A new method for non-parametric multivariate analysis of variance

Distinct alterations of gut microbiota between viral- and non-viral-related hepatocellular carcinoma

Altered gut microbiota has been connected to hepatocellular carcinoma (HCC) occurrence and advancement. This study was conducted to identify a gut microbiota signature in differentiating between viral-related HCC (Viral-HCC) and non-hepatitis B-, non-hepatitis C-related HCC (NBNC-HCC). Fecal specimens were obtained from 16 healthy controls, 33 patients with viral-HCC (17 and 16 cases with hepatitis B virus (HBV) and hepatitis C virus (HCV) infection, respectively), and 18 patients with NBNC-HCC. Compositions of fecal microbiota were assessed by 16S rRNA sequencing. Bioinformatic analysis was performed by the DADA2 pipeline in the R program. Significantly different genera from the top 50 relative abundance were used to classify between subgroups of HCC by the Random Forest algorithm. Our data demonstrated that the HCC group had a significantly decreased alpha-diversity and changed microbial composition in comparison with healthy controls. Within the top 50 relative abundance, there were 11 genera including Faecalibacterium, Agathobacter, and Coprococcus that were significantly enhanced in Viral-HCC, while 5 genera such as Bacteroides, Streptococcus, Ruminococcus gnavus group, Parabacteroides, and Erysipelatoclostridium were enhanced in NBNC-HCC. Compared to Viral-HCC, the NBNC-HCC subgroup significantly reduced various short-chain fatty acid-producing bacteria, as well as declined fecal butyrate but elevated plasma surrogate markers of microbial translocation. Based on the machine learning algorithm, a high diagnostic accuracy to classify HCC subgroups was achieved with an area under the receiver-operating characteristic (ROC) curve (AUC) of 0.94. Collectively, these data revealed that gut dysbiosis was distinct according to etiological factors of HCC, which might play an essential role in hepatocarcinogenesis. These findings underscore the possible use of a gut microbiota signature for the diagnosis and therapeutic approaches regarding different subgroups of HCC. KEY POINTS: • Gut dysbiosis is connected to hepatocarcinogenesis and can be used as a novel biomarker. • Gut microbiota composition is significantly altered in different etiological factors of HCC. • Microbiota-based signature can accurately distinguish between Viral-HCC and NBNC-HCC.

Hemp hull fiber and two constituent compounds, N-trans-caffeoyltyramine and N-trans-feruloyltyramine, shape the human gut microbiome in vitro

Mounting evidence supports the potential of dietary bioactives to reduce chronic disease risk. N-trans-caffeoyltyramine (NCT) and N-trans-feruloyltyramine (NFT) have been hypothesized to drive regulation of gut permeability, but these components have not yet been studied in the context of the human gut microbiome. This work examined whether purified NCT and NFT, or a hemp hull product containing NCT and NFT (Brightseed® Bio Gut Fiber™), can impact the gut microbiome using an in vitro fermentation assay. Representative human gut microbiomes were treated with Bio Gut Fiber™ or NCT and NFT and compared to starch and methylcellulose, as controls, in vitro. Stronger changes were exerted by Bio Gut Fiber™, NCT, and NFT. Communities treated with Bio Gut Fiber™ saw increased productivity and diversity. We found a dose-dependent effect of NCT and NFT on microbial communities. Here, we describe novel potential for hemp-derived bioactives to shape the gut microbiome.

Investigating oral microbiome dynamics in chronic kidney disease and post-transplantation in continuous culture

The oral microbiome is influenced by environmental factors in chronic kidney disease and following kidney transplantation affecting microbial composition, which may have implications for health and recovery. A major driver of oral microbiome perturbation is the accumulation of urea in saliva. We have modelled increased salivary urea concentrations associated with CKD and subsequent reductions that may occur post-transplantation. Oral microbiota were established in constant-depth film fermenters by inoculation with saliva. Duplicate validation runs were maintained with artificial saliva with baseline urea concentrations (0.205 mg/mL) for 21 days. Triplicate treatment runs were then done with baseline urea for 10 days (healthy phase) before urea was increased for 10 days to reflect CKD concentrations (0.92 mg/mL) (CKD phase). This was followed by reversion to baseline urea concentrations (post-transplant phase). Biofilms in primary validation runs reached dynamic stability within 5 days according to viable counting. DNA sequence data indicated minimal taxonomic variation over time and between low and high urea treatments despite background noise indicating changes in bacteria belonging to the family Gemellaceae and the genera TG5 and Leptotrichia. Significant differences in alpha and beta diversity occurred between low and high urea states but not following reversion to a low urea environment. Increased abundance of the TG5 was detected in late model phases, despite apparent count stability, and independent of changes in urea concentrations.

IMPORTANCE

This study investigates dynamic changes in the oral microbiome associated with changes in salivary urea concentration, an important factor in chronic kidney disease (CKD). The in vitro system modeled increased urea concentrations and subsequent reductions post-transplantation. The study provides insight into the oral microbial shifts during different simulated clinical phases. Understanding these dynamics is crucial for advancing our comprehension of CKD-associated oral microbiome variations and their potential impact on patient well-being and recovery.

Estimating taxonomic and functional structure along a tropical estuary: linking metabolic traits and aspects of ecosystem functioning

Microbial life forms are among the most ubiquitous on Earth, yet many remain understudied in Caribbean estuaries. We report on the prokaryote community composition of the Urabá Estuary in the Colombian Caribbean using 16S rRNA gene-transcript sequencing. We also assessed potential functional diversity through 38 metabolic traits inferred from 16S rRNA gene data. Water samples were collected from six sampling stations at two depths with contrasting light-penetration conditions along an approximately 100 km transect in the Gulf of Urabá in December 2019. Non-metric multidimensional scaling analysis grouped the samples into two distinct clusters along the transect and between depths. The primary variables influencing the prokaryote community composition were the sampling station, depth, salinity, and dissolved oxygen levels. Twenty percent of genera (i.e., 58 out 285) account for 95% of the differences between groups along the transect and among depths. All of the 38 metabolic traits studied showed some significant relationship with the tested environmental variables, especially salinity and except with temperature. Another non-metric multidimensional scaling analysis, based on community-weighted mean of traits, also grouped the samples in two clusters along the transect and over depth. Biodiversity facets, such as richness, evenness, and redundancy, indicated that environmental variations-stemming from river discharges-introduce an imbalance in functional diversity between surface prokaryote communities closer to the estuary's head and bottom communities closer to the ocean. Our research broadens the use of 16S rRNA gene transcripts beyond mere taxonomic assignments, furthering the field of trait-based prokaryote community ecology in transitional aquatic ecosystems.IMPORTANCEThe resilience of a dynamic ecosystem is directly tied to the ability of its microbes to navigate environmental gradients. This study delves into the changes in prokaryote community composition and functional diversity within the Urabá Estuary (Colombian Caribbean) for the first time. We integrate data from 16S rRNA gene transcripts (taxonomic and functional) with environmental variability to gain an understanding of this under-researched ecosystem using a multi-faceted macroecological framework. We found that significant shifts in prokaryote composition and in primary changes in functional diversity were influenced by physical-chemical fluctuations across the estuary's environmental gradient. Furthermore, we identified a potential disparity in functional diversity. Near-surface communities closer to the estuary's head exhibited differences compared to deeper communities situated farther away. Our research serves as a roadmap for posing new inquiries about the potential functional diversity of prokaryote communities in highly dynamic ecosystems, pushing forward the domain of multi-trait-based prokaryote community ecology.

Connection between the gut microbiota of largemouth bass (Micropterus salmoides) and microbiota of the aquaponics system environment

The significant role played by the gut microbiota in fish growth, development, immunity, and overall health has been widely established. Nevertheless, there remains a lack of clarity regarding the interaction and origin between the environmental microbiota and the gut microbiota of aquaculture species within the aquaponics coupling system. Thus, we conducted an analysis of the gut microbiota of largemouth bass (Micropterus salmoides) obtained from an indoor enclosed circulating water aquaponics coupling system located in greenhouses in northern China. Additionally, we examined the microbiota of the fish pond water and tomato rhizosphere soil using high-throughput sequencing of the 16S rRNA gene. Our results demonstrated significant differences in the compositions of fish pond water, rhizosphere soil, and the gut microbiota of largemouth bass. Moreover, these compositions changed throughout the culture period. Approximately 11.99% of the bacterial composition in the gut microbiota of largemouth bass could be attributable to the rhizosphere soil microbiota, while 62.01% of the bacterial composition could be attributable to the fish pond water microbiota. However, the proportion of bacteria in the gut microbiota from the fish pond water microbiota remained respectively 40.90% and 56.15% in May and September, which increased markedly to 88.97% in July. Similarly, the proportion of bacteria in the pond water microbiota from the tomato rhizosphere soil microbiota were respectively 0% and 8.95% in samples collected in May and September, which increased markedly to 69.26% in July, and the proportion of bacteria in the gut microbiota from the tomato rhizosphere soil microbiota were respectively 0.07% and 0% in samples collected in May and September, which increased to 0.45% in July. The research results offer essential insights into the interactions and origins of environmental microbiota and gut microbiota in the aquaponics system of cultured fish. This knowledge could enhance green aquaponics practices for largemouth bass.

A quantitative approach to measure and predict microbiome response to antibiotics

Although antibiotics induce sizable perturbations in the human microbiome, we lack a systematic and quantitative method to measure and predict the microbiome's response to specific antibiotics. Here, we introduce such a method, which takes the form of a microbiome response index (MiRIx) for each antibiotic. Antibiotic-specific MiRIx values quantify the overall susceptibility of the microbiota to an antibiotic, based on databases of bacterial phenotypes and published data on intrinsic antibiotic susceptibility. We applied our approach to five published microbiome studies that carried out antibiotic interventions with vancomycin, metronidazole, ciprofloxacin, amoxicillin, and doxycycline. We show how MiRIx can be used in conjunction with existing microbiome analytical approaches to gain a deeper understanding of the microbiome response to antibiotics. Finally, we generate antibiotic response predictions for the oral, skin, and gut microbiome in healthy humans. Our approach is implemented as open-source software and is readily applied to microbiome data sets generated by 16S rRNA marker gene sequencing or shotgun metagenomics.

