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Storage time is considered to be one of the most important factors affecting the obnoxious odor and microbial spoilage of fresh meat. In this study, volatile organic compounds (VOCs) and bacterial community structure of chilled goose meat during storage were investigated. The results showed that numerous VOCs were produced during the fresh goose meat storage, including aldehydes (nonanal, (E)-2-octenal, hexanal, tetradecanal), alcohol (1-octen-3-ol), furan (2-pentylfuran), and carboxylic acids (methyl diethyldithiocarbamate), which might be a breakdown product during spoilage. In addition, there were slight fluctuations in fatty acid profiles and amino acid contents. Furthermore, bacterial community diversity decreased with prolonged storage. Also, Pseudomonas and Acinetobacter were the dominant spoilage bacteria contributing to nonanal and methyl diethyldithiocarbamate generation. Taken together, these data provide insights into the characterization of VOCs and the bacterial community of chilled goose meat, which will help to further control the microbial quality of chilled meat.

Plant domestication and breeding not only resulted in multiple phenotypic changes but also impacted the agricultural ecosystems in which our current crops are cultivated. Most crops to date rely on the extensive use of fertilizers and pesticides to support crop growth and health. To minimize the environmental impact of these management practices, the plant microbiome has gained renewed attention as a large yet untapped resource of microorganisms with beneficial effects on plant growth and health. In the past decade, it has become evident that the microbiome of plants plays a key role in nutrient acquisition, plant development, and tolerance to diverse abiotic and biotic stresses. Here, we review past and present knowledge of the microbiome of tomato as a model for unraveling the functional potential of plant microbiomes, the impact of domestication, and the underlying genetics of microbiome assembly and activity. We also provide perspectives on how this knowledge can be adopted to enhance crop productivity and strengthen the sustainability of agricultural management practices. [Graphic: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

ABSTRACTBackground Sufficient protein intake is essential for adequate physical condition and athletic performance. However, numerous factors can influence the absorption of consumed protein, including timing, type of protein intake, and gut microbiota. In the present study, elite male water polo players consumed a plant-based, vegan protein supplement with (n = 10) or without (n = 10) pre- and probiotics daily during the 31-day study period.Methods We determined the anthropometric characteristics and body composition, dietary habits, gut microbiota composition, and blood parameters of the players at the beginning and at the end of the study. Body composition parameters were analyzed using the InBody 970 bioimpedance analyzer. Gut microbiome composition was determined from stool samples by metagenome sequencing. Paired and unpaired t-tests were used to determine differences between body composition and blood parameters within the groups and between the two groups at the two different sampling times. The Wilcoxon test was used to determine the change in bacterial composition during the study. Correlations between changes in body composition, blood parameters, and taxonomic groups were analyzed using a linear correlation calculation.Results Skeletal muscle mass (p

Infertility is a disease with a complex pathophysiology and concurrent presence of gynaecological and reproductive disorders associated with it. A significant hurdle that infertility faces is the limitation of the success rate per couple per cycle in one assisted reproductive technology treatment. A central role is played by the complex embryo endometrial crosstalk that has been a subject of study since the very beginning of natural conception failures. The endometrium is a key player in the attempt for a healthy live birth. Thought to be previously sterile, the uterus is now known as home to a unique community of microorganisms. The microbiota and their genomic content: the endometrial microbiome is a complex and heterogeneous endocrine system that plays a pivotal role in the master orchestration of successful embryo implantation in a receptive uterine cavity. The microbial community inside the uterus is now known to influence reproductive pathologies and complex aetiologies that influence infertile outcomes. This review is aimed to understand the correlations of the endometrial microbiome and more specifically, bacterial communities and their pathophysiology in reproductive pathologies leading to infertility. The role of personalised regimens and therapies for treatment through nutritional, microbiotic or pharmaceutical interventions is discussed. The use of selected strains that are part of this bacterial community as probiotics could be a successful therapy for uterine diseases and concomitant infertility alongside nutritional and pharmaceutical interventions. Further longitudinal studies in infertile patients with specific pathologies with stratified selection are necessary to progress microbiome evaluation and eventually, modulation for infertility. [ABSTRACT FROM AUTHOR]

Objective: The objective of the study was to systematically investigate the association between gut microbiota (GM) abundance and Parkinson's disease (PD). Methods: PubMed, Medline, Cochrane Library and other literature datebase platforms were searched for eligible studies in the English-language from conception to March 1, 2024. Studies evaluating the association between GM and PD were included. The results of the included studies were analyzed using a random effects model with calculation of the mean difference (MD) with the 95 % confidence interval to quantify the incidence of differences in abundance of various bacterial families in PD patients. Continuous models were used to analyze the extracted data. Results: A total of 14 studies with 1045 PD cases and 821 healthy controls were included for data extraction and meta-analysis. All the included studies exhibited reasonable quality. The included studies reported the data on the ratios of 10 families of GM. Of these 10 microbiota families, Bifidobacteriaceae, Ruminococcaceae, Rikenellaceae, Lactobacillaceae, Verrucomicrobiaceae and Christensenellaceae were found to have increased ratios according to the pooled ratios, while Prevotellaceae, Lachnospiraceae, Erysipelotrichaceae and Faecalibacterium were decreased in PD cases. Conclusion: Patients in the PD cohort exhibited distinctive microbiota compositions compared to healthy individuals, with unique differential patterns in gut microbiome abundance at the phylum, family, and genus levels that may be associated wtih PD pathogenesis.

Wound healing is a complex process influenced by age, systemic conditions, and local factors. The wound microbiota's crucial role in this process is gaining recognition. This concise review outlines wound microbiota impacts on healing, emphasizing distinct phases like hemostasis, inflammation, and cell proliferation. Inflammatory responses, orchestrated by growth factors and cytokines, recruit neutrophils and monocytes to eliminate pathogens and debris. Notably, microbiota alterations relate to changes in wound healing dynamics. Commensal bacteria influence immune responses, keratinocyte growth, and blood vessel development. For instance, Staphylococcus epidermidis aids keratinocyte progression, while Staphylococcus aureus colonization impedes healing. Other bacteria like Group A Streptococcus spp. And Pseudomonas affect wound healing as well. Clinical applications of microbiota-based wound care are promising, with probiotics and specific bacteria like Acinetobacter baumannii aiding tissue repair through molecule secretion. Understanding microbiota influence on wound healing offers therapeutic avenues. Tailored approaches, including probiotics, prebiotics, and antibiotics, can manipulate the microbiota to enhance immune modulation, tissue repair, and inflammation control. Despite progress, critical questions linger. Determining the ideal microbiota composition for optimal wound healing, elucidating precise influence mechanisms, devising effective manipulation strategies, and comprehending the intricate interplay between the microbiota, host, and other factors require further exploration. [ABSTRACT FROM AUTHOR]

Norovirus infection is influenced by the presence of commensal bacteria, and both human and murine norovirus (MNV) bind to these bacteria. These virus–bacterial interactions, as well as MNV infection, promote the increased production of bacterial extracellular vesicles (bEVs). However, no correlation has been made between specific bacterial groups, their vesicles, and their impact on norovirus infection. The current study evaluated the impact of select bacterial compositions of murine microbiomes using antibiotic (ABX) cocktails on MNV infection and bEV production. The goal of this research was to determine if increases in bEVs following MNV infection in mice were associated with changes in specific bacterial populations. Bacterial taxa were found to be differentially abundant in both ABX-treated and untreated mice, with the greatest change in bacterial taxa seen in mice treated with a broad-spectrum ABX cocktail. Specifically, Lachnospiraeae were found to be differentially abundant between a variety of treatment factors, including MNV infection. Overall, these results demonstrate that MNV infection can alter the abundance of bacterial taxa within the microbiota, as well as their production of extracellular vesicles, and that the use of selective antibiotic treatments can allow the detection of viral impacts on the microbiome that might otherwise be masked. [ABSTRACT FROM AUTHOR]

Current visualizations in microbiome research rely on aggregations in taxonomic classifications or do not show less abundant taxa. We introduce Snowflake: a new visualization method that creates a clear overview of the microbiome composition in collected samples without losing any information due to classification or neglecting less abundant reads. Snowflake displays every observed OTU/ASV in the microbiome abundance table and provides a solution to include the data’s hierarchical structure and additional information obtained from downstream analysis (e.g., alpha- and beta-diversity) and metadata. Based on the value-driven ICE-T evaluation methodology, Snowflake was positively received. Experts in microbiome research found the visualizations to be user-friendly and detailed and liked the possibility of including and relating additional information to the microbiome’s composition. Exploring the topological structure of the microbiome abundance table allows them to quickly identify which taxa are unique to specific samples and which are shared among multiple samples (i.e., separating sample-specific taxa from the core microbiome), and see the compositional differences between samples. An R package for constructing and visualizing Snowflake microbiome composition graphs is available at https://gitlab.com/vda-lab/snowflake.

