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At least 19 recordsLinked to original sources
PubMed2026

Unveiling microbial risks in Chinese household dust: a comprehensive analysis from absolute abundance to virulence unit.

BACKGROUND: People spend the majority of their lives indoors, yet the risk and virulence potential of household microbiota remain largely unexplored, particularly in developing countries. RESULTS: Here, we conducted a nationwide survey on both dust samples and health information across 118 Chinese households. The microbiota composition and its functional units were analyzed using absolute 16S rRNA/ITS sequencing, metagenomics, and metaproteomics. Cross-domain network analysis of the core microbial communities revealed robust co-occurrence patterns in household dust. The mean absolute abundance of potentially pathogenic bacteria and fungi in households was 2.39 × 105 and 2.83 × 106 DNA copies/g dust. The potentially pathogenic community was primarily influenced by latitude, relative humidity, and average temperature. Although total absolute abundance was substantially lower in urban areas, the relative abundance of potentially pathogenic bacteria was markedly higher compared to rural environments. While urban-rural differences existed, the underlying statistical drivers were the environmental variables. The absolute abundance of potential pathogens was significantly associated with the prevalence of rhinitis, wheeze, and dermatitis in 266 participants. Children were identified as the highest-risk group from inhalation exposure of average daily dose. A total of 170 bacterial, 223 fungal virulence factors (VFs), and 370 antibiotic resistance genes (ARGs) were detected in dust and dust extracellular vesicle (EV)-associated DNA. EV-associated cargoes contributed 47.13% to the bacterial VF profiles, 11.90% to fungal VF profiles, and 44.45% to ARG profiles. Metaproteomic analysis confirmed the presence of VF profiles in dust EVs, which was further verified by curated proteomics data from 35 household pathogens. CONCLUSIONS: This study provides a comprehensive, quantitative framework linking indoor microbial exposure to health risks, highlighting EVs as a non-negligible, novel, extracellular mechanistic pathway for health impact in household environments. Video Abstract.

Child↗
PubMed2025

New insights into soil amendment: Impact of humic acid on typical antibiotic resistance in agricultural soil.

Humic acid (HA) addition can improve agricultural soil, but little is known about how it affects the soil resistome. In this study, we used selective agar plate combined with quantitative PCR (qPCR) and 16S rRNA gene sequencing to investigate how HA influences antibiotic resistant bacteria (ARB) and antibiotic resistant genes (ARGs) in soil contaminated with erythromycin and kanamycin. 0.1 % HA reduced the abundance of culturable erythromycin-resistant bacteria (ERB), while promoting the growth of kanamycin-resistant bacteria (KRB). Lysinibacillus and Paenibacillus were the dominant genera in ERB and KRB, respectively, governing the changes in their abundances. At this concentration, the Lysinibacillus abundance in ERB decreased from 96.74 % to 70.57 %. Meanwhile, that of Paenibacillus in KRB increased from 33.40 % to 77.44 %. The copy number of ermF decreased after HA addition, while that of ermB increased. Furthermore, 0.1 % HA significantly reduced the copy number and relative abundance of aadA1 and aac(6')-Ib (aka aacA4)-03 in the soil. Changes in these two types of ARB and ARGs were primarily driven by shifts in the microbial community structure. Soil physicochemical properties, particularly increased organic matter (OM), altered the absolute abundance of ermB. Meanwhile, changes in intI1 abundance determined the risk associated with aadA1 and aac(6')-Ib (aka aacA4)-03. These findings emphasize the dual role of HA in the dissemination of antibiotic resistance in agricultural soils and highlight the necessity of considering dose-dependent effects when applying HA as a soil amendment.

Soil Microbiology↗
PubMed2026

Scale reliant mixed effects models enhance microbiome data analysis.

