Gut diversity and the resistome as biomarkers of febrile neutropenia outcome in paediatric oncology patients undergoing hematopoietic stem cell transplantation

The gut microbiota of paediatric oncology patients undergoing a conditioning regimen before hematopoietic stem cell transplantation is recently considered to play role in febrile neutropenia. Disruption of commensal microbiota and evolution of opportune pathogens community carrying a plethora of antibiotic-resistance genes play crucial role. However, the impact, predictive role and association of patient´s gut resistome in the course of the therapy is still to be elucidated. We analysed gut microbiota composition and resistome of 18 paediatric oncology patients undergoing hematopoietic stem cell transplantation, including 12 patients developing febrile neutropenia, hospitalized at The Bone Marrow Transplantation Unit of the National Institute of Children´s disease in Slovak Republic and healthy individuals (n = 14). Gut microbiome of stool samples obtained in 3 time points, before hematopoietic stem cell transplantation (n = 16), one week after hematopoietic stem cell transplantation (n = 16) and four weeks after hematopoietic stem cell transplantation (n = 14) was investigated using shotgun metagenome sequencing and bioinformatical analysis. We identified significant decrease in alpha-diversity and nine antibiotic-resistance genes msr(C), dfrG, erm(T), VanHAX, erm(B), aac(6)-aph(2), aph(3)-III, ant(6)-Ia and aac(6)-Ii, one week after hematopoietic stem cell transplantation associated with febrile neutropenia. Multidrug-resistant opportune pathogens of ESKAPE, Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae and Escherichia coli found in the gut carried the significant subset of patient's resistome. Over 50% of patients treated with trimethoprim/sulfamethoxazole, piperacillin/tazobactam and amikacin carried antibiotic-resistance genes to applied treatment. The alpha diversity and the resistome of gut microbiota one week after hematopoietic stem cell transplantation is relevant predictor of febrile neutropenia outcome after hematopoietic stem cell transplantation. Furthermore, the interindividual diversity of multi-drug resistant opportunistic pathogens with variable portfolios of antibiotic-resistance genes indicates necessity of preventive, personalized approach.

The Relationship Between Gut Microbiome Estrobolome and Breast Cancer: A Systematic Review of Current Evidences

Breast cancer is the most frequent kind of cancer and the second leading cause of mortality worldwide, behind heart disease. Next-generation sequencing technologies enables for unprecedented enumeration of human resident gut microorganisms, conferring novel insights into the role of the microbiota in health and individuals with breast cancer. A growing body of research on microbial dysbiosis seems to indicate an elevated risk of health complications including cancer. Although several dysbiosis indices have been proposed, their underlying methodology, as well as the cohorts and conditions of breast cancer patients are significantly different. To date, these indices have not yet been thoroughly reviewed especially when it comes to researching the estrogen-gut microbiota axis. Instead of providing a thorough rating of the most effective diversity measurements, the current work aims to be used to assess the relevance of each study's findings across the demographic data, different subtypes, and stages of breast cancer, and tie them to the estrobolome, which controls the amount of oestrogen that circulates through humans. This review will cover 11 studies which will go into a detailed discussion for the microbiome results of the mentioned studies, leaving to the user the final choice of the most suited indices as well as highlight the observed bacteria found to be related to the estrobolome in hopes of giving the reader a better understanding for the biological cross-talk between gut microbiome and breast cancer progression.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12088-023-01135-z.

Gut microbiome in men with chronic prostatitis/chronic pelvic pain syndrome: profiling and its predictive significance

PURPOSE

To investigate the difference in gut microbiome composition between patients with chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS) and healthy controls, and to assess the potential of gut microbiota as predictive markers for CP/CPPS risk.

METHODS

The present study included 41 CP/CPPS patients and 43 healthy controls in China. Fecal specimen data were obtained and analysed using 16S rRNA gene sequencing. Alpha and beta-diversity indices, relative microbiome abundances, cluster analysis, and linear discriminant analysis effect size (LEfSe) were employed. Microbial biomarkers were selected for the development of a diagnostic classification model, and the functional prediction was conducted using PICRUSt2.

