomics indicated that the surfaces of A. jinshanensis proteases contained more positively charged amino acid residues to maintain protein stability in acidic environments. The genes HSP20 and acpP were identified as acid-resistant genes for A. jinshanensis by heterologous expression analysis. These findings not only enhance our understanding of LAB in Baijiu, providing a scientific basis for acid regulation for production process, but also offer valuable insights for studying core species in other fermentation systems.

Microbial community characteristics and pathogens detection in Rhipicephalus sanguineus and Haemaphysalis hystricis from Hainan Island, China.

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

Curcumin suppresses colorectal tumorigenesis through restoring the gut microbiota and metabolites

BackgroundCurcumin has been reported to have activity for prevention and therapy of CRC, yet its underlying mechanisms remain largely unknown. Recently, emerging evidence suggests that the gut microbiota and its metabolites contribute to the causation and progression of Colorectal cancer (CRC). In this study, we aimed to investigate if curcumin affects the tumorigenesis of CRC by modulating gut microbiota and its metabolites.MethodsForty male C57BL/6JGpt mice were randomly divided into four groups: negative control (NC), curcumin control, CRC model, and curcumin treatment (CRC-Cur) groups. CRC mouse model was induced by using azoxymethane (AOM) and dextran sodium sulfate (DSS), and the mice in CRC model and curcumin treatment groups received oral PBS or curcumin (150 mg/kg/day), respectively. Additionally, fecal samples were collected. 16 S rRNA sequencing and Liquid Chromatography Mass Spectrometry (LC-MS)-based untargeted metabolomics were used to observe the changes of intestinal flora and intestinal metabolites.ResultsCurcumin treatment restored colon length and structural morphology, and significantly inhibited tumor formation in AOM/DSS-induced CRC model mice. The 16S rRNA sequencing analysis indicated that the diversity and richness of core and total species of intestinal microflora in the CRC group were significantly lower than those in the NC group, which were substantially restored in the curcumin treatment group. Curcumin reduced harmful bacteria, including Ileibacterium, Monoglobus and Desulfovibrio, which were elevated in CRC model mice. Moreover, curcumin increased the abundance of Clostridia_UCG-014, Bifidobacterium and Lactobacillus, which were decreased in CRC model mice. In addition, 13 different metabolites were identified. Compared to the NC group, ethosuximide, xanthosine, and 17-beta-estradiol 3-sulfate-17-(beta-D-glucuronide) were elevated in the CRC model group, whereas curcumin treatment significantly reduced their levels. Conversely, glutamylleucine, gamma-Glutamylleucine, liquiritin, ubenimex, 5’-deoxy-5’-fluorouridine, 7,8-Dihydropteroic acid, neobyakangelicol, libenzapril, xenognosin A, and 7,4’-dihydroxy-8-methylflavan were decreased in the CRC group but notably upregulated by curcumin. Kyoto Encyclopedia of Genes and Genome (KEGG) pathway analysis revealed enrichment in seven pathways, including folate biosynthesis (P < 0.05).ConclusionsThe gut microecological balance was disrupted in AOM/DSS-induced CRC mice, accompanied by metabolite dysbiosis. Curcumin restored the equilibrium of the microbiota and regulated metabolites, highly indicating that curcumin may alleviate the development of AOM/DSS induced colorectal cancer in mice by regulating intestinal flora homeostasis and intestinal metabolites.

Proximity labeling defines the phagosome lumen proteome of murine and primary human macrophages.

Proteomic analyses of the phagosome has significantly improved our understanding of the proteins which contribute to critical phagosome functions such as apoptotic cell clearance and microbial killing. However, previous methods of isolating phagosomes for proteomic analysis have relied on cell fractionation with some intrinsic limitations. Here, we present an alternative and modular proximity-labeling based strategy for mass spectrometry proteomic analysis of the phagosome lumen, termed PhagoID. We optimize proximity labeling in the phagosome and apply PhagoID to immortalized murine macrophages as well as primary human macrophages. Analysis of proteins detected by PhagoID in murine macrophages demonstrate that PhagoID corroborates previous proteomic studies, but also nominates novel proteins with unexpected residence at the phagosome for further study. A direct comparison between the proteins detected by PhagoID between mouse and human macrophages further reveals that human macrophage phagosomes have an increased abundance of proteins involved in the oxidative burst and antigen presentation. Our study develops and benchmarks a new approach to measure the protein composition of the phagosome and validates a subset of these findings, ultimately using PhagoID to grant further insight into the core constituent proteins and species differences at the phagosome lumen.