Linear models, including those used for differential abundance analyses, are frequently used in microbiome research to assess how experimental conditions (e.g., disease state or age) affect microbial abundance. Linear mixed-effects models (MEMs) extend linear models to accommodate complex designs, such as longitudinal sampling or hierarchical study structures. However, when applied to microbiome data, existing MEM approaches suffer from high false positive and false negative rates because sequence counts are compositional - they reflect relative rather than absolute abundances. Current methods attempt to overcome this limitation through normalization, but these approaches rely on strong, often unrealistic assumptions about the unmeasured biological scale (e.g., total microbial load). Here we introduce scale-reliant mixed-effects models (SR-MEM), which extend our earlier scale-reliant inference framework by explicitly modeling uncertainty in the unmeasured scale via user-defined probability distributions. By treating scale as a latent variable rather than fixing it through normalization, SR-MEM enables robust inference for complex experimental designs. SR-MEM can incorporate external scale measurements (e.g., flow cytometry, qPCR) or leverage scale information from independent studies to further improve inference. Across simulations and multiple real-world case studies, SR-MEM consistently controls the false discovery rate while maintaining comparable or higher power than standard approaches relying on normalization or bias correction. In reanalyses of published datasets, SR-MEM yields results that are more reproducible across studies and more consistent with known biological and pharmacological effects. SR-MEM provides a principled and practical framework for mixed-effects modeling of microbiome sequence count data in the presence of unmeasured biological scale. By avoiding normalization-based assumptions and instead propagating scale uncertainty through inference, SR-MEM improves error control and reproducibility in longitudinal and hierarchical studies. An accessible implementation is provided in the ALDEx3 R package.

Microbiota↗
PubMed2026

Genomic wastewater surveillance of human and animal influenza A viruses in California during the 2024-2025 flu season.

BACKGROUND: Wastewater genomic surveillance provides an opportunity to detect human and animal influenza A virus (IAV). We aimed to implement an IAV genomic surveillance framework agnostic to subtype, which enables recovery of IAV from multiple hosts and estimation of proportions across subtypes. METHODS: We conducted IAV genomic surveillance in wastewater during the 2024-2025 flu season at multiple sites in California and compared these data with available human clinical IAV sequences and test positivity. We applied a custom whole-genome, multi-host IAV probe enrichment panel and adapted our custom expectation-maximization (EM) algorithm to deconvolute IAV mixtures in wastewater and infer subtype relative abundances. Absolute IAV concentrations were quantified using RT-PCR-based assays. H5N1 wastewater and clinical sequences were further characterized by constructing a whole-genome maximum-likelihood phylogenetic tree. Finally, we performed variant analysis to examine amino acid substitutions detected in wastewater. FINDINGS: Our IAV probe enrichment method and EM algorithm successfully enriched all eight segments of three circulating IAV subtypes and accurately estimated subclade relative abundances for mixed IAV samples. Seasonal human H1N1pdm09 and H3N2 were detected throughout the study period from both wastewater and clinical sequencing data, with H1N1 subclades 6B.1A.5a.2a.1 and 6B.1A.5a.2a co-circulating, and H3N2 dominated by subclade 3C.2a1b.2a.2a.3a.1. Wastewater surveillance consistently detected H5N1 clade 2.3.4.4b across three monitored wastewater sites, while clinical H5N1 detections, from anywhere in CA, were sporadic and rare. Whole-genome phylogenetic analysis revealed that wastewater H5N1 sequences clustered with reference sequences associated with dairy cow and avian infections, while all human clinical H5N1 sequences clustered exclusively with reference sequences associated with dairy cow infections. Amino acid substitutions were identified across viral segments, and no mutations associated with mammalian adaptation were observed from wastewater samples. INTERPRETATION: When IAV concentrations were dominated by seasonal human subtypes rather than H5N1, subtype patterns aligned between wastewater and clinical data. While sequencing IAV in wastewater was unable to distinguish if H5N1 detections were due to human or animal infections, it was able to provide clade-level information about H5N1 found in wastewater that could be useful in the future. Wastewater genomic surveillance can complement clinical surveillance, increasing ability to detect all circulating IAV subtypes and enhancing public health preparedness from a One Health perspective.

Journal Article↗
PubMed2026

Dual roles of static magnetic field on enhancing sulfamethoxazole biodegradation and preventing antibiotic resistance genes transfer in halotolerant fungal-bacterial sludge treating saline aquaculture wastewater.

