Lower Relative Abundance Research Articles

The plasma lipidome varies with the severity of metabolic dysfunction-associated steatotic liver disease

BackgroundMetabolic dysfunction-associated steatotic liver disease (MASLD) is closely associated with many aspects of disturbed metabolic health. MASLD encompasses a wide spectrum of liver diseases, ranging from isolated steatosis to metabolic dysfunction-associated steatohepatitis (MASH), up to fibrosis, cirrhosis, and ultimately hepatocellular carcinoma. Limited noninvasive diagnostic tools are currently available to distinguish the various stages of MASLD and as such liver biopsy remains the gold standard for MASLD diagnostics. We aimed to explore whether the plasma lipidome and its variations can serve as a biomarker for MASLD stages.MethodsWe investigated the plasma lipidome of 7 MASLD-free subjects and 32 individuals with MASLD, of whom 11 had MASH based on biopsy scoring.ResultsCompared with the MASLD-free subjects, individuals with MASLD had higher plasma concentrations of sphingolipids, glycerolipids, and glycerophospholipids. Only plasma concentrations of ceramide-1-phosphate C1P(d45:1) and phosphatidylcholine PC(O-36:3), PC(O-38:3), and PC(36:2) differed significantly between presence of MASH in individuals with MASLD. Of these lipids, the first three have a very low relative plasma abundance, thus only PC(36:2) might serve as a biomarker with higher plasma concentrations in MASLD individuals without MASH compared to those with MASH.ConclusionsPlasma lipids hold promise as biomarkers of MASLD stages, whereas plasma PC(36:2) concentrations would be able to distinguish individuals with MASH from those with MASLD without MASH.

A novel mouse model of upper tract urothelial carcinoma highlights the impact of dietary intervention on gut microbiota and carcinogenesis prevention despite carcinogen exposure.

Animal models of N-butyl-N-(4-hydroxy butyl) nitrosamine (BBN)-induced urothelial carcinoma (UC), particularly bladder cancer (BC), have long been established. However, the rare incidence of BBN-induced upper urinary tract UC (UTUC), which originates from the same urothelium as BC, remains elusive. The scarcity of animal models of UTUC has made it challenging to study the biology of UTUC. To address this problem, we tried to establish a novel mouse model of UTUC by treating multiple mice strains and sexes with BBN. The molecular consistency between the UTUC mouse model and human UTUC was confirmed using multi-omics analyses, including whole-exome, whole-transcriptome, and spatial transcriptome sequencing. 16S ribosomal RNA metagenome sequencing, metabolome analysis, and dietary interventions were employed to assess changes in the gut microbiome, metabolome, and carcinogenesis of UTUC. Of all treated mice, only female BALB/c mice developed UTUC over BC. Multi-omics analyses confirmed that the UTUC model reflected the molecular characteristics and heterogeneity of human UTUC with poor prognosis. Furthermore, the model exhibited increased Tnf-related inflammatory gene expression in the upper urinary tract and a low relative abundance of Parabacteroides distasonis in the gut. Dietary intervention, mainly without alanine, led to P. distasonis upregulation and successfully prevented UTUC, as well as suppressed Tnf-related inflammatory gene expression in the upper urinary tract despite the exposure to BBN. This is the first report to demonstrate a higher incidence of UTUC than BC in a non-engineered mouse model using BBN. Overall, this model could serve as a useful tool for comprehensively investigating UTUC in future studies.

Effect of pre-farrowing hygiene routine (sub-standard vs. optimal) and creep feeding regime (dry pelleted starter diet vs. liquid mixture of milk replacer and starter diet) on post-weaning intestinal parameters and growth to slaughter in pigs.