IMPORTANCE

Antibiotics are potent influencers of the human microbiome and can be a source for enduring dysbiosis and antibiotic resistance in healthcare. Existing microbiome data analysis methods can quantify perturbations of bacterial communities but cannot evaluate whether the differences are aligned with the expected activity of a specific antibiotic. Here, we present a novel method to quantify and predict antibiotic-specific microbiome changes, implemented in a ready-to-use software package. This has the potential to be a critical tool to broaden our understanding of the relationship between the microbiome and antibiotics.

Implementing high-throughput insect barcoding in microbiome studies: impact of non-destructive DNA extraction on microbiome reconstruction

Background

Symbiotic relationships with diverse microorganisms are crucial for many aspects of insect biology. However, while our understanding of insect taxonomic diversity and the distribution of insect species in natural communities is limited, we know much less about their microbiota. In the era of rapid biodiversity declines, as researchers increasingly turn towards DNA-based monitoring, developing and broadly implementing approaches for high-throughput and cost-effective characterization of both insect and insect-associated microbial diversity is essential. We need to verify whether approaches such as high-throughput barcoding, a powerful tool for identifying wild insects, would permit subsequent microbiota reconstruction in these specimens.

Methods

High-throughput barcoding ("megabarcoding") methods often rely on non-destructive approaches for obtaining template DNA for PCR amplification by leaching DNA out of insect specimens using alkaline buffers such as HotSHOT. This study investigated the impact of HotSHOT on microbial abundance estimates and the reconstructed bacterial community profiles. We addressed this question by comparing quantitative 16S rRNA amplicon sequencing data for HotSHOT-treated or untreated specimens of 16 insect species representing six orders and selected based on the expectation of limited variation among individuals.

Results

We find that in 13 species, the treatment significantly reduced microbial abundance estimates, corresponding to an estimated 15-fold decrease in amplifiable 16S rRNA template on average. On the other hand, HotSHOT pre-treatment had a limited effect on microbial community composition. The reconstructed presence of abundant bacteria with known significant effects was not affected. On the other hand, we observed changes in the presence of low-abundance microbes, those close to the reliable detection threshold. Alpha and beta diversity analyses showed compositional differences in only a few species.

Conclusion

Our results indicate that HotSHOT pre-treated specimens remain suitable for microbial community composition reconstruction, even if abundance may be hard to estimate. These results indicate that we can cost-effectively combine barcoding with the study of microbiota across wild insect communities. Thus, the voucher specimens obtained using megabarcoding studies targeted at characterizing insect communities can be used for microbiome characterizations. This can substantially aid in speeding up the accumulation of knowledge on the microbiomes of abundant and hyperdiverse insect species.

Vertical transfer of gut microbiota from dam to neonate calf in the early of life

The aim of this study was to investigate the vertical transfer of microbiota from dams to the offspring. We studied a pair of 20 dams and its offspring. Maternal sources (colostrum, feces and vaginal secretion) and newborn fecal samples were analyzed using 16S rDNA amplicon sequencing on days 1, 3, 7, 14 and 28. Overall, newborns were maintained healthy and did not receive antimicrobial therapy. The Source Tracker analysis indicated that the newborn fecal microbiota was similar to colostrum and vaginal secretion from day 1 up to 7. However, an unknown source (probably from the environment) showed a gradual increase in its similarity with fecal samples from calves measured from day 3 to 28. The most abundant bacteria groups on meconium (day 1) and calf fecal samples on day 3 were Escherichia-Shigella and Clostridium, respectively. On day 7, the predominant genus were Bifidobacterium and Lactobacillus, while Fusobacterium was the most abundant genus on day 14, coinciding with the diarrhea peak. Faecalibacterium showed a gradual increase throughout the neonatal period. Maternal sources contribute to the neonatal microbiota, however other unknown sources (probably environment) had a strong influence on development of the gut microbiota later in the neonate period.

Post-fire temporal dynamics of plant-pollinator communities in a tropical savanna

Fire is a major ecological and evolutionary factor promoting biodiversity and maintaining functioning of naturally fire-prone ecosystems. In tropical savannas, plant communities show a set of fire-adapted traits and both flowering and pollination services have the potential to rapidly regenerate after fire, but fire-suppression policies may disrupt this adaptability following potential woody encroachment. Understanding the effects of fire on plant-pollinator interactions are required to advance conservation of biodiversity and ecosystem functioning. We evaluated the dynamics of plant community assemblage, flower availability, composition of flower functional traits associated with attractiveness to pollinators, and activity and diversity of insect pollinator guilds over ten post-fire stand ages along a 14-year chronosequence in a naturally burned region in the Cerrado, a megadiverse savanna in Brazil. We expect to find a high resilience of plant-pollinator communities and a steady decline in the successional recovery as time-since-fire proceeds. Along the post-fire chronosequence, vegetation was dominated by subshrubs with tubular, white, and nectar flowers arranged in inflorescences, while bees were the predominant pollinators. Plant assemblage and flower number showed an initial significant increase but monotonically declined after 7-9 years after fire. Accordingly, pollinator richness and abundance significantly reached highest peaks in interim periods and a steady decline over time. In contrast, the frequency of community-wide plant-life form, flower functional traits, and pollinator diversity remained unaltered over the post-fire chronosequence. We added compelling evidence of a high post-fire resilience of plant-pollinator communities and further understanding of how fire-suppression policies may affect pollination in the Cerrado.

Using patterns of shared taxa to infer bacterial dispersal in human living environment in urban and rural areas

Contact with environmental microbial communities primes the human immune system. Factors determining the distribution of microorganisms, such as dispersal, are thus important for human health. Here, we used the relative number of bacteria shared between environmental and human samples as a measure of bacterial dispersal and studied these associations with living environment and lifestyles. We analyzed amplicon sequence variants (ASVs) of the V4 region of 16S rDNA gene from 347 samples of doormat dust as well as samples of saliva, skin swabs, and feces from 53 elderly people in urban and rural areas in Finland at three timepoints. We first enumerated the ASVs shared between doormat and one of the human sample types (i.e., saliva, skin swab, or feces) of each individual subject and calculated the shared ASVs as a proportion of all ASVs in the given sample type of that individual. We observed that the patterns for the proportions of shared ASVs differed among seasons and human sample type. In skin samples, there was a negative association between the proportion of shared ASVs and the coverage of built environment (a proxy for degree of urbanization), whereas in saliva data, this association was positive. We discuss these findings in the context of differing species pools in urban and rural environments.

IMPORTANCE

Understanding how environmental microorganisms reach and interact with humans is a key question when aiming to increase human contacts with natural microbiota. Few methods are suitable for studying microbial dispersal at relatively large spatial scales. Thus, we tested an indirect method and studied patterns of bacterial taxa that are shared between humans and their living environment.

Soil microbial identity explains home-field advantage for litter decomposition

Unraveling the mechanisms of home-field advantage (HFA) is essential to gain a complete understanding of litter decomposition processes. However, knowledge of the relationships between HFA effects and microbial communities is lacking. To examine HFA effects on litter decomposition, we identified the microbial communities and conducted a reciprocal transplant experiment, including all possible combinations of soil and litter, between sites at two elevations in cool-temperate forests. Soil origin, rather than HFA, was an important factor in controlling litter decomposition processes. Microbiome-wide association analyses identified litter fungi and bacteria specific to the source soil, which completely differed at a low taxonomic level between litter types. The relative abundance of these microbes specific to source soil was positively correlated with litter mass loss. The results indicated that the unique relationships between plant litter and soil microbes through plant-soil linkages drive litter decomposition processes. In the short term, soil disturbances resulting from land-use changes have the potential to disrupt the effect of soil origin and hinder the advancement of litter decomposition. These findings contribute to an understanding of HFA mechanisms and the impacts of land-use change on decomposition processes in forest ecosystems.

Mounting an immune response reduces male attractiveness in a lizard

Parasites impact host fitness and constitute an important selective pressure on the host's life history. According to parasite-mediated sexual selection, ornaments are presumed to honestly indicate immune capacity or resistance against parasites, and the chooser sex (typically females) obtains an advantage by selecting more ornamented, thus more immunocompetent mates. Therefore, signalers mounting an immune response must allocate resources from the sexual signal to the immune system, hence reducing the expression of the ornament and becoming less attractive to the choosing sex. Here, we test this idea in the lizard Psammodromus algirus. We inoculated a subsample of males with lipopolysaccharide (LPS) of the cell wall of Escherichia coli, while others served as sham controls. The inoculation of LPS decreased the proportion of ergosterol (pro-vitamin D2) in femoral secretions, and chemosensory tests showed that the scent of LPS-inoculated males was less attractive to females than the scent of control males. Given that ergosterol is a precursor of vitamin D, which has physiological functions as an immune modulator, immunocompromised males likely needed to divert vitamin D to the immune system, reducing the allocation of ergosterol to secretions. In this way, females could detect "sick" males, preferring the apparently healthy males. Overall, our study shows that mounting an immune response is costly in terms of reduced attractiveness. Moreover, we disentangle the underlying mechanism, which involves an honest signal based on vitamin D allocation.

Associations of plant-based foods, red and processed meat, and dairy with gut microbiome in Finnish adults

PURPOSE

Population-based studies on the associations of plant-based foods, red meat or dairy with gut microbiome are scarce. We examined whether the consumption of plant-based foods (vegetables, potatoes, fruits, cereals), red and processed meat (RPM) or dairy (fermented milk, cheese, other dairy products) are related to gut microbiome in Finnish adults.

METHODS

We utilized data from the National FINRISK/FINDIET 2002 Study (n = 1273, aged 25-64 years, 55% women). Diet was assessed with 48-hour dietary recalls. Gut microbiome was analyzed using shallow shotgun sequencing. We applied multivariate analyses with linear models and permutational ANOVAs adjusted for relevant confounders.

RESULTS

Fruit consumption was positively (beta = 0.03, SE = 0.01, P = 0.04), while a dairy subgroup including milk, cream and ice-creams was inversely associated (beta=-0.03, SE 0.01, P = 0.02) with intra-individual gut microbiome diversity (alpha-diversity). Plant-based foods (R2 = 0.001, P = 0.03) and dairy (R2 = 0.002, P = 0.01) but not RPM (R2 = 0.001, P = 0.38) contributed to the compositional differences in gut microbiome (beta-diversity). Plant-based foods were associated with several butyrate producers/cellulolytic species including Roseburia hominis. RPM associations included an inverse association with R. hominis. Dairy was positively associated with several lactic producing/probiotic species including Lactobacillus delbrueckii and potentially opportunistic pathogens including Citrobacter freundii. Dairy, fermented milk, vegetables, and cereals were associated with specific microbial functions.