Microbial core communities in activated sludge plants are strongly affected by immigration and geography

BackgroundThe microbiota in wastewater treatment plants (WWTPs) and incoming wastewater is critical for the treatment process, the preservation of natural ecosystems and human health, and for the recovery of resources and achievement of sustainability goals. Both core species and conditionally rare and abundant taxa (CRAT) are considered process-critical but little is known about identity as well as true functional and ecological importance. Here, we present a comprehensive investigation of the microbiota of 84 municipal activated sludge (AS) plants with nutrient removal treating ~ 70% of all wastewater within a confined geographical area, Denmark (43,000 km2). With the use of an ecosystem-specific database (MiDAS 5.2), species-level classification allowed us to investigate the core and CRAT species, whether they were active, and important factors determining their presence.ResultsWe established a comprehensive catalog of species with names or placeholder names showing each plant contained approx. 2,500 different species. Core and CRAT represented in total 258 species, constituting around 50% of all reads in every plant. However, not all core and CRAT could be regarded as process-critical as growth rate calculations revealed that 43% did not grow in the AS plants and were present only because of continuous immigration from the influent. Analyses of regional microbiota differences and distance decay patterns revealed a stronger effect for species than genera, demonstrating that geography had a clear effect on the AS microbiota, even across a limited geographical area such as Denmark (43,000 km2).ConclusionsThe study is the first comprehensive investigation of WWTPs in a confined geographical area providing new insights in our understanding of activated sludge microbiology by introducing a concept of combining immigration and growth calculation with identifying core and CRAT to reveal the true ecosystem-critical organisms. Additionally, the clear biogeographical pattern on this scale highlights the need for more region-level studies to find regional process-critical taxa (core and CRAT), especially at species and amplicon sequence variant (ASV) level.

A comprehensive catalog encompassing 1376 species-level genomes reveals the core community and functional diversity of anammox microbiota

Research on the microbial community and function of the anammox process for environmentally friendly wastewater treatment has achieved certain success, which may mean more universal insights are needed. However, the comprehensive understanding of the anammox process is constrained by the limited taxonomic assignment and functional characterization of anammox microbiota, primarily due to the scarcity of high-quality genomes for most organisms. This study reported a global genome catalog of anammox microbiotas based on numerous metagenomes obtained from both lab- and full-scale systems. A total of 1376 candidate species from 7474 metagenome-assembled genomes were used to construct the genome catalog, providing extensive microbial coverage (averaged of 92.40 %) of anammox microbiota. Moreover, a total of 64 core genera and 44 core species were identified, accounting for approximately 64.25 % and 43.97 %, respectively, of anammox microbiota. The strict core genera encompassed not only functional bacteria (e.g., Brocadia, Desulfobacillus, Zeimonas, and Nitrosomonas) but also two candidate genera (UBA12294 and OLB14) affiliated with the order Anaerolineales. In particular, core denitrifying bacteria with observably taxonomic diversity exhibited diverse functional profiles; for instance, the potential of carbohydrate metabolism in Desulfobacillus and Zeimonas likely improves the mixotrophic lifestyle of anammox microbiota. Besides, a noteworthy association was detected between anammox microbiota and system type. Microbiota in coupling system exhibited complex diversity and interspecies interactions by limiting numerous core denitrifying bacteria. In summary, the constructed catalog substantially expands our understanding of the core community and their functions of anammox microbiota, providing a valuable resource for future studies on anammox systems.

Historic checklist, core species and temporal composition turnover of birds in an urban protected natural area in central México over 50 years.