The objective was to evaluate the effect of providing dry pelleted starter diet (DPS) or a liquid mixture of milk replacer and starter diet (LMR+S) to suckling pigs housed in farrowing pens of sub-standard or optimal hygiene conditions on pig growth to slaughter, and post-weaning (PW) intestinal parameters. On day (d) 107 of gestation, 87 sows were randomly allocated to one of four treatments in a 2×2 factorial arrangement. The factors were creep feeding (DPS or LMR+S) and pre-farrowing hygiene routine (SUB-STANDARD or OPTIMAL). Pigs were provided with DPS (manually) from d11 to weaning (at d28±1.2 of age) or LMR+S using an automatic liquid feeding system from d4 to weaning. The SUB-STANDARD hygiene routine (pens washed and dried for ~18h, sows not washed or disinfected) and the OPTIMAL hygiene routine (pens pre-soaked, detergent applied, washed, dried for 3 days, chlorocresol-based disinfectant applied, dried for 3 more days and sows washed and disinfected with Virkon) were used to obtain SUB-STANDARD or OPTIMAL hygiene conditions, respectively in farrowing rooms prior to entry of sows. Microbiome analysis was performed on fecal samples from 8 focal pigs/treatment, before weaning and at d21 and d114 PW. On d4 PW, 10 pigs/treatment were euthanized to collect intestinal tissue and digesta samples for histological, enzyme activity and microbiome analysis. Feeding LMR+S to pigs born into the OPTIMAL hygiene increased total dry matter intake compared to all of the other groups (P ≤ 0.05) and increased weaning weight compared to DPS feeding under both OPTIMAL and SUB-STANDARD hygiene conditions (P ≤ 0.05). Pigs from OPTIMAL farrowing pens had lower clinical cases of disease, diarrhoea prevalence and were slaughtered 3.8 days earlier than those from SUB-STANDARD farrowing pens (P ≤ 0.05). Suckling piglet mortality was reduced with LMR+S (P ≤ 0.05). On d4 PW, jejunal and ileal villus height were increased by OPTIMAL hygiene and ileal sucrase activity was increased by LMR+S (P ≤ 0.05). On d4 PW, LMR+S-fed pigs from OPTIMAL farrowing pens had lower relative abundance of Clostridium_P in the jejunum. In conclusion, the OPTIMAL hygiene routine increased pre-weaning LMR+S feed intake, reduced clinical cases of disease, improved intestinal structure and reduced the weaning to slaughter duration, while LMR+S feeding increased weaning weight, intestinal maturity and reduced pre-weaning mortality.

Discerning Emittable from Extractable Chemicals Identified in Consumer Products by Suspect Screening GCxGC-TOFMS.

Characterization of chemicals in household products is important for understanding this potential source of chemical exposure. Increasingly, suspect screening and nontargeted analysis techniques are used to characterize as many chemical signatures as possible. Solids such as household products are most conveniently prepared using solvent extraction, revealing what chemicals are contained within the product matrix but providing no information about the potential of those chemicals to leave the matrix and cause actual exposure. In this work, the profile and relative abundances of "extractable" chemical signatures found after solvent extraction are compared to those "emittable" to the headspace for 81 household products analyzed by two-dimensional gas chromatography time-of-flight mass spectrometry. This study retrospectively fuses data collected in separate efforts over 3.8 years and 13 analytical batches. Management of the data is made possible by recent developments in processing systems for complex data such as Highlight. Compounds were generically classified as aromatic heteroatom, aromatic hydrocarbon, glycol, hydrocarbon, long chain heteroatom, nonaromatic heteroatom, and unknown/unclassified. Class-based retention time and abundance trends were observed. Liquid extraction resulted in the greatest number of features and the highest relative abundances, while low temperature emission conditions produced the smallest number of features and lowest relative abundances.

Microbiota composition of Culex perexiguus mosquitoes during the West Nile virus outbreak in southern Spain.

