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Results for “ecological stratification”

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PubMed2026

Genome-resolved analysis of colonization factor repertoires reveals ecological stratification in cervid gut microbiomes.

INTRODUCTION: Colonization factors (CFs) are important microbial traits associated with persistence and host adaptation in the gut, yet their large-scale organization in cervid gut microbiomes remains unclear. METHODS: A total of 3,311 non-redundant high-quality metagenome-assembled genomes (MAGs), derived from 688 cervid gut metagenomic samples across 15 publicly available projects and one in-house dataset, were analyzed. CF-associated genes were identified by comparison against the GHA CF database, and CF repertoires were characterized at genome, host-species, and gastrointestinal-segment levels. RESULTS: A total of 138,729 CF-associated genes spanning 71 CF families were identified. MAGs from Cervinae contained richer CF repertoires than those from Caprinae, and CF47 (Peptidase_C69), CF24_29 (QueH), and CF18 (Glycos_transf_2) were among the most prevalent families. CF repertoires were strongly structured by taxonomy, showed a moderate association with bacterial phylogenetic distance, and formed two recurrent genome-level configurations with distinct KEGG functional profiles. Integration of sample metadata further revealed differentiation of CF repertoires across host species and gastrointestinal segments, representing the major ecological dimensions examined in this study. Segment-associated CF variation was accompanied by redistribution of broader functional profiles, including enrichment of carbohydrate and lipid metabolism in the jejunum, membrane transport in the ileum, xenobiotics biodegradation in the cecum, and environmental adaptation in the rumen. DISCUSSION: These findings provide a genome-resolved view of CF repertoire organization in cervid gut microbiomes and demonstrate that colonization-associated functions are structured across microbial lineages and ecological contexts. This study highlights the importance of considering microbial taxonomy and host-associated environments when interpreting the distribution of CF repertoires in mammalian gut ecosystems.

Cervidae↗

PubMed1975

Distribution and ecological consideration of Breinlia booliati infecting wild rodents in Malaysia.

Seven of the 18 species of lowland forest terrestrial and semi-arboreal murids were found naturally infected with Breinlia booliati. Of these, two species, Rattus sabanus and R. cremoriventer, were found to be the most preferred hosts. None of the murids from the highland, field or human-inhabited areas was infected. This could have been due more to the greater scarcity of the vectors in these habitats than to the susceptibility of the hosts. The absence of this parasite in the squirrels examined may be attributed either to host specificity or to the normal activity cycles or vertical stratification of the vectors, separating them in space and/or time from the squirrels. The pattern of dispersion of the parasite is influenced by the wide distribution of suitable hosts, and the hypothesis that the parasite is of forest origin is discussed.

Aedes↗

PubMed1991

[Nutrition survey in the Republic of the Congo: results from a national survey conducted in 1987].

The objective was to evaluate the nutritional status of preschool children in the rural areas in order to establish a baseline for the measurement of the impact of a Government Nutrition Education Project (NUTED) in forthcoming years. The household cross-sectional survey was carried out on a representative sample of the rural population. The sample was stratified in order to portray the nutritional status of the children in the northern regions (more thinly populated) and in the southern regions: one stratum for small towns (between 2000 and 30,000 inhabitants) and 4 strata for rural localities. The sampling method used was by clusters of 30 children, distributed randomly in 20 zones per stratum. The nutritional indices of 2429 children were calculated and analysed according to WHO recommendations. The prevalence of the different types of malnutrition was 27.5% (95% confidence interval (CI), 24.2-30.8) for stunting (height-for-age retardation) and 5.5% (CI = 4.2-6.8) for wasting (weight-for-height retardation). Both types coexisted among 1.9% of the children; 23% of children were underweight for their age (CI = 21.6-26.2), and 15.8% (CI = 14.7-16.9) aged greater than 12 months had a mid-arm circumference below 135 mm. No sex difference was observed in the results. Stunting seems to appear in the second trimester of life (3-5 months), and wasting appeared between 9 and 23 months (highest rate between 12 and 17 months: 14.0% (CI = 9.3-18.8], which presents a real public health problem. The stratification did not show any significant differences in nutritional status among the children living in rural zones and those living in the small towns. However, the prevalence of malnutrition in the rural zones was 2 or 3 times higher than that observed in 1986 in Brazzaville. The division of the country into five main ecological zones allows some useful comparisons, e.g., the prevalence of stunting ranges from 15.5% (CI = 12.8-18.2) in the northern inundated forest zone to 38.8% (CI = 32.9-44.7) in the southern forests of Mayombe and Chaillu. The diet also varied, the frequency of animal protein consumption on the preceding day ranging from 76.3% to 59.1% in the different zones. The Republic of the Congo differs from other African countries in having relatively lower rates of stunting but an astonishingly high prevalence of wasting.(ABSTRACT TRUNCATED AT 400 WORDS)