To address low biological treatment efficiency in saline antibiotic wastewater and antibiotic resistance gene (ARGs) transmission risk, a static magnetic field (SMF) was applied to a salt-tolerant fungal-bacterial consortium to enhance sulfamethoxazole (SMX) biodegradation; additionally, associated ARGs transmission risks were assessed. Results demonstrated that 40 mT was the optimal SMF intensity, under which the SMX degradation efficiency achieved a relative improvement of 62.8% compared to the control. At the mechanistic level, SMF alleviated oxidative stress by stimulating extracellular polymeric substance (EPS) secretion and upregulating antioxidant defenses, thereby reducing intracellular reactive oxygen species (ROS) accumulation. Furthermore, SMF significantly suppressed the absolute abundance of mobile genetic elements (MGEs), effectively restricting the horizontal gene transfer of ARGs. SMF application is an effective strategy for improving SMX removal and reducing ARGs transfer, providing new insights for developing advanced saline aquaculture wastewater biological treatment technologies.

Sulfamethoxazole↗
PubMed2025

Uncertainty Modeling Outperforms Machine Learning for Microbiome Data Analysis.

Microbiome sequencing measures relative rather than absolute abundances, providing no direct information about total microbial load. Normalization methods attempt to compensate, but rely on strong, often untestable assumptions that can bias inference. Experimental measurements of load (e.g., qPCR, flow cytometry) offer a solution, but remain costly and uncommon. A recent high-profile study proposed that machine learning could bypass this limitation by predicting microbial load from sequencing data alone. To evaluate this claim, we assembled mutt, the largest public database of paired sequencing and load measurements, spanning 35 studies and over 15,000 samples. Using mutt, we show that published machine learning models fail to generalize: on average they perform worse than a naive baseline that always predicted the training set mean. These failures stem from covariate shift-limited shared taxa between studies, differences in community composition, and differences in preprocessing pipelines-that silently derail model inputs. In contrast, Bayesian partially identified models do not attempt to impute microbial load, but instead propagate scale uncertainty through downstream analyses. Across 30 benchmark datasets, Bayesian partially identified models consistently outperformed normalization and machine learning approaches, providing a principled and reproducible foundation for microbiome inference.

16S rRNA-seq↗
PubMedDate not supplied

[Population density of Ixodes persulcatus ticks (Ixodidae) in the western Sikhote-Alin].

The paper presents data on the population density of active ticks in different landscape zones of West Sykhote-Alyn as well as the material on the absolute abundance of ticks in four experimental 400 m2 areas. The abundance of active Ixodes persulcatus and Haemaphysalis japonica on vegetation at the peak of their activity was found to amount to half of all hibernated adult ticks.

Animals↗
PubMed2025

Absolute quantification of the living skin microbiome overcomes relic-DNA bias and reveals specific patterns across volunteers.

BACKGROUND: As the first line of defense against external pathogens, the skin and its resident microbiota are responsible for protection and eubiosis. Innovations in DNA sequencing have significantly increased our knowledge of the skin microbiome. However, current characterizations do not discriminate between DNA from live cells and remnant DNA from dead organisms (relic DNA), resulting in a combined readout of all microorganisms that were and are currently present on the skin rather than the actual living population of the microbiome. Additionally, most methods lack the capability for absolute quantification of the microbial load on the skin, complicating the extrapolation of clinically relevant information. RESULTS: Here, we integrated relic-DNA depletion with shotgun metagenomics and bacterial load determination to quantify live bacterial cell abundances across different skin sites. Though we discovered up to 90% of microbial DNA from the skin to be relic DNA, we saw no significant effect of this on the relative abundances of taxa determined by shotgun sequencing. Relic-DNA depletion prior to sequencing strengthened underlying patterns between microbiomes across volunteers and reduced intraindividual similarity. We determined the absolute abundance and the fraction of population alive for several common skin taxa across body sites and found taxa-specific differential abundance of live bacteria across regions to be different from estimates generated by total DNA (live + dead) sequencing. CONCLUSIONS: Our results reveal the significant bias relic DNA has on the quantification of low biomass samples like the skin. The reduced intraindividual similarity across samples following relic-DNA depletion highlights the bias introduced by traditional (total DNA) sequencing in diversity comparisons across samples. The divergent levels of cell viability measured across different skin sites, along with the inconsistencies in taxa differential abundance determined by total vs live cell DNA sequencing, suggest an important hypothesis for certain sites being susceptible to pathogen infection. Overall, our study demonstrates a characterization of the skin microbiome that overcomes relic-DNA bias to provide a baseline for live microbiota that will further improve mechanistic studies of infection, disease progression, and the design of therapies for the skin. Video Abstract.