RESULTS

Alpha-diversity measures revealed no statistically significant difference in bacterial community structure between CP/CPPS patients and controls. However, significant differences were observed in the relative abundances of several bacterial genera. Beta-diversity analysis revealed a distinct separation between the two groups. Significant inter-group differences were noted at various taxonomic levels, with specific bacterial genera being significantly different in abundance. The LEfSe analysis indicated that three bacterial species were highly representative and seven bacterial species were low in CP/CPPS patients as compared to the control group. A diagnostic model for CP/CPPS based on microbial biomarkers exhibited good performance. PICRUSt2 functional profiling indicated significant differences in the development and regeneration pathway.

CONCLUSION

Significant differences in the gut microbiome composition were found between groups. The study provided a novel diagnostic model for CP/CPPS based on microbiota, presenting promising potential for future therapeutic targets and non-invasive diagnostic biomarkers for CP/CPPS patients.

Metrics matter: Multiple diversity metrics at different spatial scales are needed to understand species diversity in urban environments

Worldwide, natural habitats are being replaced by artificial structures due to urbanisation. Planning of such modifications should strive for environmental net gain that benefits biodiversity and ecosystems. Alpha (α) and gamma (γ) diversity are often used to assess 'impact' but are insensitive metrics. We test several diversity measures across two spatial scales to compare species diversity in natural and artificial habitats. We show γ-diversity indicates equivalency in biodiversity between natural and artificial habitats, but natural habitats support greater taxon (α) and functional richness. Within-site β-diversity was also greater in natural habitats, but among-site β-diversity was greater in artificial habitats, contradicting the commonly held view that urban ecosystems are more biologically homogenous than natural ecosystems. This study suggests artificial habitats may in fact provide novel habitat for biodiversity, challenges the applicability of the urban homogenisation concept and highlights a significant limitation of using just α-diversity (i.e., multiple metrics are needed and recommended) for assessing environmental net gain and attaining biodiversity conservation goals.

A Matter of Metals: Copper but Not Cadmium Affects the Microbial Alpha-Diversity of Soils and Sediments - a Meta-analysis

Heavy metal (HM) accumulation in soil affects plants and soil fauna, yet the effect on microbial alpha-diversity remains unclear, mainly due to the absence of dedicated research synthesis (e.g. meta-analysis). Here, we report the first meta-analysis of the response of soil microbial alpha-diversity to the experimental addition of cadmium (Cd) and copper (Cu). We considered studies conducted between 2013 and 2022 using DNA metabarcoding of bacterial and fungal communities to overcome limitations of other cultivation- and electrophoresis-based techniques. Fungi were discarded due to the limited study number (i.e. 6 studies). Bacterial studies resulted in 66 independent experiments reported in 32 primary papers from four continents. We found a negative dose-dependent response for Cu but not for Cd for bacterial alpha-diversity in the environments, only for Cu additions exceeding 29.6 mg kg^-1 (first loss of - 0.06% at 30 mg kg^-1). The maximal loss of bacterial alpha-diversity registered was 13.89% at 3837 mg kg^-1. Our results first highlight that bacterial communities behave differently to soil pollution depending on the metal. Secondly, our study suggests that even extreme doses of Cu do not cause a dramatic loss in alpha-diversity, highlighting how the behaviour of bacterial communities diverges from soil macro-organisms.

The respiratory microbiota alpha-diversity in chronic lung diseases: first systematic review and meta-analysis

Background

While there seems to be a consensus that a decrease in gut microbiome diversity is related to a decline in health status, the associations between respiratory microbiome diversity and chronic lung disease remain a matter of debate. We provide a systematic review and meta-analysis of studies examining lung microbiota alpha-diversity in patients with asthma, chronic obstructive pulmonary disease (COPD), cystic fibrosis (CF) or bronchiectasis (NCFB), in which a control group based on disease status or healthy subjects is provided for comparison.

Results

We reviewed 351 articles on title and abstract, of which 27 met our inclusion criteria for systematic review. Data from 24 of these studies were used in the meta-analysis. We observed a trend that CF patients have a less diverse respiratory microbiota than healthy individuals. However, substantial heterogeneity was present and detailed using random-effects models, which limits the comparison between studies.