Introduction: Bats, along with their ectoparasites, harbor a wide diversity of symbiotic and potential pathogenic bacteria. Despite the enormous diversity of bats (181 species), few studies aimed to investigate the bacterial microbiome of Brazilian chiropterans and associated ectoparasites. This study aimed to characterize the bacterial microbiome of non-hematophagous bats and associated Streblidae flies and Macronyssidae and Spinturnicidae mites in the state of Mato Grosso do Sul, midwestern Brazil. Methods: Oral and rectal swabs were collected from 30 bats (Artibeus lituratus [n = 13], Artibeus planirostris [n = 9], Eptesicus furinalis [n = 5], Carollia perspicillata [n = 2], and Platyrrhinus lineatus [n = 1]). In addition, a total of 58 mites (15 Macronyssidae and 43 Spinturnicidae) and 48 Streblidae bat flies were collected from the captured bats. After DNA extraction and purification, each sample's bacterial composition was analyzed with metagenomic sequencing. Results: The microbiome composition of both oral and rectal bat swab samples showed that Gammaproteobacteria was the most abundant bacterial class. Spiroplasma, Wolbachia and Bartonella represented the most abundant genera in Streblidae flies. While Wolbachia (Alphaproteobacteria) was the most abundant genus found in Spinturnicidae, Arsenophonus (Gammaproteobacteria) was found in high abundance in Macronyssidae mites. In addition to characterizing the microbiome of each sample at the class and genus taxonomic levels, we identified medically significant bacteria able to infect both animals and humans in oral (Streptococcus and Anaplasma) and rectal swabs (Enterobacter, Klebsiella, Escherichia, Enterococcus, Streptococcus), Macronyssidae (Anaplasma, Bartonella, Ehrlichia) and Spinturnicidae (Anaplasma, Bartonella) mites as well as Streblidae flies (Spiroplasma, Bartonella). Discussion and conclusion: Besides expanding the knowledge on the bacterial microbiome of non-hematophagous bats and Streblidae flies from Brazil, the present work showed, for the first time, the bacterial community of bat-associated Macronyssidae and Spinturnicidae mites. [ABSTRACT FROM AUTHOR]

The gut microbiota plays a crucial role in animal health and homeostasis, particularly in endangered species conservation. This study investigated the fecal microbiota composition of European captive-bred African savanna elephants (Loxodonta africana) housed in French zoos, and compared it with wild African savanna elephants. Fecal samples were collected and processed for DNA extraction and amplicon sequencing of the 16S rRNA gene. The analysis of α and ß diversity revealed significant effects of factors such as diet, daily activity, and institution on microbiota composition. Specifically, provision of branches as part of the diet positively impacted microbiota diversity. Comparative analyses demonstrated distinct differences between captive and wild elephant microbiomes, characterized by lower bacterial diversity and altered co-occurrence patterns in the captive population. Notably, specific taxa were differentially abundant in captive and wild elephants, suggesting the influence of the environment on microbiota composition. Furthermore, the study identified a core association network shared by both captive and wild elephants, emphasizing the importance of certain taxa in maintaining microbial interactions. These findings underscore the impact of environment and husbandry factors on elephant gut microbiota, highlighting the benefits of dietary enrichment strategies in zoos to promote microbiome diversity and health. The study contributes to the broader understanding of host-microbiota interactions and provides insights applicable to conservation medicine and captive animal management. [ABSTRACT FROM AUTHOR]

IntroductionBats, along with their ectoparasites, harbor a wide diversity of symbiotic and potential pathogenic bacteria. Despite the enormous diversity of bats (181 species), few studies aimed to investigate the bacterial microbiome of Brazilian chiropterans and associated ectoparasites. This study aimed to characterize the bacterial microbiome of non-hematophagous bats and associated Streblidae flies and Macronyssidae and Spinturnicidae mites in the state of Mato Grosso do Sul, midwestern Brazil.MethodsOral and rectal swabs were collected from 30 bats (Artibeus lituratus [n = 13], Artibeus planirostris [n = 9], Eptesicus furinalis [n = 5], Carollia perspicillata [n = 2], and Platyrrhinus lineatus [n = 1]). In addition, a total of 58 mites (15 Macronyssidae and 43 Spinturnicidae) and 48 Streblidae bat flies were collected from the captured bats. After DNA extraction and purification, each sample’s bacterial composition was analyzed with metagenomic sequencing.ResultsThe microbiome composition of both oral and rectal bat swab samples showed that Gammaproteobacteria was the most abundant bacterial class. Spiroplasma, Wolbachia and Bartonella represented the most abundant genera in Streblidae flies. While Wolbachia (Alphaproteobacteria) was the most abundant genus found in Spinturnicidae, Arsenophonus (Gammaproteobacteria) was found in high abundance in Macronyssidae mites. In addition to characterizing the microbiome of each sample at the class and genus taxonomic levels, we identified medically significant bacteria able to infect both animals and humans in oral (Streptococcus and Anaplasma) and rectal swabs (Enterobacter, Klebsiella, Escherichia, Enterococcus, Streptococcus), Macronyssidae (Anaplasma, Bartonella, Ehrlichia) and Spinturnicidae (Anaplasma, Bartonella) mites as well as Streblidae flies (Spiroplasma, Bartonella).Discussion and conclusionBesides expanding the knowledge on the bacterial microbiome of non-hematophagous bats and Streblidae flies from Brazil, the present work showed, for the first time, the bacterial community of bat-associated Macronyssidae and Spinturnicidae mites.

The gut microbiota plays a crucial role in animal health and homeostasis, particularly in endangered species conservation. This study investigated the fecal microbiota composition of European captive-bred African savanna elephants (Loxodonta africana) housed in French zoos, and compared it with wild African savanna elephants. Fecal samples were collected and processed for DNA extraction and amplicon sequencing of the 16S rRNA gene. The analysis of α and β diversity revealed significant effects of factors such as diet, daily activity, and institution on microbiota composition. Specifically, provision of branches as part of the diet positively impacted microbiota diversity. Comparative analyses demonstrated distinct differences between captive and wild elephant microbiomes, characterized by lower bacterial diversity and altered co-occurrence patterns in the captive population. Notably, specific taxa were differentially abundant in captive and wild elephants, suggesting the influence of the environment on microbiota composition. Furthermore, the study identified a core association network shared by both captive and wild elephants, emphasizing the importance of certain taxa in maintaining microbial interactions. These findings underscore the impact of environment and husbandry factors on elephant gut microbiota, highlighting the benefits of dietary enrichment strategies in zoos to promote microbiome diversity and health. The study contributes to the broader understanding of host-microbiota interactions and provides insights applicable to conservation medicine and captive animal management.