Humans↗
PubMed2026

Estimation of chloroplast macromolecular complex copy numbers and subunit stoichiometries during the Chlamydomonas reinhardtii cell cycle.

An unbiased, quantitative view of biomolecules in a living cell is a prerequisite for accurate modeling approaches and informs our understanding of cellular metabolism at scale. In this work, we used the total protein approach (TPA), in which the total protein mass of a given proteomics sample is used as a calibrator for absolute protein quantification, to determine protein abundances during the Chlamydomonas reinhardtii diurnal cycle. We use external, independently measured quantitative markers (metals, pigments) to assess the absolute protein abundances in unlabeled whole cell extracts. We calculate protein abundances in fg cell-1 of 7322 Chlamydomonas proteins, 2266 of which were captured in every time point, including the major proteins involved in the light reactions, photoprotection, proteostasis, and fatty acid metabolism during a cell cycle. As expected, Rubisco large and small subunits are present in a 1:1 stoichiometry, with the large subunit being the most abundant protein in our data set, averaging 5.05 × 106 molecules per cell, reflecting 2.7% of the total protein mass. We noticed that PSII is the most abundant complex involved in the light reactions with 2.08 × 106 complexes per cell. PSI averages 1.75 × 106 complexes per cell and cytochrome b6f averages 0.77 × 106 complexes per cell. The TPA is a robust tool to study proteome dynamics quantitatively, while avoiding artifacts due to biochemical fractionation. Our proteome data set with an unprecedented temporal resolution is a valuable resource to assess protein abundances during the cell cycle in the reference alga Chlamydomonas.

Chlamydomonas reinhardtii↗
PubMed2026

Engineered Ratiometric Near-Infrared Probes Enable Dual-Organelle Visualization of G-Quadruplex in Living Cells.

G-quadruplexes (G4s) participate in nuclear genome regulation and mitochondrial metabolism, but tools for monitoring both compartments in the same living cell remain limited. Here, we report PEG-INR-Me, a ratiometric near-infrared (NIR) probe designed for simultaneous visualization of nuclear and mitochondrial G4-associated signals. G4 binding enhances the long-wavelength emission, whereas the short-wavelength channel serves as an operational normalization channel under matched acquisition conditions. Accordingly, cellular Channel640/Channel560 values are interpreted as relative readouts within a defined compartment and experiment, rather than as absolute comparisons of G4 abundance between organelles. PEG-INR-Me revealed parallel cell-cycle-associated changes in nuclear and mitochondrial signals, higher signals in cancer cells than in noncancerous cells, and concurrent decreases during cisplatin treatment followed by partial recovery after caspase inhibition. These observations establish temporal concordance between mitochondria and nucleus. Following direct local administration, the probe also distinguished 4T1 tumors from a contralateral subcutaneous control site. PEG-INR-Me therefore provides a dual-compartment imaging platform for investigating nuclear and mitochondrial G4-associated dynamics, and their mechanistic relationship deserves to be further investigated.

G‐Quadruplexes↗
PubMed1978

Quantitative studies on the localization of the cholinergic receptor protein in the normal and denervated electroplaque from Electrophorus electricus.