CONCLUSION

Our results suggest a potential association between plant-based foods and dairy or their subgroups with microbial diversity measures. Furthermore, our findings indicated that all the food groups were associated with distinct overall microbial community compositions. Plant-based food consumption particularly was associated with a larger number of putative beneficial species.

Co-exposure to polyethylene fiber and Salmonella enterica serovar Typhimurium alters microbiome and metabolome of in vitro chicken cecal mesocosms

Humans and animals encounter a summation of exposures during their lifetime (the exposome). In recent years, the scope of the exposome has begun to include microplastics. Microplastics (MPs) have increasingly been found in locations, including in animal gastrointestinal tracts, where there could be an interaction with Salmonella enterica serovar Typhimurium, one of the commonly isolated serovars from processed chicken. However, there is limited knowledge on how gut microbiomes are affected by microplastics and if an effect would be exacerbated by the presence of a pathogen. In this study, we aimed to determine if acute exposure to microplastics in vitro altered the gut microbiome membership and activity. The microbiota response to a 24 h co-exposure to Salmonella enterica serovar Typhimurium and/or low-density polyethylene (PE) microplastics in an in vitro broiler cecal model was determined using 16S rRNA amplicon sequencing (Illumina) and untargeted metabolomics. Community sequencing results indicated that PE fiber with and without S. Typhimurium yielded a lower Firmicutes/Bacteroides ratio compared with other treatment groups, which is associated with poor gut health, and overall had greater changes to the cecal microbial community composition. However, changes in the total metabolome were primarily driven by the presence of S. Typhimurium. Additionally, the co-exposure to PE fiber and S. Typhimurium caused greater cecal microbial community and metabolome changes than either exposure alone. Our results indicate that polymer shape is an important factor in effects resulting from exposure. It also demonstrates that microplastic-pathogen interactions cause metabolic alterations to the chicken cecal microbiome in an in vitro chicken cecal mesocosm.

IMPORTANCE

Researching the exposome, a summation of exposure to one's lifespan, will aid in determining the environmental factors that contribute to disease states. There is an emerging concern that microplastic-pathogen interactions in the gastrointestinal tract of broiler chickens may lead to an increase in Salmonella infection across flocks and eventually increased incidence of human salmonellosis cases. In this research article, we elucidated the effects of acute co-exposure to polyethylene microplastics and Salmonella enterica serovar Typhimurium on the ceca microbial community in vitro. Salmonella presence caused strong shifts in the cecal metabolome but not the microbiome. The inverse was true for polyethylene fiber. Polyethylene powder had almost no effect. The co-exposure had worse effects than either alone. This demonstrates that exposure effects to the gut microbial community are contaminant-specific. When combined, the interactions between exposures exacerbate changes to the gut environment, necessitating future experiments studying low-dose chronic exposure effects with in vivo model systems.

Microbiome-informed study of the mechanistic basis of methane inhibition by Asparagopsis taxiformis in dairy cattle

Copious amounts of methane, a major constituent of greenhouse gases currently driving climate change, are emitted by livestock, and efficient methods that curb such emissions are urgently needed to reduce global warming. When fed to cows, the red seaweed Asparagopsis taxiformis (AT) can reduce enteric methane emissions by up to 80%, but the achieved results can vary widely. Livestock produce methane as a byproduct of methanogenesis, which occurs during the breakdown of feed by microbes in the rumen. The ruminant microbiome is a diverse ecosystem comprising bacteria, protozoa, fungi, and archaea, and methanogenic archaea work synergistically with bacteria to produce methane. Here, we find that an effective reduction in methane emission by high-dose AT (0.5% dry matter intake) was associated with a reduction in methanol-utilizing Methanosphaera within the rumen, suggesting that they may play a greater role in methane formation than previously thought. However, a later spike in Methanosphaera suggested an acquired resistance, possibly via the reductive dehalogenation of bromoform. While we found that AT inhibition of methanogenesis indirectly impacted ruminal bacteria and fermentation pathways due to an increase in spared H2, we also found that an increase in butyrate synthesis was due to a direct effect of AT on butyrate-producing bacteria such as Butyrivibrio, Moryella, and Eubacterium. Together, our findings provide several novel insights into the impact of AT on both methane emissions and the microbiome, thereby elucidating additional pathways that may need to be targeted to maintain its inhibitory effects while preserving microbiome health and animal productivity.

IMPORTANCE

Livestock emits copious quantities of methane, a major constituent of the greenhouse gases currently driving climate change. Methanogens within the bovine rumen produce methane during the breakdown of feed. While the red seaweed Asparagopsis taxiformis (AT) can significantly reduce methane emissions when fed to cows, its effects appear short-lived. This study revealed that the effective reduction of methane emissions by AT was accompanied by the near-total elimination of methane-generating Methanosphaera. However, Methanosphaera populations subsequently rebounded due to their ability to inactivate bromoform, a major inhibitor of methane formation found in AT. This study presents novel findings on the contribution of Methanosphaera to ruminal methanogenesis, the mode of action of AT, and the possibility for complementing different strategies to effectively curb methane emissions.

New species of Ontocetus (Pinnipedia: Odobenidae) from the Lower Pleistocene of the North Atlantic shows similar feeding adaptation independent to the extant walrus (Odobenus rosmarus)

Ontocetus is one of the most notable extinct odobenines owing to its global distribution in the Northern Hemisphere. Originating in the Late Miocene of the western North Pacific, this lineage quickly spread to the Atlantic Ocean during the Pliocene, with notable occurrences in England, Belgium, The Netherlands, Morocco and the eastern seaboard of the United States. Reassessment of a pair of mandibles from the Lower Pleistocene of Norwich (United Kingdom) and a mandible from the Upper Pliocene of Antwerp (Belgium) that were referred to as Ontocetus emmonsi reveals existences of features of both Ontocetus and Odobenus. The presence of four post-canine teeth, a lower canine larger than the cheek-teeth and a lower incisor confirms the assignment to Ontocetus; simultaneously, characteristics such as a fused and short mandibular symphysis, a well-curved mandibular arch and thin septa between teeth align with traits usually found in Odobenus. Based on a combination of these characters, we describe Ontocetus posti, sp. nov. Its mandibular anatomy suggests, a better adaptation to suction-feeding than what was previously described in the genus suggesting that Ontocetus posti sp. nov. likely occupied a similar ecological niche to the extant walrus Odobenus rosmarus. Originating from the North Pacific Ocean, Ontocetus most likely dispersed via the Central American Seaway. Although initially discovered in the Lower Pliocene deposits of the western North Atlantic, Ontocetus also left its imprint in the North Sea basin and Moroccan Plio-Pleistocene deposits. The closure of the Isthmus of Panama during the Mio-Pliocene boundary significantly impacted the contemporary climate, inducing global cooling. This event constrained Ontocetus posti in the North Sea basin leaving the taxon unable to endure the abrupt climate changes of the Early Pleistocene, ultimately going extinct before the arrival of the extant counterpart, Odobenus rosmarus.

The microbiome of Total Suspended Particles (TSP) and its influence on the respiratory microbiome of healthy office workers

Air particulate matter (PM) is widely recognized for its potential to negatively affect human health, including changes in the upper respiratory microbiome. However, research on PM-associated microbiota remains limited and mostly focused on PM (e.g., PM 2.5 and PM 10 ). This study aims to characterize for the first time the microbiome of Total Suspended Particles (TSP) and investigate the correlations of indoor TSP with the human upper respiratory microbiome. Biological and environmental samples were collected over three collection periods lasting three weeks each, between May and July 2022 at the University of Milan and the University of Insubria Como. TSP were sampled using a filter-based technique, while respiratory samples from both anterior nares (AN) and the nasopharynx (NP) were collected using swabs. Microbiome analysis of both human (N = 145) and TSP (N = 51) samples was conducted on metagenomic sequencing data. A comparison of indoor and outdoor TSP microbiomes revealed differences in microbial diversity and taxonomic composition. The indoor samples had higher relative abundance of environmental bacteria often associated with opportunistic infections like Paracoccus sp., as well as respiratory bacteria such as Staphylococcus aureus and Klebsiella pneumoniae . Additionally, both indoor and outdoor TSP samples contained broad spectrum antibiotic resistance genes. Indoor TSP exposure was negatively associated with commensal bacteria and positively associated with Staphylococcus aureus relative abundance. Finally, a correlation between the relative abundance of respiratory bacteria identified in the indoor TSP and the upper respiratory microbiome was found, suggesting a potential interaction between TSP and the upper airways.

Geometric morphometric analysis of the brainstem and cerebellum in Chiari I malformation

Background

Chiari I malformation (CMI) is characterized by inferior descent of the cerebellar tonsils through the foramen magnum and is associated with headache and neck pain. Many morphometric research efforts have aimed to describe CMI anatomy in the midsagittal plane using classical measurement techniques such as linear dimensions and angles. These methods are less frequently applied to parasagittal features and may fall short in quantifying more intricate anatomy with fewer distinct homologous landmarks.

Methods

Landmark-based geometric morphometric techniques were used to asses CMI morphology in five anatomical planes of interest.

Results

Significant shape differences between CMI and age/sex-matched controls were found in the midsagittal (Pseudo-F = 5.4841, p = 0.001) and axial planes through the rostral medulla (Pseudo-F = 7.6319, p = 0.001). In addition to tonsillar descent, CMI principal component 1 (PC1) scores in the midsagittal protocol were associated with marked anterior concavity of the brainstem and generalized verticality of the cerebellum with anterior rotation of its anterior lobe. In the axial medulla/cerebellum protocol, CMI PC1 scores were associated with greater anterior-posterior (A-P) dimension with loss of medial-lateral (M-L) dimension.

Discussion

These results suggest that CMI is associated with greater curvature of the brainstem and spinal cord, which may perturb normal neural activities and disrupt cerebrospinal fluid movements. Previous reports on the A-P diameter of the posterior fossa in CMI have conflicted; our findings of greater A-P cerebellar dimensionality with concomitant loss of width alludes to the possibility that more caudal aspects of the posterior cranial fossa are more bowl-like (homogenous in axial dimensions) and less trough-like or elongated in the M-L direction.

