Background/aimThe increasing incidence of early-age-onset colorectal neoplasia (EAO-CRN) in individuals under 50 years old poses a global health concern. This study aimed to investigate the variations in the microbiota in individuals with EAO-CRN compared with a control group, utilizing stool, oral swab, and saliva samples.MethodsParticipants under 50 years of age provided stool, oral swab, and saliva samples. Colorectal neoplasia was classified into the serrated lesions and adenoma–carcinoma groups based on histology and compared with a control group without polyps. The alpha diversity and the taxonomic abundance differences were assessed using amplicon sequence variants obtained through 16S rRNA sequencing and matched taxonomy data.ResultsA total of 45 participants were included: 14 in the control, 13 in the serrated lesions, and 18 in the adenoma–carcinoma groups. Microbial analysis revealed no significant differences in the alpha diversity among the groups. However, the stool samples from the serrated lesions group had higher levels of the families Erysipelotrichaceae and Lachnospiraceae compared with the control group. Analysis of the oral swabs indicated relatively elevated levels of the family Streptococcaceae in both the serrated lesions and adenoma–carcinoma groups. In the saliva samples, the serrated lesions and adenoma–carcinoma groups showed higher levels of the family Lactobacillaceae, with the serrated lesions group also exhibiting elevated levels of the family Bifidobacteriaceae.ConclusionsThis study elucidates the microbiota changes associated with EAO-CRN, distinguishing between serrated lesions and adenoma–carcinoma groups using stool, oral swab, and saliva samples. These findings contribute to the understanding of the relationship between microbiota and colorectal neoplasia in the early-onset population.
Abstract The Southern Ocean (SO) plays a key role in regulating global biogeochemical cycles and climate, yet microbial genes sustaining its biological activity remain poorly characterized. We introduce a microbial genes collection from 218 metagenomes sampled during the Antarctic Circumnavigation Expedition, the majority of which are missing from functional databases. 38% even lack homologs in current reference marine gene catalogs, defining a singular genetic seascape. We show that SO gene assemblages exhibit a common polar signature with the Arctic Ocean while being structured by water masses at the SO-scale. We analyze genomic markers of diverse SO biomes, focusing on dimethylsulphoniopropionate (DMSP) cleavage by polar-adapted bacteria, organic matter consumption in the blooming Mertz polynya and adaptation to polar conditions in the ubiquitous bacteria Pelagibacter. Our work takes a step towards a comprehensive understanding of SO’s plankton ecology and evolution, capturing the current state of the unique microbial diversity in this rapidly changing Ocean.
Daniel E. Sanchez, Faith M. Walker, Savannah J. Marriott
et al.
ABSTRACT Environmental DNA (eDNA) is a valuable biomonitoring tool, but application in terrestrial settings remains challenging due to a lack of generalizable sampling approaches. With bat species needing urgent research attention, airborne eDNA may offer this generalizability, as current eDNA sampling for bats is mostly limited to conspicuous sources (e.g., guano). While previous studies detected bats from roosts and open‐air sites using active air sampling, it remains uncertain whether bats can be readily detected from the open air using passive approaches. In central Texas, we used passive air sampling to determine if we could recover bat assemblages with metabarcoding and an imperiled focal species (tricolored bat, Perimyotis subflavus) with qPCR. Outside two cave locations, we positioned passive air samplers (two collection media per sampler; n = 24 media) near artificial prey patches, monitoring acoustically for bat activity and foraging. In the lab, we subjected the media to multiple eDNA extraction methods, direct DNA extraction, and two resuspension‐concentration approaches (filtration and pelleting). Metabarcoding allowed the detection of two bat species within a single sample, while qPCR allowed detection of P. subflavus in two samples. Although the detections all came from direct extraction, pelleting substantially improved taxonomic recovery and sample success for vertebrates overall. Detection of bat eDNA from passive samplers establishes a lower bound possibility for open‐air settings, and the low number of detections highlights the need for improved sampling strategies. We offer recommendations to enhance future efforts and introduce a qPCR assay for P. subflavus that can be used in a variety of eDNA contexts.