Electroplaques dissected from the electric organ of Electrophorus electricus are labeled by tritiated alpha1-isotoxin from Naja nigricollis, a highly selective reagent of the cholinergic (nicotinic) receptor site. Preincubation of the cell with an excess of unlabeled alpha-toxin and with a covalent affinity reagent or labeling in the presence of 10(-4) M decamethonium reduces the binding of [3H]alpha-toxin by at least 75%. Absolute surface densities of alpha-toxin sites are estimated by high-resolution autoradiography on the basis of silver grain distribution and taking into account the complex geopmetry of the cell surface. Binding of [3H]alpha-toxin on the noninnervated face does not differ from background. Labeled sites are observed on the innervated membrane both between the synapses and under the nerve terminals but the density of sites is approx. 100 times higher at the level of the synapses than in between. Analysis of the distance of silver grains from the innervated membrane shows a symmetrical distribution centered on the postsynaptic plasma membrane under the nerve terminal. In extrasynaptic areas, the barycenter of the distribution lies approximately 0.5 micrometer inside the cell, indicating that alpha-toxin sites are present on the membrane of microinvaginations, or caveolae, abundant in the extrajunctional areas. An absolute density of 49,600 +/- 16,000 sites/micrometer2 of postsynaptic membrane is calculated; it is in the range of that found at the crest of the folds at the neuromuscular junction and expected from a close packing of receptor molecules. Electric organs were denervated for periods up to 142 days. Nerve transmission fails after 2 days, and within a week all the nerve terminals disappear and are subsequently replaced by Schwann cell processes, whereas the morphology of the electroplaque remains unaffected. The denervated electroplaque develops some of the electrophysiological changes found with denervated muscles (increases of membrane resting resistance, decrease of electrical excitability) but does not become hypersensitive to cholinergic agonists. Autoradiography of electroplaques dissected from denervated electric organs reveals, after labeling with [3H]alpha-toxin, patches of silver grains with a surface density close to that found in the normal electroplaque. The density of alpha-toxin binding sites in extrasynaptic areas remains close to that observed on innervated cells, confirming that denervation does not cause an increase in the number of cholinergic receptor sites. The patches have the same distribution, shape,and dimensions as in subneural areas of the normal electroplaque, and remnants of nerve terminal or Schwann cells are often found at the level of the patches. They most likely correspond to subsynaptic areas which persist with the same density of [3H]alpha-toxin sites up to 52 days after denervation. In the adult synapse, therefore, the receptor protein exhibits little if any tendency for lateral diffusion.

Action Potentials↗
PubMed1978

Patterns of protein synthesis in E. coli: a catalog of the amount of 140 individual proteins at different growth rates.

The amount of 140 individual proteins of E. coli B/r was measured during balanced growth in five different media. The abundance of each protein was determined from its absolute amount in 14C-glucose-minimal medium and a measurement of its relative amount at each growth rate using a double labeling technique. Separation of the proteins was carried out by two-dimensional gel electrophoresis. This catalog of proteins, combined with 50 additional ribosomal proteins already studied, comprises about 5% of the coding capacity of the genome, but accounts for two thirds of the cell's protein mass. The behavior of most of these proteins could be described by a relatively small number of patterns. 102 of the 140 proteins exhibited nearly linear variations with growth rate. The remaining 38 proteins exhibited levels which seemed to depend more on the chemical nature of the medium than on growth rate. Proteins, including the ribosomal proteins, that increase in amount with increasing growth rate account for 20% of total cell protein by weight during growth on acetate, 32% on glucose-minimal medium and 55% on glucose-rich medium. Proteins with invariant levels in the various media comprise about 4% of the cell's total protein.

Bacterial Proteins↗
PubMed2025

ChIP-Rx: Arabidopsis Chromatin Profiling Using Quantitative ChIP-Seq.

Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) is widely used to probe the chromatin landscape of transcription factors, chromatin components, and associated proteins. Conventional ChIP normalization procedures robustly allow estimating differences in local enrichment across genomic regions. Yet, inter-sample comparisons can be biased by technical variability and biological differences. This is notably the case when samples display large differences in the abundance of the target protein or its enrichment at chromatin. For example, epigenome defects are improperly detected or quantified upon large-effect genetic or chemical inhibition of chromatin modifiers. To circumvent these caveats and robustly determine biological variations while minimizing technical variability, ChIP adaptations using an external reference have flourished. Here, we describe a step-by-step protocol employing a reference exogenous chromatin (ChIP-Rx) that allows absolute comparisons of epigenome variations in Arabidopsis samples displaying drastic differences in chromatin mark abundance. In contrast to the originally published ChIP-Rx approach, which assumes that exogenous spike-in references are constant across samples, the method detailed here involves the sequencing of each input sample to account for technical variability in initial reference chromatin contents. We also report a detailed computational workflow with an accompanying Github resource to help in calculating spike-in normalization factors, applying them to normalize epigenome tracks, and performing spike-in normalized inter-sample differential analyses. We propose two ways of computing the spike-in factor: a classically used method based on raw counts and a noise-corrected method using peak detection on the exogenous genome.