Identification and characterization of a skin microbiome on Caenorhabditis elegans suggests environmental microbes confer cuticle protection

In the wild, C. elegans are emersed in environments teeming with a veritable menagerie of microorganisms. The C. elegans cuticular surface serves as a barrier and first point of contact with their microbial environments. In this study, we identify microbes from C. elegans natural habitats that associate with its cuticle, constituting a simple "skin microbiome." We rear our animals on a modified CeMbio, mCeMbio, a consortium of ecologically relevant microbes. We first combine standard microbiological methods with an adapted micro skin-swabbing tool to describe the skin-resident bacteria on the C. elegans surface. Furthermore, we conduct 16S rRNA gene sequencing studies to identify relative shifts in the proportion of mCeMbio bacteria upon surface-sterilization, implying distinct skin- and gut-microbiomes. We find that some strains of bacteria, including Enterobacter sp. JUb101, are primarily found on the nematode skin, while others like Stenotrophomonas indicatrix JUb19 and Ochrobactrum vermis MYb71 are predominantly found in the animal's gut. Finally, we show that this skin microbiome promotes host cuticle integrity in harsh environments. Together, we identify a skin microbiome for the well-studied nematode model and propose its value in conferring host fitness advantages in naturalized contexts.

IMPORTANCE

The genetic model organism C. elegans has recently emerged as a tool for understanding host-microbiome interactions. Nearly all of these studies either focus on pathogenic or gut-resident microbes. Little is known about the existence of native, nonpathogenic skin microbes or their function. We demonstrate that members of a modified C. elegans model microbiome, mCeMbio, can adhere to the animal's cuticle and confer protection from noxious environments. We combine a novel micro-swab tool, the first 16S microbial sequencing data from relatively unperturbed C. elegans, and physiological assays to demonstrate microbially mediated protection of the skin. This work serves as a foundation to explore wild C. elegans skin microbiomes and use C. elegans as a model for skin research.

Mapping the geographical distribution of the mucosa-associated gut microbiome in GI-symptomatic children with autism spectrum disorder

Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by cognitive, behavioral, and communication impairments. In the past few years, it has been proposed that alterations in the gut microbiota may contribute to an aberrant communication between the gut and brain in children with ASD. Consistent with this notion, several studies have demonstrated that children with ASD have an altered fecal microbiota compared with typically developing (TD) children. However, it is unclear where along the length of the gastrointestinal (GI) tract these alterations in microbial communities occur. In addition, the variation between specific mucosa-associated communities remains unknown. To address this gap in knowledge of the microbiome associated with ASD, biopsies from the antrum, duodenum, ileum, right colon, and rectum of children with ASD and age- and sex-matched TD children were examined by 16S rRNA sequencing. We observed an overall elevated abundance of Bacillota and Bacteroidota and a decreased abundance of Pseudomonadota in all GI tract regions of both male and female children with ASD compared with TD children. Further analysis at the genera level revealed unique differences in the microbiome in the different regions of the GI tract in children with ASD compared with TD children. We also observed sex-specific differences in the gut microbiota composition in children with ASD. These data indicate that the microbiota of children with ASD is altered in multiple regions of the GI tract and that different anatomic locations have unique alterations in mucosa-associated bacterial genera.NEW & NOTEWORTHY Analysis in stool samples has shown gut microbiota alterations in children with autism spectrum disorder (ASD) compared with typically developing (TD) children. However, it is unclear which segment(s) of the gut exhibit alterations in microbiome composition. In this study, we examined microbiota composition along the gastrointestinal (GI) tract in the stomach, duodenum, ileum, right colon, and rectum. We found site-specific and sex-specific differences in the gut microbiota of children with ASD, compared with controls.

Does ecology shape geographical parthenogenesis? Evidence from the facultatively parthenogenetic stick insect Megacrania batesii

Closely related sexual and parthenogenetic species often show distinct distribution patterns, known as geographical parthenogenesis. Similar patterns, characterized by the existence of separate sexual and parthenogenetic populations across their natural range, can also be found in facultative parthenogens - species in which every female is capable of both sexual and parthenogenetic reproduction. The underlying mechanisms driving this phenomenon in nature remain unclear. Features of the habitat, such as differences in host-plant phenotypes or niche breadth, could favour sexual or asexual reproductive modes and thus help to explain geographical parthenogenesis in natural insect populations. Megacrania batesii is a facultatively parthenogenetic stick insect that displays geographical parthenogenesis in the wild. We aimed to explore whether sexual and parthenogenetic populations of M. batesii displayed niche differentiation or variations in niche breadth that could explain the separation of the two population types. To do this, we sampled host plants from across the range of M. batesii and quantified phenotypic traits that might affect palatability or accessibility for M. batesii, including leaf thickness, toughness, spike size and density, plant height, and chemical composition. We also quantified host-plant density, which could affect M. batesii dispersal. We found little evidence of phenotypic differences between host plants supporting sexual versus asexual M. batesii populations, and no difference in host-plant density or niche breadth between the two population types. Our results suggest that habitat parameters do not play a substantial role in shaping patterns of geographical parthenogenesis in wild populations of M. batesii. Instead, population sex ratio variation could result from interactions between the sexes or dispersal dynamics.

Behavioral Diversity Among Odonata Larvae Increases in Water with Greater Turbidity Under Captivity Conditions

Various factors, including environmental variables, influence the behavior of aquatic insects. However, our understanding of insect behavior and their relationships with these variables remains limited. One important variable is water turbidity, which may be exacerbated by soil erosion, directly impacting visibility in the water and potentially affecting the organism's behaviors. In this study, we investigated larval behavior across seven Odonata species under controlled conditions, examining variations in behavioral diversity (frequency and type) associated with sex and three levels of water turbidity. Our findings revealed that heightened water turbidity correlated with increased behavior frequency, possibly attributable to predator avoidance in darker, seemingly safer habitats. Furthermore, behavior diversity differed between sexes, being higher for males in certain categories and for females in others. Anisoptera species predominantly displayed behaviors like resting, eating, and prey capture, whereas Zygoptera larvae were often observed perching and walking, possibly indicative of distinct predator response strategies. Behaviors shared by Anisoptera larvae could be associated with similar responses to predators and capture of prey. Our study found an increased frequency of behaviors when the larvae are in water with higher turbidity. Behavior frequency disparities between the sexes were observed across various behaviors, likely influenced by species-specific activity levels and individual behavioral plasticity in response to environmental cues. Overall, individuals exhibited heightened behavioral activity in environments with elevated turbidity, potentially reflecting a perceived lower risk environment.

Desert plants, arbuscular mycorrhizal fungi and associated bacteria: Exploring the diversity and role of symbiosis under drought

Desert plants, such as Agave tequilana, A. salmiana and Myrtillocactus geometrizans, can survive harsh environmental conditions partly due to their symbiotic relationships with microorganisms, including arbuscular mycorrhizal fungi (AMF). Interestingly, some of these fungi also harbour endosymbiotic bacteria. Our research focused on investigating the diversity of these AMFs and their associated bacteria in these plants growing in arid soil. We found that agaves have a threefold higher AMF colonization than M. geometrizans. Metabarcoding techniques revealed that the composition of AMF communities was primarily influenced by the plant host, while the bacterial communities were more affected by the specific plant compartment or niche they inhabited. We identified both known and novel endofungal bacterial taxa, including Burkholderiales, and confirmed their presence within AMF spores using multiphoton microscopy. Our study also explored the effects of drought on the symbiosis between A. tequilana and AMF. We discovered that the severity of drought conditions could modulate the strength of this symbiosis and its outcomes for the plant holobiont. Severe drought conditions prevented the formation of this symbiosis, while moderate drought conditions promoted it, thereby conferring drought tolerance in A. tequilana. This research sheds light on the diversity of AMF and associated bacteria in Crassulacean Acid Metabolism (CAM) plants and underscores the crucial role of drought as a factor modulating the symbiosis between A. tequilana and AMF. Further research is needed to understand the role of endofungal bacteria in this response.

The growth promotion in endophyte symbiotic plants does not penalise the resistance to herbivores and bacterial microbiota

A trade-off between growth and defence against biotic stresses is common in plants. Fungal endophytes of the genus Epichloë may relieve this trade-off in their host grasses since they can simultaneously induce plant growth and produce antiherbivore alkaloids that circumvent the need for host defence. The Epichloë ability to decouple the growth-defence trade-off was evaluated by subjecting ryegrass with and without Epichloë endophytes to an exogenous treatment with gibberellin (GA) followed by a challenge with Rhopalosiphum padi aphids. In agreement with the endophyte-mediated trade-off decoupling hypothesis, the GA-derived promotion of plant growth increased the susceptibility to aphids in endophyte-free plants but did not affect the insect resistance in endophyte-symbiotic plants. In line with the unaltered insect resistance, the GA treatment did not reduce the concentration of Epichloë-derived alkaloids. The Epichloë mycelial biomass was transiently increased by the GA treatment but at the expense of hyphal integrity. The response of the phyllosphere bacterial microbiota to both GA treatment and Epichloë was also evaluated. Only Epichloë, and not the GA treatment, altered the composition of the phyllosphere microbiota and the abundance of certain bacterial taxa. Our findings clearly demonstrate that Epichloë does indeed relieve the plant growth-defence trade-off.

The immediate metabolomic effects of whole-genome duplication in the greater duckweed, Spirodela polyrhiza

PREMISE

In plants, whole-genome duplication (WGD) is a common mutation with profound evolutionary potential. Given the costs associated with a superfluous genome copy, polyploid establishment is enigmatic. However, in the right environment, immediate phenotypic changes following WGD can facilitate establishment. Metabolite abundances are the direct output of the cell's regulatory network and determine much of the impact of environmental and genetic change on the phenotype. While it is well known that an increase in the bulk amount of genetic material can increase cell size, the impact of gene dosage multiplication on the metabolome remains largely unknown.

METHODS

We used untargeted metabolomics on four genetically distinct diploid-neoautotetraploid pairs of the greater duckweed, Spirodela polyrhiza, to investigate how WGD affects metabolite abundances per cell and per biomass.

RESULTS

Autopolyploidy increased metabolite levels per cell, but the response of individual metabolites varied considerably. However, the impact on metabolite level per biomass was restricted because the increased cell size reduced the metabolite concentration per cell. Nevertheless, we detected both quantitative and qualitative effects of WGD on the metabolome. Many effects were strain-specific, but some were shared by all four strains.