Conclusions

Knowledge on respiratory microbiota is under construction, and for the moment, it seems that alpha-diversity measurements are not enough documented to fully understand the link between microbiota and health, excepted in CF context which represents the most studied chronic respiratory disease with consistent published data to link alpha-diversity and lung function. Whether differences in respiratory microbiota profiles have an impact on chronic respiratory disease symptoms and/or evolution deserves further exploration.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12931-022-02132-4.

Unused railway lines for conservation of pollinators in the intensively managed agricultural landscape

Pollinating insects are under high human pressure due to agricultural intensification and urbanization. Although many research and conservation projects have been applied worldwide, there is still a need for a comprehensive approach that meets local conditioning and capabilities. This paper investigated the composition, abundance, richness, alpha, beta, and gamma-diversity of pollinators between unused railway embankments and semi-natural grasslands. On 50 study sites (25 sites in unused railways and 25 their reference on grasslands), we collected data on the abundance, species richness and species diversity of bees, butterflies, and hoverflies. We conducted five samplings yearly (April-September) for two years, 2017-2018. To assess differences in abundance, species richness, alpha and beta diversity of pollinators between unused railways and controls, we used generalized linear mixed models (GLMM). To compare the composition of pollinator species, we applied non-metric multidimensional scaling (NMDS). Abundance, species richness, and Shannon-Wiener diversity index of all three groups of pollinators were significantly higher in unused railway lines than in control grasslands. Pollinator communities were more constant in unused railway lines than in grasslands. The NMDS analysis highlighted the importance of these structures for bee, butterfly and hoverfly communities, which were a subset of grassland species, but were more abundant. We indicated the highest total taxonomic beta-diversity for bees, butterflies, and hoverflies and species turnover for bees and butterflies in control grassland compared with unused railway lines. The taxonomical nestedness was significantly higher in unused railways lines for bees and butterflies than in control grasslands. In the case of hoverflies, we did not found any significant differences in species turnover and nestedness. Unused railway lines may act as a conservation tool for pollinator communities in intensively managed farmland and complement the declining semi-natural habitats.

The interplay of flow processes shapes aquatic invertebrate successions in floodplain channels - A modelling applied to restoration scenarios

The high biotic diversity supported by floodplains is ruled by the interplay of geomorphic and hydrological processes at various time scales, from daily fluctuations to decennial successions. Because understanding such processes is a key question in river restoration, we attempted to model changes in taxonomic richness in an assemblage of 58 macroinvertebrate taxa (21 gastropoda and 37 ephemeroptera, plecoptera and trichoptera, EPT) along two successional sequences typical for former braided channels. Individual models relating the occurrence of taxa to overflow and backflow durations were developed from field measurements in 19 floodplain channels of the Rhône floodplain (France) monitored over 10 years. The models were combined to simulate diversity changes along a progressive alluviation and disconnection sequence after the reconnection with the main river of a previously isolated channel. Two scenarios were considered: (i) an upstream + downstream reconnection creating a lotic channel, (ii) a downstream reconnection creating a semi-lotic channel. Reconnection led to a direct increase in invertebrate richness (on average x2.5). However, taxonomical richness showed a constant decrease as isolation progressed and reached an average of 2 for EPT and 7 for gastropods at the end of the scenarios. With more than 80% of the taxonomic models with an AUC equal or higher than 0.7 and slopes of linear relations between observed and predicted richness of 0.75 (gastropods) and 1 (EPT), the Boosted Regression Trees (BRT) provided a good basis for prediction of species assemblages. These models can be used to quantify a priori the sustainability and ecological efficiency of restoration actions and help floodplain restoration planning and management.