Child Nutrition Disorders↗

PubMed2026

Characteristics and assembly mechanisms of tobacco-associated bacteria in typical tobacco-planting regions across China.

INTRODUCTION: Plant-associated microbiota critically modulates host growth and environmental adaptation, yet assembly mechanisms, niche differentiation, and ecological strategies of bacterial communities inhabiting tobacco microhabitats remain poorly elucidated across geographical gradients. METHODS: Here, we systematically characterized bacterial microbiome assembly across five tobacco-associated niches (bulk soil, rhizosphere soil, root, stem, and leaf) from seven typical tobacco-planting regions using 16S rRNA amplicon sequencing, genome annotation, and niche breadth analysis. The independent and interactive effects of geographical location and host compartment on community structure, and further compared genomic traits, functional profiles, and life-history strategies between specialist and generalist bacterial populations were quantified. RESULTS: The results revealed a deterministic soil-plant continuum stratification of bacterial communities and diversity, with progressively simplified communities and decreasing alpha diversity from bulk soil to above-ground tissues, accompanied by progressive dominance of Proteobacteria. Geographical factors predominantly structured soil microbial communities via divergent edaphic properties, while host filtering acted as a universal dominant driver shaping endophytic microbiome assembly. Niche differentiation analysis demonstrated that niche-specialized bacterial ASVs overwhelmingly dominated all microhabitats and geographical sites, whereas generalist taxa only constituted auxiliary populations. Although specialist and generalist microbes exhibited highly conserved core genomic architectures and overall functional repertoires, they displayed distinct niche-specific functional divergence in metabolic pathways, stress resistance, and secondary metabolism across host compartments. Life-history strategy analysis further revealed that Y-strategist represented the core adaptive bacterial population, especially enriched in above-ground tobacco tissues. DISCUSSION: Our study establishes a hierarchical dual-filtering assembly model for tobacco microbiota, clarifies the ecological differentiation and functional adaptation of specialist and generalist bacteria, and provides fundamental insights into the assembly rules and adaptive mechanisms of crop-associated microbiomes for future microbial resource utilization and agricultural microbiome regulation.

biogeography↗

PubMed1978

[Comparative analysis of the neuronal and synaptic organization of the mesencephalic visual center of Greek and steppe turtles].

The stratification, neuronal structure and synaptic organization of tectum opticum have been studied in two species of tortoises (Testudo graeca and Testudo horsfieldi, Gray) by means of Golgi methods and electron microscopy. The midbrain tectum in these closely related animals has some common properties, but at the same time it possesses certain species specific features. Their properties in common appear to be connected with the common ecology and closely systematic place of Testudo graeca and Testudo horsfieldi. The specific features appear to be connected with the species differences in visual behavior of these species.

Animals↗

PubMed1992

Epidemiological risk stratification of malaria in the Americas.