Objective: The objective of this study is to compare the microbiome of healthy peri-implant sulcus (C) and peri-implantitis sulcus (U) from the same patient and analyze the difference in the microbiome composition. Materials and methods: DNA samples of subgingival biofilms from 10 C (control group) and 10 U (uncontrolled group) sites were sent to Microbiome Center in Korea Research Institute of Biomedical Science and analyzed using 16s rRNA gene amplification and sequencing (MiSeq, Illumina) and human oral microbiome database (HOMD). Results: At the phylum level, Firmicutes and Proteobacteria were more abundant in group C, while Firmicutes and Bacteroidetes were dominant in group U. At the genus level, the core peri-implant microbiome was Streptococcus in group C. On the other hand, the core peri-implant microbiome was Porphyromonas, especially P. gingivalis in group U. Conclusion: In this study, the microbiome composition of peri-implantitis sulcus was different from that of healthy peri-implant sulcus from the same patient. The peri-implantitis microbiome was pathogen-enriched and was similar to the microbiome associated with periodontitis.

Wound healing is a complex process influenced by age, systemic conditions, and local factors. The wound microbiota’s crucial role in this process is gaining recognition. This concise review outlines wound microbiota impacts on healing, emphasizing distinct phases like hemostasis, inflammation, and cell proliferation. Inflammatory responses, orchestrated by growth factors and cytokines, recruit neutrophils and monocytes to eliminate pathogens and debris. Notably, microbiota alterations relate to changes in wound healing dynamics. Commensal bacteria influence immune responses, keratinocyte growth, and blood vessel development. For instance, Staphylococcus epidermidis aids keratinocyte progression, while Staphylococcus aureus colonization impedes healing. Other bacteria like Group A Streptococcus spp. And Pseudomonas affect wound healing as well. Clinical applications of microbiota-based wound care are promising, with probiotics and specific bacteria like Acinetobacter baumannii aiding tissue repair through molecule secretion. Understanding microbiota influence on wound healing offers therapeutic avenues. Tailored approaches, including probiotics, prebiotics, and antibiotics, can manipulate the microbiota to enhance immune modulation, tissue repair, and inflammation control. Despite progress, critical questions linger. Determining the ideal microbiota composition for optimal wound healing, elucidating precise influence mechanisms, devising effective manipulation strategies, and comprehending the intricate interplay between the microbiota, host, and other factors require further exploration.

Norovirus infection is influenced by the presence of commensal bacteria, and both human and murine norovirus (MNV) bind to these bacteria. These virus–bacterial interactions, as well as MNV infection, promote the increased production of bacterial extracellular vesicles (bEVs). However, no correlation has been made between specific bacterial groups, their vesicles, and their impact on norovirus infection. The current study evaluated the impact of select bacterial compositions of murine microbiomes using antibiotic (ABX) cocktails on MNV infection and bEV production. The goal of this research was to determine if increases in bEVs following MNV infection in mice were associated with changes in specific bacterial populations. Bacterial taxa were found to be differentially abundant in both ABX-treated and untreated mice, with the greatest change in bacterial taxa seen in mice treated with a broad-spectrum ABX cocktail. Specifically, Lachnospiraeae were found to be differentially abundant between a variety of treatment factors, including MNV infection. Overall, these results demonstrate that MNV infection can alter the abundance of bacterial taxa within the microbiota, as well as their production of extracellular vesicles, and that the use of selective antibiotic treatments can allow the detection of viral impacts on the microbiome that might otherwise be masked.

Abstract Background Breast cancer (BC) is the most common malignancy in women, in whom it reaches 20% of the total neoplasia incidence. Most BCs are considered sporadic and a number of factors, including familiarity, age, hormonal cycles and diet, have been reported to be BC risk factors. Also the gut microbiota plays a role in breast cancer development. In fact, its imbalance has been associated to various human diseases including cancer although a consequential cause-effect phenomenon has never been proven. Methods The aim of this work was to characterize the breast tissue microbiome in 34 women affected by BC using an NGS-based method, and analyzing the tumoral and the adjacent non-tumoral tissue of each patient. Results The healthy and tumor tissues differed in bacterial composition and richness: the number of Amplicon Sequence Variants (ASVs) was higher in healthy tissues than in tumor tissues (p = 0.001). Moreover, our analyses, able to investigate from phylum down to species taxa for each sample, revealed major differences in the two richest phyla, namely, Proteobacteria and Actinobacteria. Notably, the levels of Actinobacteria and Proteobacteria were, respectively, higher and lower in healthy with respect to tumor tissues. Conclusions Our study provides information about the breast tissue microbial composition, as compared with very closely adjacent healthy tissue (paired samples within the same woman); the differences found are such to have possible diagnostic and therapeutic implications; further studies are necessary to clarify if the differences found in the breast tissue microbiome are simply an association or a concausative pathogenetic effect in BC. A comparison of different results on similar studies seems not to assess a universal microbiome signature, but single ones depending on the environmental cohorts’ locations.

ABSTRACT Cancer pagurus is highly susceptible to shell disease syndrome. However, little is known about concomitant changes in the epibacterial community. We compared the bacterial communities of black spot affected and nonaffected areas of the carapace by amplicon sequencing of 16S rRNA genes and 16S rRNA. Within each spot, bacterial communities of affected areas were less diverse compared to communities from nonaffected areas. Communities of different affected spots were, however, more divergent from each other, compared to those of different nonaffected areas. This indicates a reduced and shifted microbial community composition caused by the black spot disease. Different communities found in black spots likely indicate different stages of the disease. In affected areas, Flavobacteriaceae rose to one of the most abundant and active families due to the increase of Aquimarina spp., suggesting a significant role in shell disease syndrome. We isolated 75 bacterial strains from diseased and healthy areas, which are primarily affiliated with Proteobacteria and Bacteroidetes, reflecting the dominant phyla detected by amplicon sequencing. The ability to degrade chitin was mainly found for Gammaproteobacteria and Aquimarina spp. within the Flavobacteriia, while the ability to use N-acetylglucosamine, the monomer of the polysaccharide chitin, was observed for most isolates, including many Alphaproteobacteria. One-third of the isolates, including most Aquimarina spp., showed antagonistic properties, indicating a high potential for interactions between the bacterial populations. The combination of bacterial community analysis and the physiological properties of the isolates provided insights into a functional complex epibacterial community on the carapace of C. pagurus. IMPORTANCE In recent years, shell disease syndrome has been detected for several ecologically and economically important crustacean species. Large proportions of populations are affected, e.g., >60% of the widely distributed species Cancer pagurus in different North Sea areas. Bacteria play a significant role in the development of different forms of shell disease, all characterized by microbial chitinolytic degradation of the outer shell. By comparing the bacterial communities of healthy and diseased areas of the shell of C. pagurus, we demonstrated that the disease causes a reduced bacterial diversity within affected areas, a phenomenon co-occurring also with many other diseases. Furthermore, the community composition dramatically changed with some taxa rising to high relative abundances and showing increased activity, indicating strong participation in shell disease. Characterization of bacterial isolates obtained from affected and nonaffected spots provided deeper insights into their physiological properties and thus the possible role within the microbiome.