Arabidopsis↗
PubMed2026

Quantitative proteomics of molybdenum cofactor biosynthesis and utilization in Caenorhabditis elegans.

The molybdenum cofactor (Moco) is a chemically labile prosthetic group required by a small but essential set of metazoan enzymes, including sulfite oxidase, xanthine dehydrogenase, aldehyde oxidases, and the mitochondrial amidoxime reducing components (MARC). Disruption of Moco biosynthesis in humans causes Molybdenum Cofactor Deficiency (MoCD), a severe neonatal encephalopathy. Caenorhabditis elegans is unique among animals studied so far in that it can meet its Moco requirement through both endogenous biosynthesis and direct uptake of mature Moco from its bacterial diet. However, the organism-wide abundance of the Moco biosynthetic machinery and Moco-dependent enzymes, and their response to altered Moco supply, have remained unknown. Here, using data independent acquisition proteomics with histone anchored absolute quantification, we generated an organism wide quantitative atlas of Moco biosynthesis and utilization in C. elegans under standard and Moco limiting conditions. Components of the biosynthetic pathway showed a strikingly asymmetric abundance. The mitochondrial enzyme MOC-5, which catalyzes the first committed step in Moco biosynthesis, was present at only about 120 copies per genome equivalent, roughly fifty-fold below the downstream cytoplasmic biosynthetic machinery, which ranged from about 5,000 to 8,500 copies per genome equivalent, identifying MOC-5 as a stoichiometric bottleneck. On the utilization side, the MARC paralogs were the dominant Moco consumers, with MARC-1 exceeding 20,000 copies per genome equivalent. Loss of dietary or endogenous Moco selectively depleted the nonsulfurated clients SUOX-1 and MARC-1, whereas biosynthetic proteins remained unchanged, indicating that protein stability, rather than compensatory expression, is the main response to Moco limitation.

Caenorhabditis elegans↗
PubMed1978

Mouse spleen lymphoblasts generated in vitro. Recovery in high yield and purity after floatation in dense bovine plasma albumin solutions.

Mouse spleen lymphoblasts, stimulated to divide in vitro, acquired a low cell density and could be separated by isopycnic techniques. Cultured cells were suspended in BPA columns, rho = 1.080, and spun to equilibrium. The method was simple, fast, accomodated large numbers of cells, and was reproducible. It provided lymphoblasts in high yield and purity (at least 80% of the low density cells were blasts). It allowed for the recovery of proliferating cells in their first cell cycle, and did not alter the subsequent ability of cells to proliferate when recultured in vitro. Certain properties of mouse spleen lymphoblasts were analyzed in detail. Lymphoblasts induced by LPS, FCS, con A (tetravalent and succinylated), and MLC were very similar except in the absolute numbers that were induced. The blasts exhibited the classic cytologic features of enlarged nucleoli and abundant cytoplasmic polyribosomes (basophilia). As a population, they were enlarged in size relative to nondividing cells, but this seemed to apply primarily to cells in the S and G2+ M phase of the cell cycle rather than G1. The cell cycle distribution of lymphoblasts was analyzed by flow microfluorometry. By analyzing low density cells obtained at varying intervals after mitogen stimulation, FMF indicated that lymphoblasts enter the S phase of their first cell cycle beginning at 20-24 h after stimulation.

Animals↗
PubMed1976

The amoebocytic corpuscles in the circulating fluid of the lamelli-branches, Indonaia caerulia and Parreysia (Parreysia) favidens.