West Nile virus (WNV) is a flavivirus naturally circulating between mosquito vectors and birds, occasionally infecting horses and humans and causing epidemiologically relevant outbreaks. In Spain, the first big WNV outbreak was recorded in 2020, resulting in 77 people infected and 8 fatalities, most of them in southern Spain. Culex perexiguus was identified as the primary vector of WNV maintaining its enzootic circulation of the virus. Growing evidence highlights the role of mosquito microbiota as a key component determining the vectorial capacity of mosquitoes, largely contributing to disease epidemiology. Here, we develop, to our knowledge, the first identification of the microbiota composition of this mosquito vector under natural conditions and test for the potential relationship between mosquito microbiota composition and WNV infection. To do so, we collected mosquitoes in a natural area of southern Spain during the 2020 WNV outbreak and identified the microbiota composition of mosquitoes using a 16S rRNA gene metabarcoding approach. The microbiota of Cx. perexiguus was dominated by the phylum Proteobacteria. The most abundant families were Burkholderiaceae and Erwiniaceae, including the genera Burkholderia, Erwinia, and Pantoea. The genus Wolbachia, which use to dominate the microbiota of Cx. pipiens and negatively interact with WNV according to the literature, had a low prevalence and relative abundance in Cx. perexiguus and its abundance did not differ between WNV-positive and WNV-negative mosquito pools. The microbiota diversity and composition of Cx. perexiguus were not significantly related to the WNV infection status. These results provide the first identification of the mosquito microbiota in an endemic area of WNV circulation in Spain.

A pronounced deep water cooling in the Indian Ocean at ∼ 3.3–2.3 Ma linked to a major increase in the Antarctic ice volume

This study investigates changes in the bottom water circulation of the Indian Ocean since 6.5 Ma, based on benthic foraminiferal relative abundances and their stable isotope ratios from Ocean Drilling Program (ODP) Sites 709 and 758. A significant shift, from dominant North Indian Deep Water (NIDW) to Antarctic Bottom Water (AABW) circulation, is documented at ∼3.3 Ma. Principal Component Analysis (PCA) reveals two major benthic foraminiferal assemblages (PCA1 and PCA2). PCA2 is dominated by Nuttallides umbonifera, Globocassidulina subglobosa, and Epistominella exigua, representing cold and well‑oxygenated bottom water conditions between 3.3 and 2.3 Ma. The increased δ18O values of Cibicides wuellerstorfi and high relative abundance of N. umbonifera between ∼3.3 and 2.3 Ma at both sites, indicate an increased influence of AABW in the Indian Ocean due to a major increase in Antarctic ice volume. PCA1 is dominated by Uvigerina proboscidea, Fissurina spp., and miliolids, indicating oxygen-poor bottom waters and high surface productivity between 1.7 and 0.5 Ma associated with an influence of NIDW. The high relative abundance of U. proboscidea and low relative abundance of E. exigua signify low seasonality and sustained flux of organic matter with a signature of strong South Equatorial Counter Current formed by the seasonal reversal of winds during 1.7–0.5 Ma at Site 709.

Enterobacter-infecting phages in nitrogen-deficient paddy soil impact nitrogen-fixation capacity and rice growth by shaping the soil microbiome

Bacteriophages (“phage”) play important roles in nutrient cycling and ecology in environments by regulating soil microbial community structure. Here, metagenomic sequencing showed that a low relative abundance of nitrogen-fixing bacteria but high abundance of Enterobacter-infecting phages in paddy soil where rice plants showed nitrogen deficiency. From soil in the same field, we also isolated and identified a novel virulent phage (named here as Apdecimavirus NJ2) that infects several species of Enterobacter and characterized its impact on nitrogen fixation in the soil and in plants. It has the morphology of the Autographiviridae family, with a dsDNA genome of 39,605 bp, 47 predicted open reading frames and 52.64 % GC content. Based on genomic characteristics, comparative genomics and phylogenetic analysis, Apdecimavirus NJ2 should be a novel species in the genus Apdecimavirus, subfamily Studiervirinae. After natural or sterilized field soil was potted and inoculated with the phage, soil nitrogen-fixation capacity and rice growth were impaired, the abundance of Enterobacter decreased, along with the bacterial community composition and biodiversity changed compared with that of the unadded control paddy soil. Our work provides strong evidence that phages can affect the soil nitrogen cycle by changing the bacterial community. Controlling phages in the soil could be a useful strategy for improving soil nitrogen fixation.