During the last years, malaria had a significant increase in Latin America, emerging again as one critical health problem in the Region of the Americas. More than 1.04 million new cases were reported in 1990. This resurgence of malaria needed a comprehensive strategy for its prevention and control. National malaria control programs recognized the epidemiological stratification of malaria as a valuable method to assist them in the recognition of local variations and factors that specifically contribute to the level and intensity of transmission in critical malarious areas. Also it serves as a useful instrument for the selection of needed malaria prevention and control activities. The principal feature of this approach is to provide a dynamic and ongoing process for assessing the epidemiological importance of different risk factors (socio-economic, ecological, organization of health services) in malaria transmission. Health interventions are based on this assessment and are aimed directly at the reduction or elimination of the identified risk factors operating at the local level. Intersectorial co-participation and the integration of malaria programs in local health services are also important aspects of this public health approach.

Epidemiologic Methods↗

PubMed2026

Spatiotemporal genomic analysis and risk assessment of the plasmids carrying blaOXA-48-like genes based on a large-scale international dataset.

BACKGROUND: The spread of OXA-48-like carbapenemases represents a major public health challenge. Although previous studies have investigated OXA-48-like carbapenemases risk factors, nosocomial dissemination, and plasmid dynamics, an integrated plasmid-centered framework combining complete plasmid mining, transmission-unit analysis, phylogenetic reconstruction, and machine learning-based risk assessment remains limited. METHODS: We systematically collected 747 complete plasmid sequences carrying blaOXA-48-like genes from the NCBI database, establishing the largest collections of complete plasmid sequences to date. Using an integrative framework of population genomics, phylogenetic dating, and machine learning, this study aimed to characterize the dissemination patterns, plasmid replicon diversity, transmission units, mobile genetic elements, co-resistance profiles, and risk classification of these plasmid. RESULTS: Plasmids carrying blaOXA-48-like genes were detected across 50 countries on six continents, with blaOXA-48 predominating in Europe, blaOXA-181 in South Asia, and blaOXA-232 largely in Asia. IncL and ColKP3/IncX3 replicons, together with Tn1999.2 and other MGEs, were central drivers of plasmid maintenance and spread. Sixteen transmission units were defined, with AA068_Cluster3 estimated to have originated in the Netherlands around 2005 before expanding to Europe, the Middle East, Asia, and North America. Co-resistance analyses revealed frequent modules involving aminoglycoside and quinolone resistance, with qnrS1 and aph(3'')-Ib most prevalent. Notably, high-risk transposon structures were often identified in non-clinical environments, underscoring their cross-ecological transmission potential. Machine learning-based classification models showed good internal performance for predefined composite-risk categories, with plasmid mobility, clinical/non-clinical source composition, and host background contributing to the classification results. CONCLUSIONS: This study provides a large-scale plasmid-centered genomic analysis of publicly available complete plasmid sequences carrying blaOXA-48-like genes, integrating transmission-unit inference, phylogeographic reconstruction, mobile genetic element and co-resistance profiling, and composite genomic risk stratification. This gene-centered framework may support future One Health-oriented antimicrobial resistance surveillance and prioritization of plasmids with higher dissemination and resistance potential.

Plasmids↗

PubMed1979

Feeding behaviour and diet of chimpanzees (Pan troglodytes troglodytes) in the Okorobikó Mountains of Rio Muni (West Africa).

Some aspects of the nutritional behaviour of the Okorobikó-Matama (Rio Muni, West Africa) chimpanzees have been studied over two periods--from June 1963 to September 1964 and from July 1966 to February 1969. This research totaled 640 h, 119 of which were in sustained contact with the animals. We have complied a list of 43 plant and two termite species consumed by the chimpanzees. We studied the relative importance of the plants consumed in terms of the four principal biotopes and seasonal cycles, the feeding behavior, the rhythm of activity and chimpanzees' vertical stratification during feeding. We also took into accout group dynamics as a function of feeding, communication and polyspecific associations with other primates. We finally compared some aspects of the nutrition of these chimpanzees with that of gorillas living in nearby zones.

Africa, Western↗

PubMed1990

Stratification in perception and action.