Abstract Metagenomic evidence of great genetic diversity within the nonconserved regions of the human gut microbial genomes appeals for new methods to elucidate the species‐level variability at high resolution. However, current approaches cannot satisfy this methodologically challenge. In this study, we proposed an efficient binning‐first‐and‐assembly‐later strategy, named MetaTrass, to recover high‐quality species‐resolved genomes based on public reference genomes and the single‐tube long fragment read (stLFR) technology, which enables cobarcoding. MetaTrass can generate genomes with longer contiguity, higher completeness, and lower contamination than those produced by conventional assembly‐first‐and‐binning‐later strategies. From a simulation study on a mock microbial community, MetaTrass showed the potential to improve the contiguity of assembly from kb to Mb without accuracy loss, as compared to other methods based on the next‐generation sequencing technology. From four human fecal samples, MetaTrass successfully retrieved 178 high‐quality genomes, whereas only 58 ones were provided by the optimal performance of other conventional strategies. Most importantly, these high‐quality genomes confirmed the high level of genetic diversity among different samples and unveiled much more. MetaTrass was designed to work with metagenomic reads sequenced by stLFR technology, but is also applicable to other types of cobarcoding libraries. With the high capability of assembling high‐quality genomes of metagenomic data sets, MetaTrass seeks to facilitate the study of spatial characters and dynamics of complex microbial communities at enhanced resolution. The open‐source code of MetaTrass is available at https://github.com/BGI-Qingdao/MetaTrass.

Microbiomes are shaped by abiotic factors like nutrients, oxygen availability, pH, temperature, and so on, but also by biotic factors including low molecular weight organic compounds referred to as natural products (NPs). Based on genome analyses, millions of these compounds are predicted to exist in nature, some of them have found important applications e.g. as antibiotics. Based on recent data I propose a model that some of these compounds function as microbial hub signaling compounds, i.e. they have a higher hierarchical influence on microbiomes. These compounds have direct effects e.g. by inhibiting microorganisms and thereby exclude them from a microbiome (excluded). Some microorganisms do not respond at all (nonresponder), others respond by producing themselves NPs like a second wave of information molecules (message responder) influencing other microorganisms, but conceivably a more limited spectrum. Some microorganisms may respond to the hub compounds with their chemical modification (message modifiers). This way, the modified NPs may have themselves signaling function for a subset of microorganisms. Finally, it is also likely that NPs act as food source (C- and/or N-source) for microorganisms specialized on their degradation. As a consequence, such specialized microorganisms are selectively recruited to the microbiota., Competing Interests: None declared., (© The Author(s) 2024. Published by Oxford University Press on behalf of FEMS.)

Pederin, a group of antitumor compounds, is produced by an endosymbiotic bacterium of Paederus fuscipes. Pederin content differed between male and female P. fuscipes, but the reason why these differences are maintained remains unexplored. Here, the pederin‐producing bacteria (PPB) infection rate in P. fuscipes was investigated. Furthermore, we assessed the microbiota structure differences in male and female P. fuscipes harbouring PPB and sequenced the transcriptome of both sexes to shed light on genes of interest. Of the 625 analysed beetles (275 females, 350 males), 96.36% of females and 31.14% of males were positive for PPB infection. PPB accounted for 54.36%–82.70% of the bacterial population in females but showed a much lower abundance in males (0.92%–3.87%). Reproductive organs possessed the highest PPB abundance compared with other parts of females, but no such relationships existed in males. Moreover, we provide the first transcriptome analysis of male and female P. fuscipes harbouring PPB and identified 8893 differentially expressed unigenes. Our results indicated that the pederin content difference between males and females might be caused by the PPB density difference in hosts. The biosequence data would be helpful for illustrating the mechanism that regulates PPB density in P. fuscipes. [ABSTRACT FROM AUTHOR]

The gut microbiota is involved in a range of physiological processes in animals, and modulating the microbiome composition is considered a novel target for identifying animal traits. Tibetan pigs show better fat deposition and disease resistance compared to Yorkshire pigs. However, studies investigating the correlation between favorable characteristics in Tibetan pigs and the gut microbial community remain scarce. In the current study, 1,249,822 high-quality sequences were obtained by amplicon sequencing of the colon contents of Tibetan and Yorkshire pigs. We found that at the boundary level, the abundance and relative abundance of colon bacterial community in Tibetan pigs were higher than that in Yorkshire pigs (P > 0.05). Phylum level, Firmicutes were the dominant colonic microflora of Tibetan and Yorkshire pigs, and the ratio of Firmicutes to Bacteroides in Tibetan pigs was slightly higher than in Yorkshire pigs. Actinobacteria and Spirobacteria were significantly higher in Tibetan pigs than in Yorkshire pigs (P < 0.05). At the genus level, the relative abundance of Bifidobacterium, Lactobacillus, and Bacteriologist, which are related to disease resistance, was significantly higher than that in Yorkshire pigs in Yorkshire pigs. In conclusion, the composition and abundance of colonic intestinal microflora in Tibetan pigs were closely related to their superior traits. Bifidobacteria, Ruminococcaceae, and Family-XIII-AD3011-Group are conducive to improving disease resistance in Tibetan pigs. Lactobacillus and Solobacterium were observed to be the main bacterial communities involved in fat deposition in Tibetan pigs. This study will provide a new reference for the development and utilization of Tibetan pigs in future. [ABSTRACT FROM AUTHOR]

Arid zones represent 44% of the world's agricultural land where crops are exposed to stressful conditions, mainly water deficiency and high solar radiation. Under such conditions, arbuscular mycorrhizal fungi (AMF) may improve plant stress resistance by increasing water and nutrient uptake but their diversity and community in dryland agroecosystems remains underexplored. The objective of this study was to investigate the AMF species diversity and community associated with five economically relevant crops (alfalfa, pepper, maize, onion and walnut) grown in an arid zone of northern Mexico. DNA was extracted and PCR-amplified with AMF specific primers from root and rhizosphere soil samples. Libraries were constructed and sequenced using the Illumina MiSeq system; representative sequences were assigned to 30 species in 12 genera. AMF community composition was similar among the crops but significantly different between the roots and the rhizosphere soil. A strong dominance, in terms of DNA sequence read abundance of Septoglomus sp. was found in root samples. On the contrary, in rhizosphere soil Rhizophagus spp. and Funneliformis mosseae were more abundant. Most of the Septoglomus sequences were affiliated to a node in-between the branches of the species S. viscosum and S. titan, indicating an undescribed or uncharacterized highly abundant species in this ecosystem. Describing and understanding plant associated AMF communities in drylands may provide valuable information for future tailored made inocula efforts. [ABSTRACT FROM AUTHOR]

The objective of the study was to systematically investigate the association between gut microbiota (GM) abundance and Parkinson's disease (PD). PubMed, Medline, Cochrane Library and other literature datebase platforms were searched for eligible studies in the English-language from conception to March 1, 2024. Studies evaluating the association between GM and PD were included. The results of the included studies were analyzed using a random effects model with calculation of the mean difference (MD) with the 95 % confidence interval to quantify the incidence of differences in abundance of various bacterial families in PD patients. Continuous models were used to analyze the extracted data. A total of 14 studies with 1045 PD cases and 821 healthy controls were included for data extraction and meta-analysis. All the included studies exhibited reasonable quality. The included studies reported the data on the ratios of 10 families of GM. Of these 10 microbiota families, Bifidobacteriaceae , Ruminococcaceae , Rikenellaceae , Lactobacillaceae , Verrucomicrobiaceae and Christensenellaceae were found to have increased ratios according to the pooled ratios, while Prevotellaceae , Lachnospiraceae , Erysipelotrichaceae and Faecalibacterium were decreased in PD cases. Patients in the PD cohort exhibited distinctive microbiota compositions compared to healthy individuals, with unique differential patterns in gut microbiome abundance at the phylum, family, and genus levels that may be associated wtih PD pathogenesis. • Gastrointestinal dysfunction before motor symptoms is known as initial PD symptom. • Previous studies reported that approximately 80 % of PD patients suffer constipation. • PD cases showed a distinctive microbiota composition compared to healthy individuals. • Alterations in gut microbiome patterns might be associated with PD. [ABSTRACT FROM AUTHOR]

Abstract Microbes can form complex communities that perform critical functions in maintaining the integrity of their environment or their hosts' wellbeing. Rationally managing these microbial communities requires improving our ability to predict how different species assemblages affect the final species composition of the community. However, making such a prediction remains challenging because of our limited knowledge of the diverse physical, biochemical, and ecological processes governing microbial dynamics. To overcome this challenge, we present a deep learning framework that automatically learns the map between species assemblages and community compositions from training data only, without knowing any of the above processes. First, we systematically validate our framework using synthetic data generated by classical population dynamics models. Then, we apply our framework to data from in vitro and in vivo microbial communities, including ocean and soil microbiota, Drosophila melanogaster gut microbiota, and human gut and oral microbiota. We find that our framework learns to perform accurate out‐of‐sample predictions of complex community compositions from a small number of training samples. Our results demonstrate how deep learning can enable us to understand better and potentially manage complex microbial communities.