Soil microbial communities are essential for the natural attenuation of organic pollutants, yet their ecological responses under long-term contamination remain insufficiently understood. This study examined the bacterial community structure and the abundance of dechlorinating bacteria at a decommissioned pharmaceutical-chemical site in northern Jiangsu Province, China, where the primary pollutants were dichloromethane, 1,2-dichloroethane, and toluene. Eighteen soil samples from the surface (0.2 m) and deep (2.2 m) layers were collected using a Geoprobe-7822DT system and analyzed for physicochemical properties and microbial composition via 16S rRNA gene amplicon sequencing. The results showed that the bacterial community composition was significantly shaped by the soil pH, moisture content, pollutant type, and depth. Dechlorinating bacteria were detected at all sites but exhibited low relative abundance, with higher concentrations in the surface soils. <i>Desulfuromonas</i>, <i>Desulfitobacterium</i>, and <i>Desulfovibrio</i> were the dominant dechlorinators, while <i>Dehalococcoides</i> appeared only in the deep soils. A network analysis revealed positive correlations between the dechlorinators and BTEX-degrading and fermentative taxa, indicating potential cooperative interactions in pollutant degradation. However, the low abundance of dechlorinators suggests that the intrinsic bioremediation capacity is limited. These findings provide new insights into microbial ecology under complex organic pollution, and support the need for integrated remediation strategies that enhance microbial functional potential in legacy-contaminated soils.
Frahad Ali, Zulikha Shah, Nadeem Ahmad Sheikh
et al.
Bioconvection flows occur in working fluids where the growth of microorganisms is subject to convective flows. Understanding the flow behavior of these fluids is essential for many biological and environmental processes, such as the purification of water, drug delivery, and microbial ecology. This article explores the bioconvection flow over a vertical flat plate, involving a micropolar fluid with mass and heat transfer. In the beginning, partial differential equations (PDEs) are used to formulate the problem, which use a non-singular and non-local kernel to take into consideration the memory impacts of the system. The problem is formulated and exact solutions are obtained by using the Laplace transform technique, finding solutions that satisfy both the governing equations and specific conditions, and then representing these solutions graphically. The statement highlights the importance of considering variable Prandtl number in thermal boundary layer modeling. When viscosity and thermal conductivity depend on temperature, treating Prandtl number as a variable is crucial for accurate results. Specifically, as thermal conductivity parameter increases, it leads to higher velocities and temperatures within the boundary layers being studied. Understanding the effect of mass Schmidt number is essential in various practical applications such as chemical engineering processes, where precise control of mass transfer is important for optimizing reactions and product quality in micropolar fluid systems. When Schmidt number increases, it means that momentum diffusion (viscosity) dominates over mass diffusion, causing species to diffuse more slowly in the fluid. One of the key advantages of fractional derivatives like the ABC operator is their ability to model memory effects in systems, where past states influence current behavior. This is particularly important in fields like control theory, neurodynamics, fluid dynamics, and finance, where historical data impacts future behavior. Engineering interest quantities are also calculated and shown in tabular form.