This paper discusses the concept of stratification, in the sense of levels of analysis and levels of control, in relation to human perception and performance. It is contended that functional analysis is the proper level of analysis for the domain of perception and action. This is illustrated by means of models of cognitive energetics and motor control. The functional level of analysis can be situated in between the level of symbolic representations and the level of neurophysiological mechanisms. It is also argued that the concept of levels of control provides a way of integrating or relating ecological and information-processing approaches to psychology, in the sense that ecological psychology is concerned with lower and more peripheral levels of control (coordinative structures). Finally, some remarks are made on the relation between cognition and perception and action, drawing on Piaget, and it is proposed that the concept of schema is more appropriate for the domain of perception and action than is the notion of symbolic representations.

Attention↗

PubMed1990

Relationship between diabetes mellitus mortality rates and drinking water magnesium levels in Iowa.

A recent ecologic study has suggested a relationship between mortality from diabetes mellitus and levels of magnesium in drinking water. However, diabetes mortality rates were from aggregate data for the entire geographic area under study. The state of Iowa has data resources available to determine diabetes mortality rates for individuals on known water supplies in Iowa and magnesium levels for raw drinking water supplies. To determine the presence of this relationship in the state of Iowa, mortality rates from 1976 through 1985 for diabetes as an underlying cause of death and for major cardiovascular disease with diabetes as an ancillary cause of death were compared for individuals from towns in Iowa with populations of 1,000 to 10,000. At the stratification levels of magnesium in municipal drinking water used in this study, no significant differences were found in diabetes mortality rates.

Cardiovascular Diseases↗

PubMed1991

Selective decontamination of the digestive tract: a stratified, randomized, prospective study in a mixed intensive care unit.

To evaluate the use of selective decontamination of the digestive tract (SDD) (polymyxin, amphotericin, tobramycin, and intravenous cefotaxime) in a mixed intensive care unit, we performed a stratified, randomized, prospective study. The 331 patients were recruited over an 18-month period, with 256 patients remaining more than 48 hours. Stratification by acute physiology and chronic health evaluation (APACHE II) preceded randomization to control (standard antibiotic therapy) or treatment (SDD) groups. Nosocomial infection was significantly reduced in the SDD group (16.7%; 21 of 126 patients) compared with the control group (30.8%; 40 of 130 patients; p = 0.008). No difference was found in overall mortality rate or length of stay between the two groups. Those patients with admission APACHE II scores 10 to 19 demonstrated the most significant reduction in nosocomial infection (23 of 70 control vs 13 of 76 SDD; p = 0.03) and mortality (15 of 70 control vs 8 of 76 SDD; p = 0.07). Emergence of multiresistant microorganisms was not a clinical problem, but a definite change occurred in the ecology of environmental and colonizing bacteria. With the exception of cefotaxime, a reduction was noted in systemic antibiotic usage in the SDD group. We conclude that SDD is useful in selected patients in a mixed intensive care unit.

Adolescent↗

PubMed2026

GiantHost: a domain-adaptive and uncertainty-aware framework for giant virus host prediction.

MOTIVATION: Nucleocytoplasmic large DNA viruses (NCLDVs) play crucial roles in global ecosystems. Although metagenomics has vastly accelerated the discovery of novel NCLDVs, predicting their hosts from fragmented contigs remains a critical bottleneck, with no dedicated end-to-end computational tools currently available. Addressing this gap requires overcoming three fundamental challenges: the extreme scarcity of labeled reference genomes, the severe domain shift between laboratory isolates and diverse environmental metagenomes, and the inability of traditional deterministic models to quantify prediction uncertainty-a crucial requirement for reliable ecological profiling where novel, divergent viruses are prevalent. RESULTS: We present GiantHost, the first NCLDV host prediction tool with domain adaptation and uncertainlty awareness. GiantHost employs a dual-tower neural network to integrate dense genome traits and sparse GVOG profiles, allowing better integration of heterogeneous features. To overcome label scarcity and domain shift, we leverage 1400 environmental viral genomes (GVMAGs) via semi-supervised multi-task learning and Domain Adversarial Neural Networks (DANN), effectively bridging the distributional gap between RefSeq and environmental data. Additionally, GiantHost incorporates Conformal Prediction (CP) to output statistically guaranteed prediction sets rather than overconfident single labels. Evaluated under rigorous genome-level cross-validation, GiantHost demonstrates robust predictive power. Applied to the Tara Ocean dataset, GiantHost successfully captured the vertical stratification of NCLDV hosts-revealing a depth-dependent decline of phytoplankton-infecting viruses and a relative enrichment of Amoebozoa-infecting viruses in the mesopelagic zone. AVAILABILITY: The source code of GiantHost is available via: https://github.com/FuchuanQu/GiantHost.