Background: Sufficient protein intake is essential for adequate physical condition and athletic performance. However, numerous factors can influence the absorption of consumed protein, including timing, type of protein intake, and gut microbiota. In the present study, elite male water polo players consumed a plant-based, vegan protein supplement with ( n  = 10) or without ( n  = 10) pre- and probiotics daily during the 31-day study period., Methods: We determined the anthropometric characteristics and body composition, dietary habits, gut microbiota composition, and blood parameters of the players at the beginning and at the end of the study. Body composition parameters were analyzed using the InBody 970 bioimpedance analyzer. Gut microbiome composition was determined from stool samples by metagenome sequencing. Paired and unpaired t-tests were used to determine differences between body composition and blood parameters within the groups and between the two groups at the two different sampling times. The Wilcoxon test was used to determine the change in bacterial composition during the study. Correlations between changes in body composition, blood parameters, and taxonomic groups were analyzed using a linear correlation calculation., Results: Skeletal muscle mass ( p  < 0.001), body cell mass ( p  = 0.002), arm circumference ( p  = 0.003), and protein mass ( p  < 0.001) increased, while body fat mass ( p  = 0.004) decreased significantly in the intervention group which consumed pre- and probiotics in addition to protein supplement. Activated acetate (reductive TCA cycle I) and propionate (pyruvate fermentation to propanoate I) pathways correlated positively with increased skeletal muscle mass ( p  < 0.01 and p  < 0.05), and the relative abundance of butyrate-producing species showed a significant positive correlation with changes in body fat mass in the intervention group ( p  < 0.05). These correlations were not observed in the control group without the intake of pre- and probiotics., Conclusions: The composition of the gut microbiota may influence protein absorption and therefore body composition and consequently physical condition and sports performance.

Background: Breast cancer (BC) is the most common malignancy in women, in whom it reaches 20% of the total neoplasia incidence. Most BCs are considered sporadic and a number of factors, including familiarity, age, hormonal cycles and diet, have been reported to be BC risk factors. Also the gut microbiota plays a role in breast cancer development. In fact, its imbalance has been associated to various human diseases including cancer although a consequential cause-effect phenomenon has never been proven.Methods: The aim of this work was to characterize the breast tissue microbiome in 34 women affected by BC using an NGS-based method, and analyzing the tumoral and the adjacent non-tumoral tissue of each patient.Results: The healthy and tumor tissues differed in bacterial composition and richness: the number of Amplicon Sequence Variants (ASVs) was higher in healthy tissues than in tumor tissues (p = 0.001). Moreover, our analyses, able to investigate from phylum down to species taxa for each sample, revealed major differences in the two richest phyla, namely, Proteobacteria and Actinobacteria. Notably, the levels of Actinobacteria and Proteobacteria were, respectively, higher and lower in healthy with respect to tumor tissues.Conclusions: Our study provides information about the breast tissue microbial composition, as compared with very closely adjacent healthy tissue (paired samples within the same woman); the differences found are such to have possible diagnostic and therapeutic implications; further studies are necessary to clarify if the differences found in the breast tissue microbiome are simply an association or a concausative pathogenetic effect in BC. A comparison of different results on similar studies seems not to assess a universal microbiome signature, but single ones depending on the environmental cohorts' locations. [ABSTRACT FROM AUTHOR]

Storage time is considered to be one of the most important factors affecting the obnoxious odor and microbial spoilage of fresh meat. In this study, volatile organic compounds (VOCs) and bacterial community structure of chilled goose meat during storage were investigated. The results showed that numerous VOCs were produced during the fresh goose meat storage, including aldehydes (nonanal, (E)-2-octenal, hexanal, tetradecanal), alcohol (1-octen-3-ol), furan (2-pentylfuran), and carboxylic acids (methyl diethyldithiocarbamate), which might be a breakdown product during spoilage. In addition, there were slight fluctuations in fatty acid profiles and amino acid contents. Furthermore, bacterial community diversity decreased with prolonged storage. Also, Pseudomonas and Acinetobacter were the dominant spoilage bacteria contributing to nonanal and methyl diethyldithiocarbamate generation. Taken together, these data provide insights into the characterization of VOCs and the bacterial community of chilled goose meat, which will help to further control the microbial quality of chilled meat., Competing Interests: The authors declare that they have no competing interests., (© 2024 The Authors. Published by Elsevier Ltd.)

Autism spectrum disorder (ASD) is characterized by deficits in social interactions and repetitive, stereotypic behaviors. Evidence shows that bidirectional communication of the gut-brain axis plays an important role. Here, we recruited 62 patients with ASD in southern China, and performed a cross-sectional study to test the relationship between repeated behavior, gut microbiome composition, and alpha diversity. We divided all participants into two groups based on the clustering results of their microbial compositions and found Veillonella and Ruminococcus as the seed genera in each group. Repetitive behavior differed between clusters, and cluster 2 had milder repetitive symptoms than Cluster 1. Alpha diversity between clusters was significantly different, indicating that cluster 1 had lower alpha diversity and more severe repetitive, stereotypic behaviors. Repetitive behavior had a negative correlation with alpha diversity. We demonstrated that the difference in intestinal microbiome composition and altered alpha diversity can be associated with repetitive, stereotypic behavior in autism. The role of Ruminococcus and Veillonella in ASD is not yet understood. [ABSTRACT FROM AUTHOR]

Aim: The latitudinal diversity gradient (LDG) is one of the most pervasive large‐scale trends in biodiversity. However, whether microbial taxa also conform to this pattern remains poorly known. This study uses the gill and shell‐surface microbiomes of the marine bivalve Mytilus californianus to test whether the diversity of host‐associated microbial communities declines with increasing latitude, as predicted by the LDG. Location: Northeastern Pacific coast, ranging from Sitka, AK to La Jolla, CA, USA (spanning 24.12 degrees of latitude). Taxon: Bacteria and Archaea associated with M. californianus gills and shell‐surfaces. Methods: We amplified and sequenced the 16S rRNA gene from M. californianus gill and shell‐surface samples. We used linear and quadratic regressions, accounting for spatial autocorrelation when needed, of average alpha and gamma diversities of the whole microbiome, as well as individual microbial clades, to determine whether these taxa conformed to the traditional LDG. We also used permutational multivariate analysis of variance to determine the level of compositional differentiation among sampling sites. Results: Gill and shell‐surface microbiota show differing latitudinal diversity patterns, with both micro‐environments exhibiting high levels of compositional differentiation along latitude. Individual microbial clades within each micro‐environment also show different latitudinal trends, most likely due to differing ecologies and life histories. Main conclusions: Mytilus californianus‐associated microbial taxa show a flat, hump‐shaped or contrarian LDG, suggesting that a steep decline in diversity with increasing latitude may not be a universal pattern across different domains of life. [ABSTRACT FROM AUTHOR]

Autism spectrum disorder (ASD) is characterized by deficits in social interactions and repetitive, stereotypic behaviors. Evidence shows that bidirectional communication of the gut-brain axis plays an important role. Here, we recruited 62 patients with ASD in southern China, and performed a cross-sectional study to test the relationship between repeated behavior, gut microbiome composition, and alpha diversity. We divided all participants into two groups based on the clustering results of their microbial compositions and found Veillonella and Ruminococcus as the seed genera in each group. Repetitive behavior differed between clusters, and cluster 2 had milder repetitive symptoms than Cluster 1. Alpha diversity between clusters was significantly different, indicating that cluster 1 had lower alpha diversity and more severe repetitive, stereotypic behaviors. Repetitive behavior had a negative correlation with alpha diversity. We demonstrated that the difference in intestinal microbiome composition and altered alpha diversity can be associated with repetitive, stereotypic behavior in autism. The role of Ruminococcus and Veillonella in ASD is not yet understood.