The circulating amoebocytes of the freshwater mussels, Indonaia caerulia and Parreysia favidens have been studied. The total number of amoebocytes is low and variable, and the individual to individual variation in total counts is particularly significant. The amoebocytes are of 3 main types: Acidophils, Large Basophils and Small Basophils. Acidophils contain large acidophilic granules and basophils fine basophilic granules within the cytoplasm. Acidophils are the largest and small basophils the smallest. The greater volume of the cell is occupied by cytoplasm in acidophils and large basophils and by the nucleus in small basophils. Large basophils are the most and small basophils the least abundant. Amoebocytes clump together by means of filipodia. Large basophils possess these protoplasmic processes in the greatest abundance, and partake most actively and in largest numbers in clumping; while small basophils lack filipodia and play an absolutely passive role. Clumping progressively becomes more extensive with passage of time following cardiac injury inflicted during blood collection. I. caerulia appears to be generally more efficient than P. favidens with regard to clumping reaction. The different structural, numerical and behavioural aspects of the amoebocytes have been considered with reference to their probable causative factors and functional import.

Animals↗
PubMed1977

Geographic distribution and habitat diversity of the Barbary Macaque sylvanus L.

During a 15-month behavioral study in Morocco and a 3-month survey in Morocco and Algeria, the present distribution of the Barbary macaque was determined. In Algeria, monkeys are found in seven constricted and disjunct localities in the Grande and Petite Kabylie mountain ranges. These localities are severely restricted in space and are located in remote or inaccessible areas which support only small populations. Their habitats include mixed cedar and holm oak forests, humid Portuguese and cork oak mixes and gorges dominated by scrub vegetation. In only two regions (Guerrouch and Agfadou) can population of reasonable size be found; even there they do not approach the abundance found in the central Middle Atlas zone of Morocco. Distribution was more extensive earlier in this century and some areas have become unoccupied within the past 15 years. Today, their absolute numbers and population densities are low in all but two locations. Algeria contains approximately 23% (5,500 maximum) of the total number of surviving Barbary macaques in North Africa. About 77% of the total number of Barbary macaques occur in Morocco. Moroccan habitats include high cedar forests, cedar/holm-oak mixtures and pure holm oak forests. Macaque distribution in the High Atlas is restricted to the Ourika valley where only a small relict population survives. There are between five and eight small, disjunct forest pockets in the Rif which support small groups of monkeys. In the Middle Atlas, monkeys are found in high numbers and in relatively wide stretches of distribution, although there are constricted areas of low densities in this region also. 65% (14,000 maximum) of the animals and their highest densities occur in the high mixed cedar forests of the Central zone, and mixed cedar forest appears to be the preferred habitat for the species. With the exception of the Central zone, their remaining distribution is typically disjunct and constricted, and population densities aer low. As in Algeria, distribution in Morocco was wider earlier this century, and several areas have recently become unoccupied.

Algeria↗
PubMed2025

StrainR2 accurately deconvolutes strain-level abundances in synthetic microbial communities.

MOTIVATION: Synthetic microbial communities offer an opportunity to conduct reductionist research in tractable model systems. However, deriving abundances of highly related strains within these communities is currently unreliable. 16S rRNA gene sequencing does not resolve abundance at the strain level and other methods such as quantitative polymerase chain reaction (qPCR) scale poorly and are resource prohibitive for complex communities. We present StrainR2, which utilizes shotgun metagenomic sequencing to provide high accuracy strain-level abundances for all members of a synthetic community, provided their genomes. RESULTS: Both in silico, and using sequencing data derived from gnotobiotic mice colonized with a synthetic fecal microbiota, StrainR2 resolves strain abundances with greater accuracy and efficiency than other tools utilizing shotgun metagenomic sequencing reads. We demonstrate that StrainR2's accuracy is comparable to that of qPCR on a subset of strains resolved using absolute quantification. AVAILABILITY AND IMPLEMENTATION: Software is available at GitHub and implemented in C, R, and Bash. Software is supported on Linux and MacOS, with packages available on Bioconda or as a Docker container. The source code at the time of publication is also available on figshare at the doi: 10.6084/m9.figshare.29420780.

Mice↗