Pregnancy during COVID 19 pandemic associated with differential gut microbiome composition as compared to pre-pandemic.

The first two years of the COVID-19 pandemic and subsequent health mandates resulted in significant disruptions to daily life, creating a period of heightened psychosocial stress in myriad aspects. Understanding the impact of this period on pregnant individuals' bacteriomes is crucial as pregnancy is a period of heightened vulnerability to stress and its sequelae, anxiety and mood disorders, which have been demonstrated to alter gut microbiome composition. In a prospective cohort study (N = 12-26) conducted from February 2019 to August 2021, we examined psychometric responses and rectal microbiome swabs from pregnant individuals. Full-length 16S rRNA sequencing followed by calculation of diversity metrics and relative abundance values were used to interrogate fecal microbiome community composition across pandemic groups. Distinct shifts in bacterial diversity and composition were observed during early to late pregnancy in the pandemic group, including lower relative abundance of pathogenic and lesser-known taxa. However, distribution of stress and depressive symptoms did not significantly differ from the pre-pandemic period while the correlation between stress and depressive symptoms dissipated during the pandemic. Our findings suggest that living through the COVID-19 pandemic altered the gut microbiome of pregnant individuals, independent of perceived stress.

Vineyard maturity increases arbuscular mycorrhizal and decreases plant pathogen fungal relative abundance in bulk soil across a 1,000 km Chilean gradient

Societal Impact StatementWine production has a significant impact on the global economy. Despite this, the microbial composition of the terroir has not been studied sufficiently, particularly in the southern hemisphere. Here, we investigated how bulk soil fungal communities are affected by several abiotic and biotic factors across 1,000 km of Chilean vineyards. We found that geographical distance was the main driver of vineyard soil fungal communities. Irrespective of variety, older vineyards host a higher relative abundance of arbuscular mycorrhizal fungi (AMF) and a lower relative abundance of plant pathogenic fungi. This result could lead to significant recommendations on when to apply AMF‐based inoculants.Summary The microbial dimension of the terroir has been increasingly recognized as an essential factor determining vineyard productivity and quality. Despite this, few studies have analyzed the factors affecting soil fungal communities of vineyards in the southern hemisphere. Across a 1,000 km gradient encompassing 34 Chilean vineyards, we investigated the effects of grapevine variety, geographical distance, maturity, and soil chemical properties on the diversity and composition of soil fungi. We implemented standard soil chemical analyses and ITS‐based DNA metabarcoding of bulk soil. We found that the total soil fungal composition was significantly affected by geographical distance but not by grapevine variety and maturity. Soil chemical dissimilarity also significantly affected soil fungal composition. When analyzing specific fungal guilds, we found a contrasting successional pattern: arbuscular mycorrhizal fungal relative abundance was significantly higher at medium and old‐maturity vineyards compared with young vineyards, on which plant pathogenic fungi had a markedly lower abundance. Our results present several caveats: the molecular marker was not the most commonly used for arbuscular mycorrhizal fungi, bulk soil was sampled (instead of roots), and all abundances were relative. Still, this study constitutes one of the most extensive studies on soil fungi – both for vineyards and Chile – and might have practical implications, as knowing the drivers of fungal and mycorrhizal biodiversity can inform agricultural management decisions.