Thanks to advances in high-throughput sequencing technologies, the importance of microbiome to human health and disease has been increasingly recognized. Analyzing microbiome data from sequencing experiments is challenging due to their unique features such as compositional data, excessive zero observations, overdispersion, and complex relations among microbial taxa. Clustered microbiome data have become prevalent in recent years from designs such as longitudinal studies, family studies, and matched case–control studies. The within-cluster dependence compounds the challenge of the microbiome data analysis. Methods that properly accommodate intra-cluster correlation and features of the microbiome data are needed. We develop robust and powerful differential composition tests for clustered microbiome data. The methods do not rely on any distributional assumptions on the microbial compositions, which provides flexibility to model various correlation structures among taxa and among samples within a cluster. By leveraging the adjusted sandwich covariance estimate, the methods properly accommodate sample dependence within a cluster. The two-part version of the test can further improve power in the presence of excessive zero observations. Different types of confounding variables can be easily adjusted for in the methods. We perform extensive simulation studies under commonly adopted clustered data designs to evaluate the methods. We demonstrate that the methods properly control the type I error under all designs and are more powerful than existing methods in many scenarios. The usefulness of the proposed methods is further demonstrated with two real datasets from longitudinal microbiome studies on pregnant women and inflammatory bowel disease patients. The methods have been incorporated into the R package "miLineage" publicly available at https://tangzheng1.github.io/tanglab/software.html. [ABSTRACT FROM AUTHOR]

• Microbial flora in cold and produced hot boiler water was studied in 14 buildings. • Microbiotas were characterized using flow cytometry and metagenomic analysis. • Microbiomes and flow cytometric fingerprints of cold water differed from hot water. • Hot waters contained active thermophilic microbiotas able to grow at 50–60 °C. • Heating of cold water generates nutrients for growth of thermophilic microbiomes. Running cold and hot water in buildings is a widely established commodity. However, interests regarding hygiene and microbiological aspects had so far been focussed on cold water. Little attention has been given to the microbiology of domestic hot-water installations (DHWIs), except for aspects of pathogenic Legionella. World-wide, regulations consider hot (or warm) water as 'heated drinking water' that must comply (cold) drinking water (DW) standards. However, the few reports that exist indicate presence and growth of microbial flora in DHWIs, even when supplied with water with disinfectant residual. Using flow cytometric (FCM) total cell counting (TCC), FCM-fingerprinting, and 16S rRNA-gene-based metagenomic analysis, the characteristics and composition of bacterial communities in cold drinking water (DW) and hot water from associated boilers (operating at 50 – 60 °C) was studied in 14 selected inhouse DW installations located in Switzerland and Austria. A sampling strategy was applied that ensured access to the bulk water phase of both, supplied cold DW and produced hot boiler water. Generally, 1.3- to 8-fold enhanced TCCs were recorded in hot water compared to those in the supplied cold DW. FCM-fingerprints of cold and corresponding hot water from individual buildings indicated different composition of cold- and hot-water microbial floras. Also, hot waters from each of the boilers sampled had its own individual FCM-fingerprint. 16S rRNA-gene-based metagenomic analysis confirmed the marked differences in composition of microbiomes. E.g., in three neighbouring houses supplied from the same public network pipe each hot-water boiler contained its own thermophilic bacterial flora. Generally, bacterial diversity in cold DW was broad, that in hot water was restricted, with mostly thermophilic strains from the families Hydrogenophilaceae, Nitrosomonadaceae and Thermaceae dominating. Batch growth assays, consisting of cold DW heated up to 50 – 60 °C and inoculated with hot water, resulted in immediate cell growth with doubling times between 5 and 10 h. When cold DW was used as an inoculum no significant growth was observed. Even boilers supplied with UVC-treated cold DW contained an actively growing microbial flora, suggesting such hot-water systems as autonomously operating, thermophilic bioreactors. The generation of assimilable organic carbon from dissolved organic carbon due to heating appears to be the driver for growth of thermophilic microbial communities. Our report suggests that a man-made microbial ecosystem, very close to us all and of potential hygienic importance, may have been overlooked so far. Despite consumers having been exposed to microbial hot-water flora for a long time, with no major pathogens so far been associated specifically with hot-water usage (except for Legionella), the role of harmless thermophiles and their interaction with potential human pathogens able to grow at elevated temperatures in DHWIs remains to be investigated. [Display omitted] [ABSTRACT FROM AUTHOR]

Összefoglaló. Az immunrendszer nem megfelelő működése meghatározó szerepet játszik a daganatok kialakulásában, progressziójában és az egyes terápiák hatékonyságában is. A bélrendszer baktériumai a szervezet immunitásán keresztül képesek befolyásolni a szervezet gyógyszeres terápiákra adott válaszreakcióját, kiváltképpen az immunellenőrzőpont-gátló kezelések hatását. Az újgenerációs nukleinsav-szekvenálási technológiák felhasználásával részletes képet kaphatunk a szervezetben jelen lévő baktériumok minőségi és mennyiségi viszonyairól. A közelmúltban összefüggést igazoltak a vastagbéldaganat, a melanoma, a vesesejtes carcinoma és a nem kissejtes tüdőrák esetén alkalmazott immunellenőrzőpont-gátló terápiák hatékonysága és a bél mikrobiom-összetétele között. Számos olyan baktériumot azonosítottak, melynek jelenlétéből, illetve mennyiségéből következtethetünk az egyes kezelésekkel szembeni egyéni érzékenységre. Ezzel összhangban, az antibiotikumkezelés által okozott dysbiosis növelte az immunellenőrzőpont-gátló terápia sikertelenségének kockázatát. Ezen eredmények tükrében a jövőben a mikrobiom-összetétel meghatározása is fontos tényező lehet az immunterápiák hatékonyságának előrejelzésében, illetve egyre inkább bizonyított, hogy a széles spektrumú antibiotikumkezelés a legtöbbször csökkenti a daganatellenes immunterápiák hatékonyságát. Jelenleg folyó klinikai vizsgálatok pedig a mikrobiom-összetétel mesterséges úton történő megváltoztatásának terápiás lehetőségeit tanulmányozzák. Bebizonyosodott, hogy a korábbi állásponttal szemben a vizelet nem steril. DNS-szekvenálás alkalmazásával számos olyan, a vizeletben előforduló baktériumot sikerült azonosítani, melynek jelenléte hozzájárulhat a húgyhólyagrák kialakulásához és progressziójához, illetve a húgyhólyagban lokálisan alkalmazott BCG-terápia hatékonyságához. Jelen munkában a közelmúlt publikációit feldolgozva összefoglaljuk, mely baktériumok jelenléte hozható összefüggésbe a különböző daganatok kialakulásával, progressziójával és terápiarezisztenciájával. Orv Hetil. 2020; 162(15): 579–586. Summary. Dysfunction of the immune system plays a crucial role in the development and progression of cancer as well as the effectiveness of antitumor therapies. Gut microbiota, due to their impact on the immune system, are able to influence response to anticancer drug therapies. Next-generation DNA-sequencing technologies enabled a comprehensive quantitative and qualitative exploration of the gut microbiome. An increasing body of evidence indicates the association between the efficacy of immune checkpoint inhibitor therapies and gut microbiome composition in colorectal cancer, malignant melanoma, renal cell carcinoma, and non-small cell lung cancer. Recently, several bacterial strains and species were shown to be associated with treatment efficacies. In accordance, dysbiosis caused by antibiotic treatment was found to increase the risk of failure to immune checkpoint inhibitor therapies. In the light of these results, examination of microbiome composition may become an important factor for the prediction of immunotherapies. Currently ongoing clinical trials are investigating the potential of therapeutic alteration of microbiome composition. Contrary to the previous view, urine has been shown not to be sterile. By using sensitive DNA-sequencing technologies, several urinary bacteria could be identified which may contribute to the development and progression of bladder cancer and may influence the efficacy of intravesical BCG therapy. In the present work, we summarize recent studies that identified the presence of certain bacteria associated with the development, progression, and therapy resistance of various cancers. Orv Hetil. 2020; 162(15): 579–586. [ABSTRACT FROM AUTHOR]