Soil fungal taxonomic diversity along an elevation gradient on the semi-arid Xinglong Mountain, Northwest China

Elevation gradients, often regarded as "natural experiments or laboratories", can be used to study changes in the distribution of microbial diversity related to changes in environmental conditions that typically occur over small geographical scales. We exploited this feature by characterizing fungal composition and diversity along an elevation gradient on Xinglong Mountain, northwest China. For this, we used MiSeq sequencing to obtain fungal sequences and clustered them into operational taxonomic units (OTUs). In total, we obtained 1,203,302 reads, 133,700 on average in each sample of soil collected at three selected elevations (2807, 3046, and 3536 m). The reads were assigned to 2192 OTUs. Inconsistent variations were observed in fungal alpha-diversity in samples from the three elevations. However, Principal Coordinate Analysis based on Bray-Curtis and UniFrac (weighted and unweighted) distance metrics revealed that fungal communities in soil samples from 3046 and 3536 m elevations were most similar. Principal Component Analysis based on relative abundances of shared OTUs confirmed that OTUs in samples from 3536 m elevation were more closely related to OTUs from 3046 m than samples from 2807 m elevation. Ascomycota, Basidiomycota, Glomeromycota, Cercozoa and Chytridiomycota were the most abundant fungal phyla across the elevation gradient. Our study also provides valuable indications of relations between fungal communities and an array of soil chemical properties, and variations in fungal taxonomic diversity across a substantial elevation gradient.

Gut microbiota differences between healthy older adults and individuals with Parkinson's disease: A systematic review

The 'Dual Hit' hypothesis, stating that Parkinson's disease (PD) begins via olfactory pathways and the gut, and the gastrointestinal symptoms PD individuals face, have largely driven the interest of the gut's involvement in PD. Studies have since observed gut microbiota differences between PD groups and controls, with these alterations potentially relating to PD pathophysiology. However, differences in the studies' methodologies precludes unanimity on the relationships of gut microbiota to PD. Thirteen observational case-control studies investigating gut microbiota in PD and controls were reviewed to assess how microbiota abundance and diversity relates to PD. Nine studies showed butyrate producing gut microbiota had lower abundances in PD compared to controls. Three studies reported α-diversity was higher, with one reporting it was lower, in PD compared to controls. Given most studies show abundance, not diversity, differences of butyrate producing bacteria between groups, we propose abundance differences are more associated with PD than microbiota diversity. As current research is observational, investigating how specific bacteria and their metabolites may alter throughout PD progression is warranted.

Rhea: a transparent and modular R pipeline for microbial profiling based on 16S rRNA gene amplicons

The importance of 16S rRNA gene amplicon profiles for understanding the influence of microbes in a variety of environments coupled with the steep reduction in sequencing costs led to a surge of microbial sequencing projects. The expanding crowd of scientists and clinicians wanting to make use of sequencing datasets can choose among a range of multipurpose software platforms, the use of which can be intimidating for non-expert users. Among available pipeline options for high-throughput 16S rRNA gene analysis, the R programming language and software environment for statistical computing stands out for its power and increased flexibility, and the possibility to adhere to most recent best practices and to adjust to individual project needs. Here we present the Rhea pipeline, a set of R scripts that encode a series of well-documented choices for the downstream analysis of Operational Taxonomic Units (OTUs) tables, including normalization steps, alpha- and beta-diversity analysis, taxonomic composition, statistical comparisons, and calculation of correlations. Rhea is primarily a straightforward starting point for beginners, but can also be a framework for advanced users who can modify and expand the tool. As the community standards evolve, Rhea will adapt to always represent the current state-of-the-art in microbial profiles analysis in the clear and comprehensive way allowed by the R language. Rhea scripts and documentation are freely available at https://lagkouvardos.github.io/Rhea.

Using Different Grazing Practices for Increasing Plant Biodiversity in the Dykes and Embankments Along the Rhône River (Southern France)

Extensive grazing by domestic herbivores is a widespread management practice used since the 80s in many European agro-ecosystems such as semi-natural grasslands to maintain open habitats and to enhance biodiversity. Such grazing systems have principally been tested in cultural ecosystems of high nature value threatened by grazing abandonment. However, there have been few case studies of grazing management in very anthropized ecosystems, such as the new ecosystems created by urban or industrial conversions. In Southern France, the Rhône channeling for navigation and electricity production generated in the 1950s the construction of thousands of hectares of dams and dykes which were colonized naturally by diverse plant communities. Yet shrub encroachment and the consequent recourse to mechanical cutting to facilitate control and maintenance, raise the question of how best to maintain and manage these new habitats. Consequently, since 1999, different low-intensity grazing management systems using rustic breeds of cattle, horses and goats have been tested on a protected reserve of 1454 ha located in the lower part of the Rhône river. Extensive grazing, more than cutting or no management, positively modified vegetation heterogeneity (beta-diversity), the target open grassland species, but not plant species richness (alpha-diversity). However, the current monitoring shows that these benefits of grazing will be confirmed only if low-intensity grazing systems are sustained and if new adaptations can be also made, such as the use of mixed stocking and the establishment of multiyear contracts with breeders.