Esme Ashe-Jepson, Edgar C. Turner, Andrew J. Bladon
Climate change is a threat to global biodiversity, with changes to mean temperatures and increasing frequency and intensity of extreme weather events. Heatwaves in particular pose a threat to species’ persistence, as temperatures may rise above physiological tolerance. However, individuals rarely experience temperatures measured at the macroclimatic scale: topographic or vegetation differences result in microclimates that provide cool refugia (local temperatures below ambient) or even result in heat traps (local temperatures above ambient) during heatwaves. However, little is known about the stability of microclimates through a period of regional warming. In this study, we recorded microclimate temperatures across different microhabitats within a calcareous grassland nature reserve in Bedfordshire, UK, in 2018, 2019 and 2022. During this time, six heatwave events occurred, including the highest air temperatures ever recorded in the UK. We found that the ability of microhabitats to offset air temperatures varied with topographic aspect, slope, amount of bare ground, shelter, vegetation height, and vegetation type, with encroaching scrub and north-facing slopes showing the strongest abilities to maintain relatively stable microclimate temperatures with increasing air temperatures, in contrast to short vegetation on south-facing slopes which became heat traps. However, no combinations of environmental structures consistently maintained cool refugia during heatwaves. Microclimate temperatures were amplified close to the ground, whereas at 50 cm height temperatures were more stable and similar to the macroclimate temperature, therefore surface-dwelling species, such as many insects, may be particularly vulnerable to extreme heat. We identified a breakdown in the ability of microhabitats to maintain cool refugia above 7 °C, implying cool refugia become increasing rare and unpredictable with increasing temperatures. Our results indicate that many microhabitats will amplify the effects of climate change rather than mitigate them. Highlights The innate unpredictability and scarcity of extreme temperature events makes them an evolutionary challenge; instead, microclimatic refugia are often suggested as a way for species to cope under climate change. By comparing microclimate temperatures to macroclimate temperatures (from a nearby weather station) in central England, we highlight how variable local temperatures can be at fine scales relevant to small surface-dwelling organisms, with microclimate temperatures differing by as much as 20 °C. Microclimate performance changed with increasing temperature, with more heat traps (microclimate temperatures above ambient) and fewer cool refugia (microclimate temperatures below ambient). No environmental variables tested reliably maintained cool refugia at high temperatures. Ground-level microclimate temperatures were amplified compared to temperatures at 50 cm height, implying that surface-dwelling organisms in grasslands, including many insects, may be particularly vulnerable compared to species that fly, climb, or live in tall vegetation.
Dominik Antoni, Antje Wichels, Maarten Boersma
et al.
Anthropogenic climate change caused by CO2 emissions forces humanity to reduce the usage of fossil fuels. Along with the task of emission reduction, societies face the task of removing excess CO2 from the atmosphere by using negative emission technologies (NETs). Ocean alkalinity enhancement (OAE) is a proposed NET, aiming at increasing oceanic CO2 uptake through the addition of alkaline substances. This is an anthropogenically accelerated version of rock weathering, a natural global process for atmospheric CO2 regulation. The environmental impacts of OAE remain poorly understood. This study was part of a comprehensive OAE-mesocosm experiment in the North Sea (RETAKE), and focused on the effects of OAE on the pelagic bacterial community during the experiment. We assessed changes in bacterial community structure with 16S rRNA amplicon sequencing and abundance with flow cytometry, to evaluate responses to alkalinity addition. Beta diversity analysis showed that sampling time was the primary driver for community variation, with only marginal structural differences linked to alkalinity treatments. PERMANOVA tests conducted on predictions of functional metabolic pathways of the community revealed significant differences between treatments and baseline controls. A deeper analysis of the identified metabolic pathways revealed little evidence for alkalinity-induced changes. In contrast, total bacterial cell counts were influenced by alkalinity additions, showing delayed abundance peaks at higher concentrations and a non-linear response threshold between 500–750 µmol/L. These dynamics were linked to shifts in chlorophyll concentrations, suggesting an indirect effect of OAE on bacteria mediated by phytoplankton derived resources. This study is one of the first to assess ecological impacts of OAE on bacteria. Our findings highlight a structural resilience of bacterial communities to OAE but also show a quantitative response. By discussing our findings, this study aims to provide focus points, such as a threshold for save levels of alkalinity addition, to direct future research.
Mateus Pepinelli, Alejandro José Biganzoli‐Rangel, Katherine Lunn
et al.