The use of additives in food products has become an important public health concern. In recent reports, dietary emulsifiers have been shown to affect the gut microbiota, contributing to a pro-inflammatory phenotype and metabolic syndrome. So far, it is not yet known whether similar microbiome shifts are observable for a more diverse set of emulsifier types and to what extent these effects vary with the unique features of an individual’s microbiome. To bridge this gap, we investigated the effect of five dietary emulsifiers on the fecal microbiota from 10 human individuals upon a 48 h exposure. Community structure was assessed with quantitative microbial profiling, functionality was evaluated by measuring fermentation metabolites, and pro-inflammatory properties were assessed with the phylogenetic prediction algorithm PICRUSt, together with a TLR5 reporter cell assay for flagellin. A comparison was made between two mainstream chemical emulsifiers (carboxymethylcellulose and P80), a natural extract (soy lecithin), and biotechnological emulsifiers (sophorolipids and rhamnolipids). While fecal microbiota responded in a donor-dependent manner to the different emulsifiers, profound differences between emulsifiers were observed. Rhamnolipids, sophorolipids, and soy lecithin eliminated 91 ± 0, 89 ± 1, and 87 ± 1% of the viable bacterial population after 48 h, yet they all selectively increased the proportional abundance of putative pathogens. Moreover, profound shifts in butyrate (−96 ± 6, −73 ± 24, and −34 ± 25%) and propionate (+13 ± 24, +88 ± 50, and +29 ± 16%) production were observed for these emulsifiers. Phylogenetic prediction indicated higher motility, which was, however, not confirmed by increased flagellin levels using the TLR5 reporter cell assay. We conclude that dietary emulsifiers can severely impact the gut microbiota, and this seems to be proportional to their emulsifying strength, rather than emulsifier type or origin. As biotechnological emulsifiers were especially more impactful than chemical emulsifiers, caution is warranted when considering them as more natural alternatives for clean label strategies.

Risk assessment of microplastic (MP) pollution requires understanding biodegradation processes and related changes in polymer properties. In the environment, there are two-way interactions between the MP properties and biofilm communities: (i) microorganisms may prefer some surfaces, and (ii) MP surface properties change during the colonization and weathering. In a 2-week experiment, we studied these interactions using three model plastic beads (polyethylene [PE], polypropylene [PP], and polystyrene [PS]) exposed to ambient bacterioplankton assemblage from the Baltic Sea; the control beads were exposed to bacteria-free water. For each polymer, the physicochemical properties (compression, crystallinity, surface chemistry, hydrophobicity, and surface topography) were compared before and after exposure under controlled laboratory conditions. Furthermore, we characterized the bacterial communities on the MP surfaces using 16S rRNA gene sequencing and correlated community diversity to the physicochemical properties of the MP. Significant changes in PE crystallinity, PP stiffness, and PS maximum compression were observed as a result of exposure to bacteria. Moreover, there were significant correlations between bacterial diversity and some physicochemical characteristics (crystallinity, stiffness, and surface roughness). These changes coincided with variation in the relative abundance of unique OTUs, mostly related to the PE samples having significantly higher contribution of Sphingobium, Novosphingobium, and uncultured Planctomycetaceae compared to the other test materials, whereas PP and PS samples had significantly higher abundance of Sphingobacteriales and Alphaproteobacteria, indicating possible involvement of these taxa in the initial biodegradation steps. Our findings demonstrate measurable signs of MP weathering under short-term exposure to environmentally relevant microbial communities at conditions resembling those in the water column. A systematic approach for the characterization of the biodegrading capacity in different systems will improve the risk assessment of plastic litter in aquatic environments.

During the early-life period, the hatchlings of red-eared slider turtles (Trachemys scripta elegans) rely on their own post-hatching internal yolk for several days before beginning to feed. The gut microbiome is critical for the adaptation of organisms to new environments, but, to date, how the microbiome taxa are assembled during early life of the turtle is unknown. In this study, the intestinal microbiome of red-eared slider hatchlings (fed on commercial particle food) was systematically analyzed at four different growth stages (0 d, 10 d, 20 d, 30 d) by a high-throughput sequencing approach. Results showed that the dominant phyla were Firmicutes (58.23%) and Proteobacteria (41.42%) at 0-day, Firmicutes (92.94%) at 10-day, Firmicutes (67.08%) and Bacteroidetes (27.17%) at 20-day, and Firmicutes (56.46%), Bacteroidetes (22.55%) and Proteobacteria (20.66%) at 30-day post-hatching. Members of the Bacteroidaceae family were absent in 0-day and 10-day turtles, but dominated in 20-day and 30-day turtles. The abundance of Clostridium also showed the highest value in 10-day turtles. The richness of the intestinal microbiomes was lower at 0-day and 30-day than that at 10-day and 20-day, while the diversity was higher at 10-day and 30-day than that at 0-day and 20-day. The results endowed the turtles with an ability to enhance their tolerance to the environment.

Thanks to the emergence and recent advances in high‐throughput sequencing technologies, it is becoming more evident every day that changes in the microbiome composition are linked to a myriad of health conditions. Despite this, the mechanisms of host–microbiota signalling remain largely unknown. The microbiome has an extensive metabolic activity that leads to the generation of a large number of compounds that are likely to influence host health. Therefore, the microbiome–host cross‐talk is in part mediated by microbial‐derived metabolites. Unlike metagenomics, which only provides information about microbial genes and thus the microbiome functional potential, metabolic phenotyping is well suited to capture their actual metabolic activity. Here, we provide an overview of these approaches and propose an integration of metagenomics, as a microbiome compositional readout, with faecal and plasma/urine metabolomics, as a functional readout, to unravel novel mechanisms linking the microbiome to host health and disease. [ABSTRACT FROM AUTHOR]

Previous studies showed that high concentration of particulate matter (PM) 2.5 and PM10 carried a large number of bacterial and archaeal species, including pathogens and opportunistic pathogens. In this study, pharyngeal swabs from 83 subjects working in an open air farmer’s market were sampled before and after exposure to smog with PM2.5 and PM10 levels up to 200 and 300 μg/m3, respectively. Their microbiota were investigated using high-throughput sequencing targeting the V3–V4 regions of the 16S rRNA gene. The genus level phylotypes was increased from 649 to 767 in the post-smog pharyngeal microbiota, of which 142 were new and detected only in the post-smog microbiota. The 142 new genera were traced to sources such as soil, marine, feces, sewage sludge, freshwater, hot springs, and saline lakes. The abundance of the genera Streptococcus, Haemophilus, Moraxella, and Staphylococcus increased in the post-smog pharyngeal microbiota. All six alpha diversity indices and principal component analysis showed that the taxonomic composition of the post-smog pharyngeal microbiota was significantly different to that of the pre-smog pharyngeal microbiota. Redundancy analysis showed that the influences of PM2.5/PM10 exposure and smoking on the taxonomic composition of the pharyngeal microbiota were statistically significant (p < 0.001). Two days of exposure to high concentrations of PM2.5/PM10 changed the pharyngeal microbiota profiles, which may lead to an increase in respiratory diseases. Wearing masks could reduce the effect of high-level PM2.5/PM10 exposure on the pharyngeal microbiota.