Microbial landscapes in Trinervitermes trinervoides termite colonies are affected by mound compartments and soil properties but not by symbiotic Podaxis fungi

Termites are important ecosystem engineers and play key roles in modulating microbial communities within and outside their mounds. Microbial diversity within termite mounds is generally lower than surrounding soils, due to termite-associated antimicrobial compounds and active sanitary behaviours. Microbial symbionts of termites can also influence the microbial landscape, by inhibiting or out-competing other microbes. Certain members of the arid habitat fungal genus Podaxis (Agaricomycetes; Agaricaceae) are symbiotic with savannah specialist grass-cutting termites, with the potential to influence mound-associated microbiomes. To test this, we characterized fungal (ITS2) and bacterial (16S rRNA) communities within and outside 49 Trinervitermes trinervoides mounds with and without Podaxis fruiting bodies across a 1000 km transect in South Africa. We predicted that Podaxis would be a dominant member of the fungal communities in mounds and negatively impact microbial diversity. Further, we explored how environmental variables shaped microbial communities, including whether soil elemental composition affected Podaxis presence. As expected, we observed less diverse fungal communities, but not bacterial communities, within than outside mounds, while microbial communities differed by sampling regions and mound compartments. Podaxis sequences were present in 48 out of 49 mounds in low relative abundances, and neither fruiting body presence nor sequence abundance were associated with microbial community diversity or composition. There was, however, an overall association between the presence of Podaxis fruiting bodies and elemental composition, with different elements displaying varying associations depending on geographic region. Both environmental variables and soil elements associated with fungal and bacterial taxa, indicating that they are key drivers of microbial community composition. Taken together, our findings suggest that microbial landscapes in termite mounds are not strongly influenced by Podaxis but mainly driven by termite filtering and regional abiotic variables and elemental compositions.

Distinct Escherichia coli transcriptional profiles in the guts of recurrent UTI sufferers revealed by pangenome hybrid selection

Low-abundance members of microbial communities are difficult to study in their native habitats, including Escherichia coli, a minor but common inhabitant of the gastrointestinal tract, and key opportunistic pathogen of the urinary tract. While multi-omic analyses have detailed interactions between uropathogenic Escherichia coli (UPEC) and the bladder mediating urinary tract infection (UTI), little is known about UPEC in its pre-infection reservoir, the gastrointestinal tract, partly due to its low relative abundance (<1%). To sensitively explore the genomes and transcriptomes of diverse gut E. coli, we develop E. coli PanSelect, which uses probes designed to specifically capture E. coli’s broad pangenome. We demonstrate its ability to enrich diverse E. coli by orders of magnitude, in a mock community and in human stool from a study investigating recurrent UTI (rUTI). Comparisons of transcriptomes between gut E. coli of women with and without history of rUTI suggest rUTI gut E. coli are responding to increased oxygen and nitrate, suggestive of mucosal inflammation, which may have implications for recurrent disease. E. coli PanSelect is well suited for investigations of in vivo E. coli biology in other low-abundance environments, and the framework described here has broad applicability to other diverse, low-abundance organisms.

Environmental associations and the paleoecological significance of the genus Pyxidicula Ehrenberg,1838 and Pyxidicula muskegii sp. nov. in the Hudson and James Bay region peatlands, Canada

An environmental proxy routinely used in paleoecological studies of peatlands is testate amoebae, which are used to infer successional and hydrological shifts through time. However, since many species of protists globally remain undescribed, important ecological information about community assemblages and their interaction with environmental conditions in both the past and present has potential gaps. During the analysis of testate amoeba assemblages from peat cores across the Hudson and James Bay region of Canada, a testate amoeba that has not been formally described was discovered with high abundance in subfossil assemblages (up to 50%). We describe this new species, Pyxidicula muskegii sp. nov., using morphometric measurements of tests from these peat core records and demonstrate its environmental preferences using modern samples collected from the same region. The hemispheric shape and irregular areolar surface pattern on the test, along with its preference for lawns in both fens and bogs, support that P. muskegii is a new species. This species is also found in much lower relative abundance in modern samples (&lt;3%) than in paleo-peat core records. This difference in modern and paleo-assemblage suggests that there is a taphonomic bias in their relative abundance with depth, which we attribute to their organic test that is less prone to decomposition. Therefore, it is critical to include rare taxa within future transfer function models to incorporate their environmental tolerances and improve model predictions.