CONCLUSIONS

The nature and impact of metabolic changes after WGD depended strongly on the genotype. Dosage effects have the potential to alter the plant metabolome qualitatively and quantitatively, but were largely balanced out by the reduction in metabolite concentration due to an increase in cell size in this species.

Population structure and pathogen interaction of Escherichia coli in freshwater: Implications of land-use for water quality and public health in Aotearoa New Zealand

Freshwater samples (n = 199) were obtained from 41 sites with contrasting land-uses (avian, low impact, dairy, urban, sheep and beef, and mixed sheep, beef and dairy) and the E. coli phylotype of 3980 isolates (20 per water sample enrichment) was determined. Eight phylotypes were identified with B1 (48.04%), B2 (14.87%) and A (14.79%) the most abundant. Escherichia marmotae (n = 22), and Escherichia ruysiae (n = 1), were rare (0.68%) suggesting that these environmental strains are unlikely to confound water quality assessments. Phylotypes A and B1 were overrepresented in dairy and urban sites (p < 0.0001), whilst B2 were overrepresented in low impact sites (p < 0.0001). Pathogens ((Salmonella, Campylobacter, Cryptosporidium or Giardia) and the presence of diarrhoeagenic E. coli-associated genes (stx and eae) were detected in 89.9% (179/199) samples, including 80.5% (33/41) of samples with putative non-recent faecal inputs. Quantitative PCR to detect microbial source tracking targets from human, ruminant and avian contamination were concordant with land-use type and E. coli phylotype abundance. This study demonstrated that a potential recreational health risk remains where pathogens occurred in water samples with low E. coli concentration, potential non-recent faecal sources, low impact sites and where human, ruminant and avian faecal sources were absent.

Neuroanatomy and pneumaticity of the extinct Malagasy "horned" crocodile Voay robustus and its implications for crocodylid phylogeny and palaeoecology

Voay robustus, the extinct Malagasy "horned" crocodile, was originally considered to be the only crocodylian representative in Madagascar during most part of the Holocene. However, Malagasy crocodylian remains have had confused taxonomic attributions and recent studies have underlined that Crocodylus and Voay populations coexisted on the island for at least 7500 years. Here, we describe the inner braincase anatomy of Voay robustus using x-ray computed tomography on four specimens, to provide new anatomical information that distinguishes Voay from Crocodylus, especially features of the brain endocast and the paratympanic sinuses. Geometric morphometric analyses are performed on 3D models of the internal organs to compare statistically Voay with a subset of extant Crocodylidae. Following these comparisons, we build an endocranial morphological matrix to discuss the proposed phylogenetic affinities of Voay with Osteolaeminae from an endocranial point of view. Additionally, we discuss the use of internal characters in systematic studies and find that they can have a major impact on morphological analyses. Finally, new radiocarbon data on Voay and subfossil Crocodylus specimens are recovered between 2010 and 2750 cal BP, which confirm the cohabitation of the two species in the same area for a long period of time. We thus assess several extinction scenarios, and propose a slightly different ecology of Voay compared to Crocodylus, which could have allowed habitat partitioning on the island. Our approach complements information obtained from previous molecular and morphological phylogenies, as well as previous radiocarbon dating, together revealing past diversity and faunal turnovers in Madagascar.

Stable flies are bona fide carriers of mastitis-associated bacteria

Hematophagous Stomoxys (stable) fly populations in dairy barns are sustained by a constant availability of cattle hosts and manure, which serve as major reservoirs of both zoonotic and opportunistic bacterial pathogens. However, the composition of the Stomoxys fly microbiota, the mechanisms by which flies acquire their microbiome, and the ability of potentially pathogenic bacteria to colonize and persist in fly hosts remain to be investigated. Here, we longitudinally collected fly and manure samples from two connected dairy facilities. High throughput 16S rRNA gene amplicon sequencing was then used to characterize and compare bacterial communities present on or within flies and in manure collected from the same facility, while culture-dependent methods were used to verify the viability of clinically relevant bacteria. Bacterial alpha diversity was overall higher in manure samples as compared to fly samples, with manure-associated bacterial communities being dominated by members of the Bacteroidales, Eubacteriales, and Oscillospirales. In contrast, flies harbored relatively low-complexity communities dominated by members of the Enterobacterales, Staphylococcales, and Lactobacillales. Clinically relevant bacterial strains, including Escherichia spp. and other taxa associated with mastitic cows housed in the same facilities, were detected in paired fly and manure samples but exhibited dramatically elevated abundances in fly samples as compared to manure samples. Viable colonies of Escherichia, Klebsiella, and Staphylococcus spp. were also readily isolated from fly samples, confirming that flies harbor culturable mastitis-associated bacteria. This study identifies biting flies as bona fide carriers of opportunistically pathogenic bacterial taxa on dairy farms.

IMPORTANCE

Disease prevention on dairy farms has significant implications for cattle health, food security, and zoonosis. Of particular importance is the control of bovine mastitis, which can be caused by diverse bacteria, including Klebsiella, Escherichia coli, Streptococcus, and Staphylococcus spp. Despite being one of the most significant and costly cattle diseases worldwide, the epidemiology of bovine mastitis is not well understood. This study provides parallel culture-independent and culture-dependent evidence to support the carriage of opportunistically pathogenic bacteria by Stomoxys flies on dairy farms. We further show that the fly microbiota is enriched in clinically relevant taxa-the vast majority of which can be traced to the manure habitats in which flies breed. Altogether, our results identify biting flies as underrecognized carriers of bacterial taxa associated with environmental bovine mastitis and other opportunistic infections in vertebrates and offer important insights into mechanisms of microbial acquisition by these and other medically important insects.

Measurements of soil protist richness and community composition are influenced by primer pair, annealing temperature, and bioinformatics choices

Protists are a diverse and understudied group of microbial eukaryotic organisms especially in terrestrial environments. Advances in molecular methods are increasing our understanding of the distribution and functions of these creatures; however, there is a vast array of choices researchers make including barcoding genes, primer pairs, PCR settings, and bioinformatic options that can impact the outcome of protist community surveys. Here, we tested four commonly used primer pairs targeting the V4 and V9 regions of the 18S rRNA gene using different PCR annealing temperatures and processed the sequences with different bioinformatic parameters in 10 diverse soils to evaluate how primer pair, amplification parameters, and bioinformatic choices influence the composition and richness of protist and non-protist taxa using Illumina sequencing. Our results showed that annealing temperature influenced sequencing depth and protist taxon richness for most primer pairs, and that merging forward and reverse sequencing reads for the V4 primer pairs dramatically reduced the number of sequences and taxon richness of protists. The data sets of primers that targeted the same 18S rRNA gene region (e.g., V4 or V9) had similar protist community compositions; however, data sets from primers targeting the V4 18S rRNA gene region detected a greater number of protist taxa compared to those prepared with primers targeting the V9 18S rRNA region. There was limited overlap of protist taxa between data sets targeting the two different gene regions (80/549 taxa). Together, we show that laboratory and bioinformatic choices can substantially affect the results and conclusions about protist diversity and community composition using metabarcoding.IMPORTANCEEcosystem functioning is driven by the activity and interactions of the microbial community, in both aquatic and terrestrial environments. Protists are a group of highly diverse, mostly unicellular microbes whose identity and roles in terrestrial ecosystem ecology have been largely ignored until recently. This study highlights the importance of choices researchers make, such as primer pair, on the results and conclusions about protist diversity and community composition in soils. In order to better understand the roles protist taxa play in terrestrial ecosystems, biases in methodological and analytical choices should be understood and acknowledged.

Consistent prokaryotic community patterns along the radial root axis of two Zea mays L. landraces across two distinct field locations

The close interconnection of plants with rhizosphere- and root-associated microorganisms is well recognized, and high expectations are raised for considering their symbioses in the breeding of future crop varieties. However, it is unclear how consistently plant-mediated selection, a potential target in crop breeding, influences microbiome members compared to selection imposed by the agricultural environment. Landraces may have traits shaping their microbiome, which were lost during the breeding of modern varieties, but knowledge about this is scarce. We investigated prokaryotic community composition along the radial root axis of two European maize (Zea mays L.) landraces. A sampling gradient included bulk soil, a distal and proximal rhizosphere fraction, and the root compartment. Our study was replicated at two field locations with differing edaphic and climatic conditions. Further, we tested for differences between two plant developmental stages and two precipitation treatments. Community data were generated by metabarcoding of the V4 SSU rRNA region. While communities were generally distinct between field sites, the effects of landrace variety, developmental stage, and precipitation treatment were comparatively weak and not statistically significant. Under all conditions, patterns in community composition corresponded strongly to the distance to the root. Changes in α- and β-diversity, as well as abundance shifts of many taxa along this gradient, were similar for both landraces and field locations. Most affected taxa belonged to a core microbiome present in all investigated samples. Remarkably, we observed consistent enrichment of Actinobacteriota (particularly Streptomyces, Lechevalieria) and Pseudomonadota (particularly Sphingobium) toward the root. Further, we report a depletion of ammonia-oxidizers along this axis at both field sites. We identified clear enrichment and depletion patterns in microbiome composition along the radial root axis of Z. mays. Many of these were consistent across two distinct field locations, plant developmental stages, precipitation treatments, and for both landraces. This suggests a considerable influence of plant-mediated effects on the microbiome. We propose that the affected taxa have key roles in the rhizosphere and root microbiome of Z. mays. Understanding the functions of these taxa appears highly relevant for the development of methods aiming to promote microbiome services for crops.