Effective numbers in the partitioning of biological diversity

Admissible measures of diversity allow specification of the number of types (species, alleles, etc.) that are "effectively" involved in producing the diversity (the "diversity effective number", also referred to as "true diversity") of a community or population. In metacommunities, effective numbers additionally serve in partitioning the total diversity (symbolized by γ) into one component summarizing the diversity within communities (symbolized by α) and an independent component summarizing the differences between communities (symbolized by β). There is growing consensus that the β-component should be treated in terms of an effective number of "distinct" communities in the metacommunity. Yet, the notion of distinctness is shown in the present paper to remain conceptually ambiguous at least with respect to the diversity within the "distinct" communities. To overcome this ambiguity and to provide the means for designing further desirable effective numbers, a new approach is taken that involves a generalized concept of effective number. The approach relies on first specifying the distributional characteristics of partitioning diversity among communities (among which are differentiation, where the same types tend to occur in the same communities, and apportionment, where different types tend to occur in different communities), then developing the indices which measure these characteristics, and finally inferring the effective numbers from these indices.

MAJOR RESULTS

(1) The β-component reflects apportionment characteristics of metacommunity structure and is quantified by the "apportionment effective number" of communities (number of effectively monomorphic communities). Since differentiation between communities arises only as a side effect of apportionment, the common interpretation of the β-component in terms of differentiation is unwarranted. (2) Multiplicative as well as additive methods of partitioning the total type diversity (γ) involve apportionment effective numbers of communities that are based on different apportionment indices. (3) "Differentiation effective numbers" of communities exist but do not conform with the classical concept of partitioning total type diversity into components within and between communities. (4) Differentiation characteristics are measured as effective numbers of distinct types (rather than communities) from the dual perspective, in which the roles of type and community membership are exchanged. This is relevant e.g. in studies of endemism and competitive exclusion. (5) For Shannon-Wiener diversity, all of the differentiation and apportionment effective numbers are equal, with the exception of those representing additive partitioning. (6) Under either perspective, that is dual or non-dual, measures of compositional differentiation (as originally suggested for the assessment of β-diversity) do not figure in the partitioning of total diversity into components, since they do not build on the intrinsic concept of diversity.

Responses of microbial community from tropical pristine coastal soil to crude oil contamination

Brazilian offshore crude oil exploration has increased after the discovery of new reservoirs in the region known as pré-sal, in a depth of 7.000 m under the water surface. Oceanic islands near these areas represent sensitive environments, where changes in microbial communities due oil contamination could stand for the loss of metabolic functions, with catastrophic effects to the soil services provided from these locations. This work aimed to evaluate the effect of petroleum contamination on microbial community shifts (Archaea, Bacteria and Fungi) from Trindade Island coastal soils. Microcosms were assembled and divided in two treatments, control and contaminated (weathered crude oil at the concentration of 30 g kg(-1)), in triplicate. Soils were incubated for 38 days, with CO2 measurements every four hours. After incubation, the total DNA was extracted, purified and submitted for target sequencing of 16S rDNA, for Bacteria and Archaea domains and Fungal ITS1 region, using the Illumina MiSeq platform. Three days after contamination, the CO2 emission rate peaked at more than 20 × the control and the emissions remained higher during the whole incubation period. Microbial alpha-diversity was reduced for contaminated-samples. Fungal relative abundance of contaminated samples was reduced to almost 40% of the total observed species. Taxonomy comparisons showed rise of the Actinobacteria phylum, shifts in several Proteobacteria classes and reduction of the Archaea class Nitrososphaerales. This is the first effort in acquiring knowledge concerning the effect of crude oil contamination in soils of a Brazilian oceanic island. This information is important to guide any future bioremediation strategy that can be required.