The Pedregal de San Ángel Ecological Reserve (REPSA) is located within the central campus of the National Autonomous University of Mexico (UNAM), in southwestern Mexico City. This area is known for its bird richness, which has been documented over time. However, this historical information has not been compiled, nor has it been assessed whether species composition has changed over time. In this study, we generated the historical checklist of avifauna in the REPSA by integrating data from systematic monitoring, bibliographic review and citizen science. Additionally, we calculated Jaccard's dissimilarity Index (nestedness and species turnover) among bird checklists from each year and evaluated whether this index and its components changed over time. In addition, we estimate whether the proportion of species arriving and becoming extinct in the REPSA is influenced by time (census interval) and by the migratory status of the species. Finally, we identified the core species of the REPSA. Our results indicate that from 1967 to 2023, 258 bird species have been recorded in the REPSA. The Jaccard's dissimilarity and turnover increased and reached an asymptotic trend over time while nestedness showed similar values throughout time. The time and species residency status did not have significant effect on the proportion of species that arrival and become extinct in the reserve. We identified 58 core species based on their persistence; 35 of these are residents, 22 have some migratory movement and one exotic species. Our results highlight the importance of the REPSA as a fundamental habitat for the avifauna of Mexico City, including a wide variety of migratory bird species.

Non-typical fractionation behaviors in a lepidolite-subtype pegmatite: Implications for the internal evolution of a naturally fluxed system

Despite their relatively rare occurrence, lepidolite-subtype pegmatites host abundant Li–Nb–Ta–Cs–Sn mineralization and represent a high-flux pegmatitic system with abnormally high F and Li activity. Characterization of highly fluxed melts and the impact of fluxes and exsolved fluids on fractionation of peraluminous melts have mainly been studied in experimental systems, with natural system correlations remaining poorly understood. Consequently, we conducted a systematic mineralogical study of a lepidolite-subtype pegmatite in the North Qinling orogenic belt, Central China. An abnormal “concave downward” fractionation trend for primary columbite-group minerals on the quadrilateral diagram is identified, and irregularly zoned columbite crystals coexist with F-rich minerals in one of the core zones have the highest Ta contents (normally 50.17–63.13 wt% Ta2O5) and Ta/(Nb + Ta) ratios (up to 0.65). Despite the consistently Ta-dominated B-site in the crystal lattice of microlite-group minerals, extreme compositional variations at the A- and Y-sites are observed. Compared with microlites in intermediate zones, the abrupt increase in U in microlite crystals in core zones and late units (up to 20.16 wt% UO2), is ascribed to the melt-fluid interaction with exsolved U-rich aqueous fluids. In addition, the fractional crystallization of F-bearing minerals resulted in a gradual decrease in F contents in microlite-group minerals from extremely F-rich (2.68–4.84 wt% F) in intermediate zones to low F species (mainly 0.82–1.71 wt% F) in core and late zones. Moreover, autometasomatism by a late fluxed melt and hydrothermal metasomatism by late aqueous fluids are identified in columbite- and microlite-group minerals. This work highlights that these non-typical fractionation behaviors related to the activity of fluxes (especially F) and the exsolution of aqueous fluids during the internal evolution of pegmatitic melts, are critical for the generation of lepidolite-subtype pegmatites. Fluorine was gradually enriched in the pegmatitic melt, and reached its highest level during crystallization of the (inner) intermediate and core zones. Non-equilibrium crystallization occurred throughout pegmatite evolution, and late units were most probably formed from aqueous fluid-enriched residual melts, rather than by hydrothermal replacement.

Clinical Investigation of Bacteriome in Primary Endodontic Infections With Apical Periodontitis Using High-Throughput Sequencing Analysis