ABSTRACT Environmental DNA (eDNA) refers to genetic material collected from the environment and not directly from an organism. eDNA is best known as a tool in aquatic ecology but has been found associated with almost every substrate examined including soils, surfaces, and riding around on other animals. The collection of eDNA from air is one of the most recent advances and has been used to monitor a variety of organisms, including plants, animals, and microorganisms. Current evidence suggests a high turnover rate providing a recent signal for the presence of DNA associated with an organism. Here, we test whether material carried in air can be collected from honey bee hives to evaluate recent foraging behavior and colony health. We sampled air using purpose built “bee safe” air filters operating for 5–6 h at each colony. We successfully recovered plant, fungal and microbial DNA from the air within hives over a 3‐week pilot period. From these data we identified the core honey bee microbiome and plant interaction data representing foraging behavior. We calculated beta diversity to estimate the effects of apiary sites and sampling date on data recovery. We observed that variance in ITS data was influenced by sampling date. Given that honey bees are generalist pollinators our ability to detect temporal signals in associated plant sequence data suggest this method opens new avenues into the ecological analysis of short term foraging behavior at the colony level. In comparison variance in microbial 16S sequencing data was more influenced by sampling location. As the assessment of colony health needs to be localized, spatial variance in these data indicate this may be an important tool in detecting infection. This pilot study demonstrates that colony air filtration has strong potential for the rapid screening of honey bee health and for the study of bee behavior.
Amin Valiei, Andrew Dickson, Javad Aminian-Dehkordi
et al.
Abstract The gut microbiome plays a major role in human health; however, little is known about the structural arrangement of microbes and factors governing their distribution. In this work, we present an in silico agent-based model (ABM) to conceptually simulate the dynamics of gut mucosal bacterial communities. We explored how various types of metabolic interactions, including competition, neutralism, commensalism, and mutualism, affect community structure, through nutrient consumption and metabolite exchange. Results showed that, across scenarios with different initial species abundances, cross-feeding promotes species coexistence. Morphologically, competition and neutralism resulted in segregation, while mutualism and commensalism fostered high intermixing. In addition, cooperative relations resulted in community properties with little sensitivity to the selective uptake of metabolites produced by the host. Moreover, metabolic interactions strongly influenced colonization success following the invasion of newcomer species. These results provide important insights into the utility of ABM in deciphering complex microbiome patterns.
Piotr B. Heczko, Milena Giemza, Weronika Ponikiewska
et al.
As an extraordinarily diverse group of bacteria, lactobacilli are now classified into several genera, many of which still include “Lactobacillus” in their names. Despite their names, this group of lactic acid bacteria comprises microorganisms that are crucial for human health, especially during the early development of the human microbiota and immune system. The interactions between lactobacilli and components of the mucosal immunity lead to its shaping and development, which is possibly considered a prime mover in the advancement of the human immune system. Although much of the evidence backing the pivotal role of lactobacilli in maintaining human health comes from studies on probiotics aiming to elucidate the mechanisms of their functional activities and studies on mucosal immunity in germ-free mice, it is justifiable to extend observations on the properties of the individual probiotic Lactobacillus that are related to health benefits onto other strains sharing common characteristics of the species. In this review, we will discuss the acquisition, presence, and functions of lactobacilli in different human microbiota throughout their whole life, including those arising in the amnion and their interactions with mucosal and immune cells. Examples of immune system modulation by probiotic lactobacilli include their colonic competition for available nutrients, interference with colonization sites, competition for binding sites on gut epithelial cells, bacteriocin production, reduction of colonic pH, and nonspecific stimulation of the immune system.
ABSTRACT
Introduction. In Cameroon, the lack of data on local microbial ecology favours the use of empirical antibiotic therapies extrapolated from foreign studies. The aim of this study was to identify bacterial and fungal causes of bloodstream infections and to report their antimicrobial sensitivities in paediatric cancer patients in Cameroon. Methods. We performed a prospective study from January to September 2021 on in paediatric cancer patients at the Chantal Biya Foundation Mother-Child Centre (CME-FBC) in Cameroon. Blood samples were taken from each febrile patient and analysed using standard laboratory procedures for culture, identification and antibiotic susceptibility testing. Results. We observed 61 patients for which 238 blood cultures were drawn. Mean participant age was 6.62 years and the children less than 5 years were the most represented (41%). The blood culture positivity rate was 28.1%, with Gram-negative bacilli being the most commonly isolated organisms (50.9% of isolates). The susceptibility of Gram-negative bacilli to first-line treatment (ceftriaxone and gentamicin) was less than 50%, while susceptibility to 4th-generation cephalosporins, carbapenems and quinolones remained acceptable, with values between 60% and 80%. Antibiotic resistance was present, with 38% of gram-negative bacilli multi-resistant and 100% of methicillin-resistant S. aureus. Conclusion. Gram-negative bacilli are the main aetiological agent of bacteraemia in febrile MCC-CBF cancer patients, with a significant proportion of isolated pathogens showing high levels of antimicrobial resistance. It is important to rely on local epidemiological data for the development of empirical antibiotic therapies.