Assessment of Changes in the Composition and Distribution of Large and Medium-Sized Mammals in Xishuangbanna, Southwest China.

Given the vulnerability of large and medium-sized mammal communities to climate change and human disturbances, understanding the spatial-temporal dynamics of these communities is essential for effective conservation planning. However, in many biodiversity hotspots, precise biological community assessments are insufficient. From 2012 to 2022, we deployed 784 camera traps in eight nature reserves (including sub-reserves) and one State Forest Farm (SFF, less strictly protected than a reserve) to study the composition and distribution of large and medium-sized mammals in tropical Xishuangbanna. The findings revealed the following: (1) Forty-three species, encompassing six orders, 17 families, and 37 genera, were documented. Among the species in historical data, nine species were not detected in this survey. (2) Smaller and more fragmented reserves lacked larger body-sized predators and herbivores, and most common species showed lower relative population abundance. Conversely, the SFF exhibited high mammal diversity. (3) The community composition of large and medium-sized mammals varied significantly across the nine sites, particularly among threatened species. Our findings highlight the uneven distribution of these mammal communities in Xishuangbanna, with rare and large-sized species facing increased vulnerability to rapid environmental changes. Moreover, the findings demonstrate the importance of considering species specificity and uniqueness in conservation planning for maintaining regional-scale biodiversity.

Developmental trajectories of atopic dermatitis with multi-omics approaches in the infant gut: COCOA birth cohort

BackgroundAn understanding of the phenotypes and endotypes of atopic dermatitis (AD) is essential for developing precision therapies. Recent studies have demonstrated evidence for the gut-skin axis in AD. ObjectiveTo determine the natural course and clinical characteristics of AD phenotypes and investigate their mechanisms based on multi-omics analyses. MethodsLatent class trajectory analysis was used to AD phenotype in 2247 children who were followed until 9 years of age from the COhort for Childhood Origin of Asthma and allergic diseases (COCOA) birth cohort study. Multi-omics analyses (microbiome, metabolites, and gut epithelial cell transcriptome) using stool samples collected at 6 months of age were performed to elucidate the underlying mechanisms of AD phenotypes. ResultsFive AD phenotypes were classified as follows: never/infrequent, early-onset transient, intermediate-transient, late-onset, and early-onset persistent. Early-onset persistent and late-onset phenotypes showed increased risks of food allergy and wheezing treatment ever, with bronchial hyperresponsiveness only evident in the early-onset persistent phenotype. Multi-omics analyses revealed a significantly lower relative abundance of Ruminococcus gnavus and a decreased gut acetate level in the early-onset persistent phenotype, with potential associations to ACSS2, JAK-STAT signaling, and systemic Th2 inflammation. The early-onset transient phenotype was associated with AMPK and/or chemokine signaling regulation, whereas the late-onset phenotype was linked with IL-17 and barrier dysfunction. ConclusionsMulti-omics profiling in early life may offer insights into different mechanisms underlying AD phenotypes in children.

Investigating the inhibitory mechanism of methanogenesis during composting under the combined influence of amoxicillin and copper pollution

This study investigated the effects of different levels of combined amoxicillin and copper (Cu) pollution on the methanogenesis of microbial communities during aerobic composting of dairy manure. Three groups were established: the control group (CK), a low-level combined pollution group (L), and a high-level combined pollution group (H). As the level of pollution increased, carbohydrate metabolism decreased during the thermophilic phase of composting, while signal translation increased. Compared with the initial phase, functional genes related to the acetoclastic pathway decreased significantly in abundance during the thermophilic phase, and cdh had the lowest relative abundance among acetoclastic pathway with a decrease of 81.52%, 81.88%, and 84.73% in groups CK, L, and H, respectively. The cumulative methane emissions in group H decreased by 31.56% and 9.23%, respectively, compared with those from groups CK and L. These results contribute to understanding the effects of combined amoxicillin and Cu pollution on methane emissions during composting.