IntroductionThis study characterized the bacteriome in primary endodontic infection (PEI) with apical periodontitis (AP), identified core and rare bacteriome species and community diversity metrics, and analyzed the relationship between the bacteriome composition, diversity and features, and patient variables. MethodsTwenty-seven patients with PEI and AP were sampled. The DNA was extracted and quantified using quantitative polymerase chain reaction. Raw V3-V4 amplicon sequencing data were processed with the DADA2 pipeline to generate amplicon sequence variants, and taxonomic assignment of the amplicon sequence variants up to the species level was done against the Human Oral Microbiome Database. Core bacteriome and differential abundance analyses were performed using ANCOM. Alpha diversity was determined using Chao1, Shannon, and Simpson indexes. LeFse analysis was used to identify abundant taxa. Sparse Estimation of Correlations among Microbiomes analysis estimated linear and nonlinear relationships among bacteria. ResultsOf 27, 24 root canal samples were analyzed, and 3 root canal sampling were filtered out with a low read count. The bacterial phyla with top mean relative abundance were Bacteroidetes, Firmicutes, Synergistetes, Fusobacteria, and Actinobacteria. A total of 113 genera and 215 species were identified. The samples were gathered into 3 clusters. LefSe analysis identified differences in abundant taxa between distinct age, gender, symptomatology, and lesion size groups. Sparse Estimation of Correlations among Microbiomes distance analysis indicated Slackia exigua as the node with the highest degree. ConclusionsThe bacteriome in PEI with AP among the patients in this study was complex and displayed high microbial heterogeneity. Moreover, age, gender, symptomatology, and lesion size were associated with differences in bacteriome features in PEI with AP.

Loss of species and functions in a deforested megadiverse tropical forest.

Tropical species richness is threatened by habitat degradation associated with land-use conversion, yet the consequences for functional diversity remain little understood. Progress has been hindered by difficulties in obtaining comprehensive species-level trait information to characterize entire assemblages and insufficient appreciation that increasing land-cover heterogeneity potentially compensates for species loss. We examined the impacts of tropical deforestation associated with land-use heterogeneity on bird species richness, functional redundancy, functional diversity, and associated components (i.e., alpha diversity, species dissimilarity, and interaction strength of the relationship between abundance and functional dissimilarity). We analyzed over 200 georeferenced bird assemblages in the Atlantic Forest of Brazil. We characterized the functional role of the species of each assemblage and modeled biodiversity metrics as a function of forest cover and land-cover heterogeneity. Replacement of native Atlantic Forest with a mosaic of land uses (e.g., agriculture, pastures, and urbanization) reduced bird species richness in a nonrandom way. Core forest species, or species considered sensitive to edges, tended to be absent in communities in heterogenous environments. Overall, functional diversity and functional redundancy of bird species were not affected by forest loss. However, birds in highly heterogenous habitats were functionally distinct from birds in forest, suggesting a shift in community composition toward mosaic-exclusive species led by land-cover heterogeneity. Threatened species of the Atlantic Forest did not seem to tolerate degraded and heterogeneous environments; they remained primarily in areas with large forest tracts. Our results shed light on the complex effects of native forest transformation to mosaics of anthropogenic landscapes and emphasize the importance of considering the effects of deforestation and land-use heterogeneity when assessing deforestation effects on Neotropical biodiversity.

Construction and application of a synthetic microbial community in reduced salinity fermentation of raw-materials based broad bean paste

Raw-materials based broad bean paste (rmBBP) is popular among consumers. Though high salinity can select functional microbial community for fermentation, it also impaired the fermentation efficiency of rmBBP and unfavored human health. Therefore, this study aimed to construct a synthetic microbial community based on key functional microbes for reduced salt rmBBP fermentation based on the elucidation of the microbial community succession during fermentation. Based on the tracked determination and multivariate statistical analysis of the physicochemical parameters, metabolites and the structure of microbial community, salinity and microbial interactions were key drivers for the succession of microbial community. Aspergillus, Staphylococcus, Weissella and Tetragenococcus were predicted to play key roles during fermentation. After that, core species were isolated from rmBBP mash and their salinity tolerance and metabolic characteristics were evaluated. Finally, a synthetic microbial community (Aspergillus oryzae, Staphylococcus carnosus, Tetragenococcus halophilus and Weissella confusa) was constructed and applied in reduced-salt rmBBP fermentation. The bioaugmentation contributed to the accumulation of volatile metabolites while effectively maintaining the acidity during rmBBP fermentation when salinity was reduced from 12% to 10%. In general, this study developed a synthetic microbial community with desired characteristics for successful reduced-salinity rmBBP fermentation.

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.