RESUME
Introduction. Au Cameroun, le manque de données sur l'écologie microbienne locale favorise l'utilisation d'antibiothérapies empiriques extrapolées à partir d'études étrangères. Le but de cette étude était d'identifier les causes bactériennes et fongiques des infections sanguines et de rapporter leurs sensibilités antimicrobiennes chez les patients pédiatriques atteints de cancer au Cameroun. Méthodologie. Nous avons réalisé une étude prospective de janvier à septembre 2021 sur des patients atteints de cancer pédiatrique au Centre Mère-Enfant de la Fondation Chantal Biya (CME-FBC) au Cameroun. Des échantillons de sang ont été prélevés sur chaque patient fébrile et analysés en utilisant des procédures de laboratoire standard pour la culture, l'identification et l'antibiogramme. Résultats. Nous avons observé 61 patients pour lesquels 238 hémocultures ont été prélevées. L'âge moyen des participants était de 6,62 ans et les enfants de moins de 5 ans étaient les plus représentés (41%). Le taux de positivité des hémocultures était de 28,1 %, les bacilles à Gram négatif étant les organismes les plus fréquemment isolés (50,9 % des isolats). La sensibilité des bacilles à Gram négatif au traitement de première intention (ceftriaxone et gentamicine) était inférieure à 50 %, tandis que la sensibilité aux céphalosporines de quatrième génération, aux carbapénèmes et aux quinolones restait acceptable, avec des valeurs comprises entre 60 et 80 %. La résistance aux antibiotiques était présente, avec 38 % de bacilles gram-négatifs multirésistants et 100 % de S. aureus résistants à la méthicilline. Conclusion. Les bacilles à Gram négatif sont le principal agent étiologique des bactériémies chez les patients fébriles atteints de cancer MCC-CBF, avec une proportion significative d'agents pathogènes isolés présentant des niveaux élevés de résistance aux antimicrobiens. Il est important de s'appuyer sur les données épidémiologiques locales pour développer des antibiothérapies empiriques.
Ercan Arıcan, Hatice Kübra Kızıl Pat, Neşe Akçay
et al.
Lake Beysehir, located in the Central Anatolia Region, is the biggest lake in Central Anatolia, providing drinking water and irrigation. It is Turkey's third-largest lake and the largest freshwater lake. Its waters are fresh water and its depth is around 8-9 m at most. The deepest point is mentioned as 12, 14, and 15 m in different sources. Although there is a lake used by such a large population in our country, there are not enough studies on microbial diversity, so revealing the diversity is important for the lake and the population around the lake. Next-generation sequencing (NGS) research has made it possible to sequence RNA and DNA considerably quicker and cheaply than in by assessing the PCR amplicon, we utilized NGS high-throughput methods for the metagenomic research of Lake Beyşehir sequences of 16S rDNA (regions V3–V4). The analyzes revealed the phylum Proteobacteria, Verrucomicrobia, Bacteroidetes and Actinobacteria.