Giant Viruses↗

PubMed2026

Integrated metagenomic and metabolomic analysis identifies severity-specific inflammatory and metabolic signatures in post-stroke depression.

Post-stroke depression (PSD) is a common complication that significantly impacts patient prognosis. This study aimed to systematically characterize the associations among gut microbial ecology, metabolic profiles, and inflammatory responses across different severities of PSD. We conducted metagenomic sequencing, non-targeted metabolomics, and serum cytokine analysis (IL-1β, IL-6, IL-10, IL-18, TNF-α, IFN-γ, and CRP) in 91 patients with varying degrees of PSD and non-PSD controls. Bioinformatics analyzes were employed to construct multi-omics association networks and machine learning models. Results indicated that PSD patients exhibited significantly increased gut microbiota alpha-diversity, suggesting dysbiosis. Mild depression was characterized by compensatory neural signaling activation, whereas the moderate depression group exhibited abnormalities in tryptophan/indole metabolism, oxidative stress-related metabolic imbalances, and functional decompensation. Further analyzes suggested that Alistipes, Blautia_A, Evtepia gabavorous, and Lachnospira were associated with inflammatory features, GABA-related metabolic alterations, aromatic amino acid/indole metabolism, and lipid-amino acid metabolism, respectively. Under a more rigorous 10-fold cross-validation framework, the performance of different multi-omics combination models showed heterogeneity; however, some combinations still demonstrated superior discriminatory ability compared to single-omics approaches. This study provides multi-omics clues suggesting associations between different PSD severity levels and features such as increased Alistipes abundance, reduced antioxidant capacity, and altered tryptophan metabolism. It provides candidate biomarker combinations that may be useful for PSD stratification and suggests that the gut microbiome may represent a potential target for future PSD intervention. In summary, PSD may be associated with dynamic alterations along the "gut-brain-inflammation-metabolism" axis. These findings provide integrated evidence for microbial, metabolic, and inflammatory abnormalities across different PSD severity levels, but still require validation in larger samples, longitudinal cohorts, and mechanistic studies.

Humans↗

PubMedDate not supplied

[The isolation of tick-borne encephalitis virus strains and the determination of the scope of immune stratification among the population and the domestic animals on the northern Russian plain].

Between 1986 and 1987 the authors conducted virological survey of 689 Ixodes persulcatus and 420 mouse-like and insectivorous rodents at the territory of Arkhangelsk Province and the Republic of Komi. A total of 8 strains of tick-borne encephalitis virus were isolated. Out of them 3 strains were isolated from small mammalians (2 from Clethrionomys glareolus, 1 from Microtus oeconomus) at the southeastern areas of Arkhangelsk Province within the middle taiga subarea, 5 strains were isolated from I. persulcatus (the rate of infection was 1.25 per cent) gathered in the southeastern Komi within the southern margins of the middle taiga subarea. PHAT investigation of the sera (2064 human, 656 cow and 171 dear specimens) evidenced almost the absence of immunity among the studied populations of the tundra and forest tundra zones. Certain positive samples observed in the northern taiga region could be explained by the infection gained in areas situated more to the south. Among the middle taiga human populations the immunity reached 4.9 per cent.

Animals↗