Activity of novel virus families infecting soil nitrifiers is concomitant with host niche differentiation.

Chemolithoautotrophic nitrifiers are model groups for linking phylogeny, evolution, and ecophysiology. Ammonia-oxidising bacteria (AOB) typically dominate the first step of ammonia oxidation at high ammonium supply rates, ammonia-oxidising archaea (AOA) and complete ammonia-oxidising Nitrospira (comammox) are often active at lower supply rates or during AOB inactivity, and nitrite-oxidising bacteria (NOB) complete canonical nitrification. Soil virus communities are dynamic but contributions to functional processes are largely undetermined. In addition, characterising viruses infecting hosts with low relative abundance, such as nitrifiers, may be constrained by vast viral diversity, partial genome recovery, and difficulties in host linkage. Here, we describe a targeted incubation study that aimed to determine whether growth of different nitrifier groups in soil is associated with active virus populations and if process-focussed analyses facilitate characterisation of high-quality virus genomes. dsDNA viruses infecting different nitrifier groups were enriched in situ via differential host inhibition. Growth of each nitrifier group was consistent with predicted inhibition profiles and concomitant with the abundance of their viruses. These included 61 high-quality/complete virus genomes 35-173kb in length with minimal similarity to validated families. AOA viruses lacked ammonia monooxygenase sub-unit C (amoC) genes found in marine AOA viruses but some encoded AOA-specific multicopper oxidase type 1 (MCO1), previously implicated in copper acquisition, and suggesting a role in supporting energy metabolism of soil AOA. Findings demonstrate focussed incubation studies facilitate characterisation of active host-virus interactions associated with specific processes and viruses of soil AOA, AOB and NOB are dynamic and potentially influence nitrogen cycling processes.

Comparison of intestinal and pharyngeal microbiota in preterm infants on the first day of life and the characteristics of pharyngeal microbiota in infants delivered by cesarean section or vaginally.

This study aimed to explore the distribution of intestinal and pharyngeal microbiota on the first day of life in preterm infants and compare the composition of microbiota in infants delivered by cesarean section or vaginally. This study included 44 late preterm infants with a gestational age of 34-36 + 6 weeks. Stool and throat swab samples were collected from the preterm infants on the first day of life. The infants were divided into cesarean section and vaginal delivery groups. Illumina NovaSeq high-throughput sequencing technology was used to sequence the V3-V4 hypervariable region of the 16S rRNA gene of all bacteria in the samples. Venn diagram was used to identify shared operational taxonomic units (OTUs) in the intestines and pharynges. Microbial analysis was conducted at the phylum and genus levels, and α and β diversity comparisons were performed. (1) Gestational age may have significantly affected the microbial colonization of the intestines and pharynges of preterm infants on the first day after birth (p ≤ 0.001). (2) More OTUs were detected in the pharynx than in the intestines, both have a total of 819 shared OTUs. Proteobacteria, Firmicutes, and Bacteroidota were the dominant phyla in both. At the genus level, Streptococcus had a lower relative abundance in stool samples (0.5%) compared to throat samples (0.5% vs. 22.2%, p = 0.003). 3) The relative abundance of Streptococcus in pharyngeal samples was 26.2% in the cesarean section group much higher than the 3.8% in the vaginal delivery group (p = 0.01). The early postnatal period is a critical time for the establishment of an infant's microbiota. Gestational age at birth may influence microbial colonization, while birth weight, gender, and mode of delivery do not. The intestinal and pharyngeal microbiota composition of preterm infants on the first day after birth showed high similarity, but larger samples are needed for further validation.