Zygoptera / Anisoptera (Insecta: Odonata) ratio as a tool to assess anthropogenic changes in Brazilian Cerrado streams

Aquatic ecosystems are among the most affected by anthropogenic impacts, and the rapid detection and measurement of these impacts are of great importance for the maintenance of such environments. The order of aquatic insects Odonata has emerged as an important bioindicator of environmental quality due to its sensitivity to environmental changes and its ecophysiological requirements, which make them closely associated with habitat conditions. The aim of this study was to test whether the Zygoptera/Anisoptera ratio can be used as an effective tool to assess anthropogenic changes in Cerrado streams. Our hypothesis is that the proportion of Zygoptera/Anisoptera is an efficient tool for measuring environmental alterations in Cerrado streams, with a positive relationship between habitat integrity and the proportion of Zygoptera and an inverse relationship with the proportion of Anisoptera. Adults were collected in 44 streams of the Cerrado Biome in the eastern Maranhão state. The Habitat Integrity Index (HII) was used to verify the environmental gradient. Our hypothesis was corroborated, with a positive relationship between the richness and abundance of Zygoptera and HII, while an inverse relationship was observed for Anisoptera. According to our results, streams exhibiting a Zygoptera abundance of 68% or higher and richness of 58% or higher can be classified as preserved, while those showing an Anisoptera abundance and richness surpassing 31% and 41%, respectively, may be deemed altered. The patterns detected in the Cerrado were similar to those found in studies of the Amazon Biome and the Atlantic Forest, confirming the effectiveness of this method even for naturally open environments, such as the Cerrado. We conclude, therefore, that this method can be used as a tool to generate rapid results in monitoring studies, with low cost and easy application, enabling the development of mitigation, control, and conservation measures for extremely threatened environments such as those found in the Cerrado Biome.

The methane-oxidizing microbial communities of three maar lakes in tropical monsoon Asia

Methane-oxidizing bacteria (MOB) is a group of planktonic microorganisms that use methane as their primary source of cellular energy. For tropical lakes in monsoon Asia, there is currently a knowledge gap on MOB community diversity and the factors influencing their abundance. Herewith, we present a preliminary assessment of the MOB communities in three maar lakes in tropical monsoon Asia using Catalyzed Reporter Deposition, Fluorescence In-Situ Hybridization (CARD-FISH), 16S rRNA amplicon sequencing, and pmoA gene sequencing. Correlation analysis between MOB abundances and lakes' physicochemical parameters following seasonal monsoon events were performed to explain observed spatial and temporal patterns in MOB diversity. The CARD-FISH analyses detected the three MOB types (I, II, and NC10) which aligned with the results from 16S rRNA amplicons and pmoA gene sequencing. Among community members based on 16S rRNA genes, Proteobacterial Type I MOB (e.g., Methylococcaceae and Methylomonadaceae), Proteobacterial Type II (Methylocystaceae), Verrucomicrobial (Methylacidiphilaceae), Methylomirabilota/NC10 (Methylomirabilaceae), and archaeal ANME-1a were found to be the dominant methane-oxidizers in three maar lakes. Analysis of microbial diversity and distribution revealed that the community compositions in Lake Yambo vary with the seasons and are more distinct during the stratified period. Temperature, DO, and pH were significantly and inversely linked with type I MOB and Methylomirabilota during stratification. Only MOB type I was influenced by monsoon changes. This research sought to establish a baseline for the diversity and ecology of planktonic MOB in tropical monsoon Asia to better comprehend their contribution to the CH4 cycle in tropical freshwater ecosystems.

Anthropogenic land uses lead to changes in limnological variables in Neotropical streams

Streams are vulnerable to anthropogenic impacts, such as changes in land use, which reflect on water quality and can be evaluated by abiotic variables. In this context, the aims were to compare the abiotic values recorded in streams of different land use categories with the limits established by National legislation, and to analyze changes in abiotic variables in response to different land use impacts. Thus, 17 streams located in southern Brazil were sampled and grouped into urban, rural, and protected areas (PA) categories. The results showed the major impacts in urban streams. However, some variables in rural streams and PA also exceeded local legislation limits. Conductivity, total dissolved solids, salinity, ammoniacal nitrogen and coliforms were significantly higher in the urban streams. Contrary to expectations, the highest levels of manganese were found in PA streams. The relationship between abiotic variables and land uses suggests possible contamination by sewage in urban streams and by pesticides in rural streams. The abiotic similarity between rural and PA streams indicates that the conservation of these water bodies is ineffective. We suggest the monitoring of these environments and measures to mitigate the impacts to seek the restoration of ecosystem services and the well-being of human populations.

Uncovering the Role of Autochthonous Deteriogenic Biofilm Community: Rožanec Mithraeum Monument (Slovenia)

The primary purpose of the study, as part of the planned conservation work, was to uncover all aspects of autochthonous biofilm pertaining to the formation of numerous deterioration symptoms occurring on the limestone Rožanec Mithraeum monument in Slovenia. Using state-of-the-art sequencing technologies combining mycobiome data with observations made via numerous light and spectroscopic (FTIR and Raman) microscopy analyses pointed out to epilithic lichen Gyalecta jenensis and its photobiont, carotenoid-rich Trentepohlia aurea, as the origin of salmon-hued pigmented alterations of limestone surface. Furthermore, the development of the main deterioration symptom on the monument, i.e., biopitting, was instigated by the formation of typical endolithic thalli and ascomata of representative Verrucariaceae family (Verrucaria sp.) in conjunction with the oxalic acid-mediated dissolution of limestone. The domination of lichenized fungi, as the main deterioration agents, both on the relief and surrounding limestone, was additionally supported by the high relative abundance of lichenized and symbiotroph groups in FUNGuild analysis. Obtained results not only upgraded knowledge of this frequently occurring but often overlooked group of extremophilic stone heritage deteriogens but also provided a necessary groundwork for the development of efficient biocontrol formulation applicable in situ for the preservation of similarly affected limestone monuments.

No colonization resistance to Campylobacter jejuni in broilers fed brown algal extract-supplemented diets

Introduction

Campylobacter jejuni gastroenteritis is the most commonly reported zoonosis within the EU, with poultry products regarded as the primary source of transmission to humans. Therefore, finding strategies to reduce Campylobacter colonization in broilers holds importance for public health. Recent studies suggest that supplementation of broiler feed with brown algal extracts, particularly laminarin, can provide beneficial effects on broiler gut health, growth performance, and gut microbiota. However, its effect on gut microbiota development and subsequent reduction of Campylobacter loads in broiler caeca during the later stages of the birds' lives remains unclear.

Methods

Experimental colonization of Ross 308 broilers with two different strains of C. jejuni was conducted, with groups fed either a basal diet or the same basal diet supplemented with 725 ppm algal extract from Saccharina latissima to provide 290 ppm laminarin. Fecal samples were collected for bacterial enumeration, and caecal samples were obtained before and after the C. jejuni challenge for the determination of microbiota development.

Results and discussion

No significant differences in fecal C. jejuni concentrations between the groups fed different diets or exposed to different C. jejuni strains were observed. This suggests that both strains colonized the birds equally well and that the laminarin rich algal extract did not have any inhibitory effect on C. jejuni colonization. Notably, 16S rRNA amplicon sequencing revealed detailed data on the caecal microbiota development, likely influenced by both bird age and C. jejuni colonization, which can be valuable for further development of broiler feed formulations aimed at promoting gut health.

Detecting mining impacts on freshwater ecosystems using replicated sampling before and after the impact

Detecting human impact on freshwater ecosystems is problematic without rigorous assessment of temporal changes. Assessments of mining impacts are further complicated by the strong influence of local catchment geology on surface waters even in unmined environments. Such influence cannot be effectively considered by using broad-scale reference frameworks based on regionalization and stream types. Using the BACI (Before-After Control-Impact) design, we examined the impact of mining discharges on freshwater algae and macroinvertebrate communities resulting from the rerouting of treated wastewaters through a pipeline to larger water bodies in Northern and North-Eastern Finland. Impacted sites and control sites were sampled 1 to 2 years before and 1 to 3 years after the pipelines became operational. Stream diatom communities recovered from past loadings upstream of the pipeline (which was no longer impacted by wastewaters) after rerouting of the wastewaters, while no changes downstream from the pipeline were detected. Upstream from the pipeline, diatom species richness increased and changes in relative abundances of the most common diatom taxa as well as in the overall community composition were observed. The effects of the pipeline were less evident for stream macroinvertebrate communities. There was an indication that regional reference conditions used in national biomonitoring may not represent diatom communities in areas with a strong geochemical background influence. Lake profundal macroinvertebrate communities were impacted by past loadings before the construction of the pipeline, and the influence of the pipeline was observed only as changes in the abundances of a few individual species such as phantom midges (which increased in abundance in response to discharges directed through the pipeline). Our results highlight the variable influence of mining discharges on aquatic communities. Statistically strong monitoring programmes, such as BACI designs, are clearly needed to detect these influences.

Tobacco crop rotation enhances the stability and complexity of microbial networks

Introduction

The effects of continuous cropping and rotation cropping, two important tobacco cultivation practices, on soil microbial communities at different stages remain unclear. Different planting patterns have been shown to influence soil physical and chemical properties, which in turn can affect the composition and diversity of soil microbial communities.

Methods

In order to investigate the impact of different planting methods on soil microbial community structure, we selected two representative planting methods: continuous cropping (tobacco) and rotational cropping (tobacco-maize). These methods were chosen as the focal points of our research to explore the potential effects on soil microbial communities. High-throughput sequencing technology was employed to investigate the structure of soil microbial communities, as well as their relationships with soil environmental factors, by utilizing the 16S rRNA, ITS, and 18S genes. Furthermore, the interaction among microorganisms was explored through the application of the Random Matrix Theory (RMT) molecular ecological network approach.

Results

There was no significant difference in α diversity, but significant difference in β diversity based on Jaccard distance test. Compared to continuous cropping, crop rotation significantly increased the abundance of beneficial prokaryotes Verrucomicrobia and Rhodanobacter. These findings indicate that crop rotation promotes the enrichment of Verrucomicrobia and Rhodanobacter in the soil microbial community. AP and NH4-N had a greater effect on the community structure of prokaryotes and fungi in tobacco soil, while only AP had a greater effect on the community structure of protist. Molecular ecological network analysis showed that the network robustness and Cohesion of rotation were significantly higher than that of continuous cropping, indicating that the complexity and stability of molecular ecological networks were higher in the rotational, and the microbial communities cooperated more effectively, and the community structure was more stable.

Discussion

From this point of view, rotational cropping is more conducive to changing the composition of soil microbial community, enhancing the stability of microbial network structure, and enhancing the potential ecological functions in soil.