Current visualizations in microbiome research rely on aggregations in taxonomic classifications or do not show less abundant taxa. We introduce Snowflake: a new visualization method that creates a clear overview of the microbiome composition in collected samples without losing any information due to classification or neglecting less abundant reads. Snowflake displays every observed OTU/ASV in the microbiome abundance table and provides a solution to include the data's hierarchical structure and additional information obtained from downstream analysis (e.g., alpha- and beta-diversity) and metadata. Based on the value-driven ICE-T evaluation methodology, Snowflake was positively received. Experts in microbiome research found the visualizations to be user-friendly and detailed and liked the possibility of including and relating additional information to the microbiome's composition. Exploring the topological structure of the microbiome abundance table allows them to quickly identify which taxa are unique to specific samples and which are shared among multiple samples (i.e., separating sample-specific taxa from the core microbiome), and see the compositional differences between samples. An R package for constructing and visualizing Snowflake microbiome composition graphs is available at https://gitlab.com/vda-lab/snowflake., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The authors declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision., (Copyright © 2024 Peeters, Bot, Rovelo Ruiz and Aerts.)

Rapid climate change due to anthropogenic greenhouse gas emissions is pushing corals to and past their physiological limits, while their microbiome is being pressed towards dysbiosis. Microbes greatly influence the health and functioning of corals, but thermal anomalies that cause bleaching can affect certain taxa of the host-associated prokaryote and Symbiodiniaceae communities, leading corals towards a disease-prone state. In some coral species, however, even significant thermal stress may not result in visible signs of bleaching. Whether changes in the coral microbiome occur in these resilient species during temperature anomalies is not well described. In the present study, we tagged, visually assessed and sampled 10 colonies of the branching coral Pocillopora acuta on a fringing reef off Orpheus Island in the central Great Barrier Reef for 1 yr, of which the summer coincided with the 2016 mass-bleaching event. No visible signs of bleaching were observed in any of the 10 colonies throughout the study period, despite experiencing two degree heating weeks of thermal stress and observations of bleaching in other coral species on the same reef. Metabarcoding based on the Symbiodiniaceae ITS2 rDNA spacer and the bacterial 16S rRNA gene provided evidence for stability of the overall microbial community structure, although the bacterial community showed increases in a number of potentially beneficial taxa, such as diazotrophs, during the thermal stress event. These findings suggest some flexibility in the microbiome to adjust to higher than average temperatures without disrupting microbiome stability, perhaps contributing to the thermal resilience of P. acuta. [ABSTRACT FROM AUTHOR]

Graphical abstract Highlights • Bacterial (16S) and fungal (ITS) contributions to the microbiome of canine skin. • The microbiome of canine skin varies with individuality. • The most abundant bacteria observed on AD skin was Staphylococcus. • High abundance of Blumeria was observed on canine atopic skin compared to healthy skin. • Topical antimicrobial treatment significantly changed the microbiome composition. Abstract Canine atopic dermatitis is a genetically predisposed inflammatory and pruritic allergic skin disease that is often complicated by (secondary) bacterial and fungal (yeast) infections. High-throughput DNA sequencing was used to characterize the composition of the microbiome (bacteria and fungi) inhabiting specific sites of skin in healthy dogs and dogs with atopic dermatitis (AD) before and after topical antimicrobial treatment. Skin microbiome samples were collected from six healthy control dogs and three dogs spontaneously affected by AD by swabbing at (non-) predilection sites before, during and after treatment. Bacteria and fungi were profiled by Illumina sequencing of the 16S ribosomal RNA gene of bacteria (16S) and the internally transcribed spacer of the ribosomal gene cassette in fungi (ITS). The total cohort of dogs showed a high diversity of microbes on skin with a strong individual variability of both 16S and ITS profiles. The genera of Staphylococcus and Porphyromonas were dominantly present both on atopic and healthy skin and across all skin sites studied. In addition, bacterial and fungal alpha diversity were similar at the different skin sites. The topical antimicrobial treatment increased the diversity of bacterial and fungal compositions in course of time on both AD and healthy skin. [ABSTRACT FROM AUTHOR]

Previous studies showed that high concentration of particulate matter (PM) 2.5 and PM10 carried a large number of bacterial and archaeal species, including pathogens and opportunistic pathogens. In this study, pharyngeal swabs from 83 subjects working in an open air farmer's market were sampled before and after exposure to smog with PM2.5 and PM10 levels up to 200 and 300 μg/m3, respectively. Their microbiota were investigated using high-throughput sequencing targeting the V3–V4 regions of the 16S rRNA gene. The genus level phylotypes was increased from 649 to 767 in the post-smog pharyngeal microbiota, of which 142 were new and detected only in the post-smog microbiota. The 142 new genera were traced to sources such as soil, marine, feces, sewage sludge, freshwater, hot springs, and saline lakes. The abundance of the genera Streptococcus , Haemophilus , Moraxella , and Staphylococcus increased in the post-smog pharyngeal microbiota. All six alpha diversity indices and principal component analysis showed that the taxonomic composition of the post-smog pharyngeal microbiota was significantly different to that of the pre-smog pharyngeal microbiota. Redundancy analysis showed that the influences of PM2.5/PM10 exposure and smoking on the taxonomic composition of the pharyngeal microbiota were statistically significant (p < 0.001). Two days of exposure to high concentrations of PM2.5/PM10 changed the pharyngeal microbiota profiles, which may lead to an increase in respiratory diseases. Wearing masks could reduce the effect of high-level PM2.5/PM10 exposure on the pharyngeal microbiota. [ABSTRACT FROM AUTHOR]

Variations of microbial species and functional composition in coastal sediment are usually taken as the results of the provision of supplementary nutrients affected by human activities. However, responses of microbiome stability to restocking biological resources remain less understood in coastal benthic systems without nutrient supplements. Here, combined with metagenomics and microbiome co-occurrence networks, the composition, function, and community stability of microbes were evaluated in a coastal area where sea cucumbers (Apostichopus japonicus) restocked after six months. Also, the physicochemical characteristics of sediments and bottom water were analyzed. We found the total organic carbon, total nitrogen, and total phosphorus of sediment did not change significantly in the restocking area after six months, whereas the concentration of dissolved inorganic nitrogen in bottom water increased significantly. Moreover, the relative abundance of Nitrospina at the class level was increased significantly in the restocking area. Also, enzymes related to nitrate reduction and nitrous oxide reductase were increased in the restocking area. Of note, stock enhancement of sea cucumbers altered associations between bacteria rather than their composition. The elimination of negative associations and reduction of the potential keystone taxa in the restocking area indicated destabilized bacterial communities. Our work may contribute to elucidating the response of microbial stability to stock enhancement. This finding also suggests that microbial community stability can be considered as an indicator of ecological risk under the influence of stock enhancement. [Display omitted] • The concentration of dissolved inorganic nitrogen in the bottom water was increased in the restocking area. • Stock enhancement without nutrient supplements altered bacterial associations. • Sea cucumbers enrich genes related to xenobiotics biodegradation and nitrification. • The elimination of negative associations and reduction of keystone taxa destabilize microbial communities. [ABSTRACT FROM AUTHOR]