Probing the oral-brain connection: oral microbiome patterns in a large community cohort with anxiety, depression, and trauma symptoms, and periodontal outcomes

The role of the oral microbiome in mental health has recently been appreciated within the proposed oral-brain axis. This study examined the structure and composition of the salivary microbiome in a large-scale population-based cohort of individuals reporting mental health symptoms (n = 306) compared to mentally healthy controls (n = 164) using 16S rRNA sequencing. Mental health symptoms were evaluated using validated questionnaires and included depression, anxiety, and posttraumatic stress disorder (PTSD), with accompanying periodontal outcomes. Participants also indicated current or previous diagnoses of anxiety, depression, periodontitis, and gingivitis. Mental and periodontal health variables influenced the overall composition of the oral microbiome. PTSD symptoms correlated with a lower clr-transformed relative abundance of Haemophilus sputorum and a higher clr-transformed relative abundance of Prevotella histicola. The clr-transformed relative abundance of P. histicola was also positively associated with depressive scores and negatively associated with psychological quality of life. Anxiety disorder diagnosis was associated with a lower clr-transformed relative abundance of Neisseria elongate and a higher clr-transformed relative abundance of Oribacterium asaccharolyticum. A higher clr-transformed relative abundance of Shuttleworthia and lower clr-transformed relative abundance of Capnocytophaga were evident in those who reported a clinical periodontitis diagnosis. Higher Eggerthia and lower Haemophilus parainfluenzae clr-transformed relative abundances were associated with reported clinical periodontitis diagnoses and psychotherapeutic efficacy. Functional prediction analysis revealed a potential role for tryptophan metabolism/degradation in the oral-brain axis, which was confirmed by lower plasma serotonin levels across symptomatic groups. This study sheds light on the intricate interplay between oral microbiota, periodontal and mental health outcomes, and a potential role for tryptophan metabolism in the proposed oral-brain axis, emphasizing the need for further exploration to pave the way for novel therapeutic interventions and predicting therapeutic response.

Microbial composition and dynamics in environmental samples from a ready-to-eat food production facility with a long-term colonization of Listeria monocytogenes

Listeria monocytogenes is a foodborne pathogen of significant concern for the food industry due to its remarkable ability to persist through safety control efforts, posing a subsequent health threat to consumers. Understanding the microbial communities coexisting with L. monocytogenes in food processing environments provides insights into its persistence mechanisms. We investigated the microbial communities on non-food contact surfaces in a facility producing ready-to-eat foods, known to harbour a ST121 L. monocytogenes strain over multiple years. A 10-week sampling period was coordinated with the company and public health authorities. Metagenomic analysis revealed a stable microbial composition dominated by Pseudomonas fluorescens. While highly related populations were present in high-care production zones, distinctive taxa characteristic of specific areas were observed (e.g., Sphingomonas aerolata). Although Listeria spp. were not detected in metagenomes, they were detected in cultured samples, suggesting low relative abundance in factory settings. The findings suggest that a stable resident microbiota, with distinct adaptations to different areas within the factory, was selected for by their collective ability to survive control efforts in this environment. Listeria spp. was a member of this microbial community, albeit at low abundance, and may likewise benefit from the mutualism of the overall microbial community.

Predator-induced defense decreases growth rate and photoprotective capacity in a nitrogen-limited dinoflagellate, Alexandrium minutum

Some dinoflagellates produce toxic secondary metabolites that correlate with increased resistance to grazers. The allocation costs of toxin production have been repeatedly addressed, but with conflicting results. Few studies have considered the potential costs of this defense to the photosystem, even though defense toxins (e.g., karlotoxins and brevetoxins) are closely linked to the photoprotective process. Here, we used chemical cues from copepods to induce paralytic shellfish toxin (PST) production in resource-limited Alexandrium minutum and quantitatively determined the growth rate and potential trade-offs with the photosystem process. The results show that grazer-induced, more toxic A. minutum had larger cell volume, lower cell division rate, and lower pigment content under nitrogen-limited conditions than control cells. In addition, predator cues led to a lower relative abundance of photoprotective xanthophylls and a reduced de-epoxidation efficiency of the xanthophyll cycle under high light conditions, reducing the ability of the cells to resist photodamage. Decreased photoprotective capacity may reflect an overlooked defense cost of toxin production.