The impact of kit, environment, and sampling contamination on the observed microbiome of bovine milk

In low-microbial biomass samples such as bovine milk, contaminants can outnumber endogenous bacteria. Because of this, milk microbiome research suffers from a critical knowledge gap, namely, does non-mastitis bovine milk contain a native microbiome? In this study, we sampled external and internal mammary epithelia and stripped and cisternal milk and used numerous negative controls, including air and sampling controls and extraction and library preparation blanks, to identify the potential sources of contamination. Two algorithms were used to mathematically remove contaminants and track the potential movement of microbes among samples. Results suggest that the majority (i.e., >75%) of sequence data generated from bovine milk and mammary epithelium samples represents contaminating DNA. Contaminants in milk samples were primarily sourced from DNA extraction kits and the internal and external skin of the teat, while teat canal and apex samples were mainly contaminated during the sampling process. After decontamination, the milk microbiome displayed a more dispersed, less diverse, and compositionally distinct bacterial profile compared with epithelial samples. Similar microbial compositions were observed between cisternal and stripped milk samples, as well as between teat apex and canal samples. Staphylococcus and Acinetobacter were the predominant genera detected in milk sample sequences, and bacterial culture showed growth of Staphylococcus and Corynebacterium spp. in 50% (7/14) of stripped milk samples and growth of Staphylococcus spp. in 7% (1/14) of cisternal milk samples. Our study suggests that microbiome data generated from milk samples obtained from clinically healthy bovine udders may be heavily biased by contaminants that enter the sample during sample collection and processing workflows.IMPORTANCEObtaining a non-contaminated sample of bovine milk is challenging due to the nature of the sampling environment and the route by which milk is typically extracted from the mammary gland. Furthermore, the very low bacterial biomass of bovine milk exacerbates the impacts of contaminant sequences in downstream analyses, which can lead to severe biases. Our finding showed that bovine milk contains very low bacterial biomass and each contamination event (including sampling procedure and DNA extraction process) introduces bacteria and/or DNA fragments that easily outnumber the native bacterial cells. This finding has important implications for our ability to draw robust conclusions from milk microbiome data, especially if the data have not been subjected to rigorous decontamination procedures. Based on these findings, we strongly urge researchers to include numerous negative controls into their sampling and sample processing workflows and to utilize several complementary methods for identifying potential contaminants within the resulting sequence data. These measures will improve the accuracy, reliability, reproducibility, and interpretability of milk microbiome data and research.

Methanol as a co-substrate with CO2 enhances butyrate production in microbial electrosynthesis

Methanol is a promising feedstock for the bio-based economy as it can be derived from organic waste streams or produced electrochemically from CO2. Acetate production from CO2 in microbial electrosynthesis (MES) has been widely studied, while more valuable compounds such as butyrate are currently attracting attention. In this study, methanol was used as a co-substrate with CO2 to enhance butyrate production in MES. Feeding with CO2 and methanol resulted in the highest butyrate production rates and titres of 0.36 ± 0.01 g L-1 d-1 and 8.6 ± 0.2 g L-1, respectively, outperforming reactors with only CO2 feeding (0.20 ± 0.03 g L-1 d-1 and 5.2 ± 0.1 g L-1, respectively). Methanol acted as electron donor and as carbon source, both of which contributed ca. 50% of the carbon in the products. Eubacterium was the dominant genus with 52.6 ± 2.5% relative abundance. Thus, we demonstrate attractive route for the use of the C1 substrates, CO2 and methanol, to produce mainly butyrate. KEY POINTS: • Butyrate was the main product from methanol and CO2 in MES • Methanol acted as both carbon and electron source in MES • Eubacterium dominating microbial culture was enriched in MES.

Study on intestinal parasitic infections and gut microbiota in cancer patients at a tertiary teaching hospital in Malaysia

Intestinal parasitic infections (IPIs) can lead to significant morbidity and mortality in cancer patients. While they are unlikely to cause severe disease and are self-limiting in healthy individuals, cancer patients are especially susceptible to opportunistic parasitic infections. The gut microbiota plays a crucial role in various aspects of health, including immune regulation and metabolic processes. Parasites occupy the same environment as bacteria in the gut. Recent research suggests intestinal parasites can disrupt the normal balance of the gut microbiota. However, there is limited understanding of this co-infection dynamic among cancer patients in Malaysia. A study was conducted to determine the prevalence and relationship between intestinal parasites and gut microbiota composition in cancer patients. Stool samples from 134 cancer patients undergoing active treatment or newly diagnosed were collected and examined for the presence of intestinal parasites and gut microbiota composition. The study also involved 17 healthy individuals for comparison and control. Sequencing with 16S RNA at the V3-V4 region was used to determine the gut microbial composition between infected and non-infected cancer patients and healthy control subjects. The overall prevalence of IPIs among cancer patients was found to be 32.8%. Microsporidia spp. Accounted for the highest percentage at 20.1%, followed by Entamoeba spp. (3.7%), Cryptosporidium spp. (3.0%), Cyclospora spp. (2.2%), and Ascaris lumbricoides (0.8%). None of the health control subjects tested positive for intestinal parasites. The sequencing data analysis revealed that the gut microbiota diversity and composition were significantly different in cancer patients than in healthy controls (p < 0.001). A significant dissimilarity was observed in the bacterial composition between parasite-infected and non-infected patients based on Bray-Curtis (p = 0.041) and Jaccard (p = 0.021) measurements. Bacteria from the genus Enterococcus were enriched in the parasite-infected groups, while Faecalibacterium prausnitzii reduced compared to non-infected and control groups. Further analysis between different IPIs and non-infected individuals demonstrated a noteworthy variation in Entamoeba-infected (unweighted UniFrac: p = 0.008), Cryptosporidium-infected (Bray-Curtis: p = 0.034) and microsporidia-infected (unweighted: p = 0.026; weighted: p = 0.019; Jaccard: p = 0.031) samples. No significant dissimilarity was observed between Cyclospora-infected groups and non-infected groups. Specifically, patients infected with Cryptosporidium and Entamoeba showed increased obligate anaerobic bacteria. Clostridiales were enriched with Entamoeba infections, whereas those from Coriobacteriales decreased. Bacteroidales and Clostridium were found in higher abundance in the gut microbiota with Cryptosporidium infection, while Bacillales decreased. Additionally, bacteria from the genus Enterococcus were enriched in microsporidia-infected patients. In contrast, bacteria from the Clostridiales order, Faecalibacterium, Parabacteroides, Collinsella, Ruminococcus, and Sporosarcina decreased compared to the non-infected groups. These findings underscore the importance of understanding and managing the interactions between intestinal parasites and gut microbiota for improved outcomes in cancer patients.

Deterministic processes dominate microbial assembly mechanisms in the gut microbiota of cold-water fish between summer and winter

Exploring the effects of seasonal variation on the gut microbiota of cold-water fish plays an important role in understanding the relationship between seasonal variation and cold-water fish. Gut samples of cold-water fish and environmental samples were collected during summer and winter from the lower reaches of the Yalong River. The results of the 16S rRNA sequencing showed that significant differences were identified in the composition and diversity of gut bacteria of cold-water fish. Co-occurrence network complexity of the gut bacteria of cold-water fish was higher in summer compared to winter (Sum: nodes: 256; edges: 20,450; Win: nodes: 580; edges: 16,725). Furthermore, from summer to winter, the contribution of sediment bacteria (Sum: 5.3%; Win: 23.7%) decreased in the gut bacteria of cold-water fish, while the contribution of water bacteria (Sum: 0%; Win: 27.7%) increased. The normalized stochastic ratio (NST) and infer community assembly mechanisms by phylogenetic bin-based null model analysis (iCAMP) showed that deterministic processes played a more important role than stochastic processes in the microbial assembly mechanism of gut bacteria of cold-water fish. From summer to winter, the contribution of deterministic processes to gut bacteria community assembly mechanisms decreased, while the contribution of stochastic processes increased. Overall, these results demonstrated that seasonal variation influenced the gut bacteria of cold-water fish and served as a potential reference for future research to understand the adaptation of fish to varying environments.

Gut microbiota from B-cell-specific TLR9-deficient NOD mice promote IL-10+ Breg cells and protect against T1D

Introduction

Type 1 diabetes (T1D) is an autoimmune disease characterized by the destruction of insulin-producing β cells. Toll-like receptor 9 (TLR9) plays a role in autoimmune diseases, and B cell-specific TLR9 deficiency delays T1D development. Gut microbiota are implicated in T1D, although the relationship is complex. However, the impact of B cell-specific deficiency of TLR9 on intestinal microbiota and the impact of altered intestinal microbiota on the development of T1D are unclear.

Objectives

This study investigated how gut microbiota and the intestinal barrier contribute to T1D development in B cell-specific TLR9-deficient NOD mice. Additionally, this study explored the role of microbiota in immune regulation and T1D onset.

Methods

The study assessed gut permeability, gene expression related to gut barrier integrity, and gut microbiota composition. Antibiotics depleted gut microbiota, and fecal samples were transferred to germ-free mice. The study also examined IL-10 production, Breg cell differentiation, and their impact on T1D development.

Results

B cell-specific TLR9-deficient NOD mice exhibited increased gut permeability and downregulated gut barrier-related gene expression. Antibiotics restored gut permeability, suggesting microbiota influence. Altered microbiota were enriched in Lachnospiraceae, known for mucin degradation. Transferring this microbiota to germ-free mice increased gut permeability and promoted IL-10-expressing Breg cells. Rag-/- mice transplanted with fecal samples from Tlr9 fl/fl Cd19-Cre+ mice showed delayed diabetes onset, indicating microbiota's impact.

Conclusion

B cell-specific TLR9 deficiency alters gut microbiota, increasing gut permeability and promoting IL-10-expressing Breg cells, which delay T1D. This study uncovers a link between TLR9, gut microbiota, and immune regulation in T1D, with implications for microbiota-targeted T1D therapies.

Vertical Stratification of Solitary Bees and Wasps in an Urban Forest from the Brazilian Amazon

Solitary bees and wasps that nest in cavities in tree trunks are important components of terrestrial ecosystems, providing pollination services, and in the case of wasps, the regulation of their prey populations. However, little is known about the vertical strata where bees and wasps build their nests. This is especially the case of urban forest remnants in the Amazon, which is relevant in the context of the global crisis in insect losses. We investigated the existence of vertical stratification in the nesting of solitary bees and wasps in an urban forest in Rio Branco, state of Acre, in the western Brazilian Amazon. We focused on whether wood temperature, ants, and termites are predictors of bee and wasp nesting. We sampled bee and wasp nests in the forest using trap-nests made with wooden blocks containing cavities with three different diameters for twelve months. Trap-nests were installed randomly at three heights in the forest. We collected 145 nests of 25 species, belonging to 11 genera and 6 families. A higher number of nests and species were collected in the upper stratum of the forest, strengthening the hypothesis that there is vertical stratification in the assemblage of solitary bees and wasps. Wood surface temperature and termite attacks on trap-nests were significantly different between strata, which may explain the vertical stratification of bee and wasp assemblages. Considering the importance of these insects for tropical forest ecosystems, the conservation of structurally complex and stratified forests is of paramount importance to maintain the diversity of this insect group.