1. Organismal biology has undergone a dramatic paradigm shift in the last decade. The realization that host cells and genes are outnumbered by symbiotic microbial cells and their genes has forced us to rethink our focus on ‘individuals’. It is also becoming increasingly clear that the ecology and biology of animals and plants are intimately connected with their microbial partners. In the context of conserving functioning species, such revelatory insights beg the question—what exactly should we be trying to conserve? of and the concept applied
Abstract As one of the promising next-generation probiotics (NGPs), Akkermansia muciniphila, a well-known mucin-degrading bacterium, has been proven to be closely related to the metabolic diseases of its human host. However, the role of A. muciniphila in the host’s intestinal health remains ambiguous. Here, we comprehensively summarize and discuss the characteristics, the distribution, and the colonization of A. muciniphila in the human gastrointestinal tract (GIT). We propose that the application of A. muciniphila as a biomarker for longevity, for diagnostics and prognostics of intestinal diseases, or for intestinal health should be cautiously considered. Precise dietary regulation can mediate the treatment of intestinal diseases by altering the abundance of A. muciniphila. Although the beneficial role of A. muciniphila and its component in intestinal inflammation has been discovered, in gnotobiotic mice with specific gut microbiota, certain genotype, and colorectal cancer, or in animal models infected with a specific pathogen, A. muciniphila may be related to the occurrence and development of intestinal diseases. Genomic analysis, emphasizing the strain-level phylogenetic differences of A. muciniphila, indicates that a clear description and discussion of each strain is critical before its practical application. Our review provides much needed insight for the precise application of A. muciniphila.
Anthony vanRooyen, Adam D. Miller, Zach Clark
et al.
Abstract The number of human–shark interactions has increased worldwide during the past decade resulting in injuries and fatalities. In Australia, the white shark (Carcharodon carcharias), tiger shark (Galeocerdo cuvier), and bull shark (Carcharhinus leucas) are responsible for the majority of fatal incidents. On the southeast coast of Australia, monitoring programs currently rely on SMART (Shark‐Management‐Alert‐in‐Real‐Time) drumlines and mesh nets to catch, tag, and monitor shark movement. However, these methods are laborious, costly, and involve the capture of only a fraction of the total shark population. Here, we develop a multiplex environmental DNA assay capable of detecting all three shark species simultaneously from water samples by targeting conserved but specific mitochondrial sequences that are characteristic of each species. The specificity of the assay was validated by testing for cross‐amplification across a range of non‐target but co‐occurring shark species from eastern Australia. We test the sensitivity of the assay on water samples collected from shark capture events and sites where these shark species are known to frequent, and undertake DNA sequencing on positive samples to confirm species haplotype authenticity. Samples collected from one of these sites also demonstrate that eDNA detections are dependent on shark activity in the area. This assay will allow for rapid detection of DNA from each shark species in water samples, providing a cost‐effective alternative for monitoring sharks along the east coast of Australia and potentially elsewhere.
Despite the ubiquity of biofilms in many environments, most microbiological study has focussed on their existence under aqueous conditions. The ecology of bacteria at solid-air interfaces is a significant concern in clinical settings, where prevention of nosocomial infection is a priority. Although multi-species communities are predominant in the environment, most laboratory research regarding bacterial survival at solid-air interfaces has focussed on pure culture survival. Therefore, the focus of this thesis was to determine whether community interactions affect the survival of bacteria after drying on exposed surfaces. It was determined that exogenous pathogens can exhibit enhanced survival after drying in the presence of members of the indoor bacterial flora. The enhanced survival of desiccation-sensitive species in communities is likely dependent on the density of cells on the surface and is thought to involve direct or close contact between community members, allowing poor-survivors to benefit from the desiccation-tolerance mechanisms of others. This project represents an exploratory study into bacterial ecology at solid-air interfaces within indoor environments.
Despite the ubiquity of biofilms in many environments, most microbiological study has focussed on their existence under aqueous conditions. The ecology of bacteria at solid-air interfaces is a significant concern in clinical settings, where prevention of nosocomial infection is a priority. Although multi-species communities are predominant in the environment, most laboratory research regarding bacterial survival at solid-air interfaces has focussed on pure culture survival. Therefore, the focus of this thesis was to determine whether community interactions affect the survival of bacteria after drying on exposed surfaces. It was determined that exogenous pathogens can exhibit enhanced survival after drying in the presence of members of the indoor bacterial flora. The enhanced survival of desiccation-sensitive species in communities is likely dependent on the density of cells on the surface and is thought to involve direct or close contact between community members, allowing poor-survivors to benefit from the desiccation-tolerance mechanisms of others. This project represents an exploratory study into bacterial ecology at solid-air interfaces within indoor environments.