A New Paradigm for High-dimensional Data: Distance-Based Semiparametric Feature Aggregation Framework via Between-Subject Attributes

This article proposes a distance-based framework incentivized by the paradigm shift towards feature aggregation for high-dimensional data, which does not rely on the sparse-feature assumption or the permutation-based inference. Focusing on distance-based outcomes that preserve information without truncating any features, a class of semiparametric regression has been developed, which encapsulates multiple sources of high-dimensional variables using pairwise outcomes of between-subject attributes. Further, we propose a strategy to address the interlocking correlations among pairs via the U-statistics-based estimating equations (UGEE), which correspond to their unique efficient influence function (EIF). Hence, the resulting semiparametric estimators are robust to distributional misspecification while enjoying root-n consistency and asymptotic optimality to facilitate inference. In essence, the proposed approach not only circumvents information loss due to feature selection but also improves the model's interpretability and computational feasibility. Simulation studies and applications to the human microbiome and wearables data are provided, where the feature dimensions are tens of thousands.

Hunting for pigments in bacterial settlers of the Great Pacific Garbage Patch

The Great Pacific Garbage Patch, a significant collection of plastic introduced by human activities, provides an ideal environment to study bacterial lifestyles on plastic substrates. We proposed that bacteria colonizing the floating plastic debris would develop strategies to deal with the ultraviolet-exposed substrate, such as the production of antioxidant pigments. We observed a variety of pigmentation in 67 strains that were directly cultivated from plastic pieces sampled from the Garbage Patch. The genomic analysis of four representative strains, each distinct in taxonomy, revealed multiple pathways for carotenoid production. These pathways include those that produce less common carotenoids and a cluster of photosynthetic genes. This cluster appears to originate from a potentially new species of the Rhodobacteraceae family. This represents the first report of an aerobic anoxygenic photoheterotrophic bacterium from plastic biofilms. Spectral analysis showed that the bacteria actively produce carotenoids, such as beta-carotene and beta-cryptoxanthin, and bacteriochlorophyll a. Furthermore, we discovered that the genetic ability to synthesize carotenoids is more common in plastic biofilms than in the surrounding water communities. Our findings suggest that plastic biofilms could be an overlooked source of bacteria-produced carotenoids, including rare forms. It also suggests that photoreactive molecules might play a crucial role in bacterial biofilm communities in surface water.

Adolescent alcohol use is associated with differences in the diversity and composition of the oral microbiome

BACKGROUND

Adolescence is a sensitive stage of oral microbial development that often coincides with the initiation and escalation of alcohol use. Thus, adolescents may be particularly susceptible to alcohol-induced alterations in the oral microbiome, though minimal research has been done in this area. Understanding the connection between the oral microbiome and alcohol use during adolescence is important to understand fully the biological consequences of alcohol use to mitigate potential adverse outcomes.

METHODS

Saliva samples were collected from adolescents aged 17-19 who used alcohol heavily (n = 21, 52.4% female) and those who did not use alcohol or any other substances (n = 18, 44.4% female). We utilized 16S rRNA sequencing to examine differences in microbial diversity and composition between the groups.

RESULTS

For alpha diversity, evenness was significantly lower in the drinking group than the control group as indicated by Pielou's evenness, Shannon, and Simpson indices. There were no statistically significant findings for beta diversity. Differential abundance analyses revealed higher abundances of Rothia and Corynebacterium in the alcohol-using group using both centered-log-ratio and relative abundance normalization. These genera are known for their high capacity to convert alcohol into acetaldehyde, a toxic metabolite reported to play a role in the neurobiological effects of alcohol. An unclassified Clostridia UCG-014, Streptobacillus, Comamonas, unclassified Lachnospiraceae, and Parvimonas were also identified as significantly different between groups when using only one of the normalization techniques.

CONCLUSIONS

This is the first study designed specifically to compare the oral microbiome of adolescents who use alcohol with that of control participants. Our findings reveal distinct alcohol-related differences in microbial composition and taxon abundance, emphasizing the importance of understanding the impact on the oral microbiome of alcohol use during adolescence. Because the oral microbiome is malleable, this study provides foundational work for future prevention and intervention studies.

Factors associated with seedling establishment on logs of different fungal decay types-A seed-sowing experiment

Wood decay fungi alter the abiotic and biotic properties of deadwood, which are important as nurse logs for seedling regeneration. However, the relationship between fungal decay type and seedling performance has not been evaluated experimentally. In this study, we examined the germination, growth, and survival of six arbuscular mycorrhizal (AM) and six ectomycorrhizal (ECM) tree species on three substrates (pine logs with brown and white rot and soil) by conducting seed-sowing experiments in a mixed forest dominated by Pinus densiflora and Quercus serrata. Analysis using ribosomal DNA internal transcribed spacer 1 (rDNA ITS1) sequencing revealed that the fungal community was significantly different across three substrates. The richness of operational taxonomic units (OTUs) of AM and ECM fungi was the largest on brown rot logs and soil, respectively. The substrate significantly affected the seedling performance when comparing wood decay types, but these were not consistent across the mycorrhizal status of the seedlings. Nevertheless, seedlings of some AM trees showed better growth and enhanced mycorrhizal colonization on brown rot logs than on white rot logs. The wood decay type influenced fungal communities in the logs and the performance of some seedling species partly by different mycorrhizal colonization rates. However, the effect was seedling species dependent and showed no apparent difference between AM and ECM trees.

Associational Effects of Desmodium Intercropping on Maize Resistance and Secondary Metabolism

Intercropping is drawing increasing attention as a strategy to increase crop yields and manage pest pressure, however the mechanisms of associational resistance in diversified cropping systems remain controversial. We conducted a controlled experiment to assess the impact of co-planting with silverleaf Desmodium (Desmodium uncinatum) on maize secondary metabolism and resistance to herbivory by the spotted stemborer (Chilo partellus). Maize plants were grown either in the same pot with a Desmodium plant or adjacent to it in a separate pot. Our findings indicate that co-planting with Desmodium influences maize secondary metabolism and herbivore resistance through both above and below-ground mechanisms. Maize growing in the same pot with a Desmodium neighbor was less attractive for oviposition by spotted stemborer adults. However, maize exposed only to above-ground Desmodium cues generally showed increased susceptibility to spotted stemborer herbivory (through both increased oviposition and larval consumption). VOC emissions and tissue secondary metabolite titers were also altered in maize plants exposed to Desmodium cues, with stronger effects being observed when maize and Desmodium shared the same pot. Specifically, benzoxazinoids were strongly suppressed in maize roots by direct contact with a Desmodium neighbor while headspace emissions of short-chain aldehydes and alkylbenzenes were increased. These results imply that direct root contact or soil-borne cues play an important role in mediating associational effects on plant resistance in this system.

Hierarchical diversity partitioning of microscopic epibiont community on intertidal molluscan shells and inert surfaces over three geographic regions in Japan

Microscopic epibionts on molluscan shells are a component of the biodiversity of intertidal coastal areas. Because molluscan shells are discrete habitats for the epibiont community, and the molluscan basibionts belong to the local community, epibiont diversity can be evaluated hierarchically by basibiont categories including species. To evaluate the structure of epibiont diversity and effects of taxonomic resolution on the evaluation, epibionts on molluscan shells and inert surfaces were investigated at three geographically distant sites in Japan. In total, 94 species-level taxonomic units of epibionts were obtained from 31 basibiont molluscan species and inert surfaces (plastics and rock chips). The density and the species richness at the site of the lowest latitude were significantly lower than those at the other sites. The epibiont community differed between the three sites, although the major portion of the epibionts were diatoms. Between-site diversity contributed most of the total diversity of the species richness and Simpson diversity in the five levels of the hierarchical partitioning: sample (individual basibiont), basibiont species (molluscan species), surface group (bivalves, chitons + limpets, and globose gastropods), site, and the total. The taxonomic resolution did not markedly affect the variability of communities between the three sites, although the taxon richness was reduced to 51 in the genus-level analysis. The lower taxonomic resolution (genus level); however, increased the contribution of the within-sample and decreased the contribution of β diversities at the higher hierarchies, leading to a possible overestimation of biotic homogenization between the communities.

Unveiling the hidden viromes across the animal tree of life: insights from a taxonomic classification pipeline applied to invertebrates of 31 metazoan phyla

Invertebrates constitute the majority of animal species on Earth, including most disease-causing agents or vectors, with more diverse viromes when compared to vertebrates. Recent advancements in high-throughput sequencing have significantly expanded our understanding of invertebrate viruses, yet this knowledge remains biased toward a few well-studied animal lineages. In this study, we analyze invertebrate DNA and RNA viromes for 31 phyla using 417 publicly available RNA-Seq data sets from diverse environments in the marine-terrestrial and marine-freshwater gradients. This study aims to (i) estimate virome compositions at the family level for the first time across the animal tree of life, including the first exploration of the virome in several phyla, (ii) quantify the diversity of invertebrate viromes and characterize the structure of invertebrate-virus infection networks, and (iii) investigate host phylum and habitat influence on virome differences. Results showed that a set of few viral families of eukaryotes, comprising Retroviridae, Flaviviridae, and several families of giant DNA viruses, were ubiquitous and highly abundant. Nevertheless, some differences emerged between phyla, revealing for instance a less diverse virome in Ctenophora compared to the other animal phyla. Compositional analysis of the viromes showed that the host phylum explained over five times more variance in composition than its habitat. Moreover, significant similarities were observed between the viromes of some phylogenetically related phyla, which could highlight the influence of co-evolution in shaping invertebrate viromes.IMPORTANCEThis study significantly enhances our understanding of the global animal virome by characterizing the viromes of previously unexamined invertebrate lineages from a large number of animal phyla. It showcases the great diversity of viromes within each phylum and investigates the role of habitat shaping animal viral communities. Furthermore, our research identifies dominant virus families in invertebrates and distinguishes phyla with analogous viromes. This study sets the road toward a deeper understanding of the virome across the animal tree of life.