Complex Microbial Ecosystem Research Articles

LnCeCell 2.0: an updated resource for lncRNA-associated ceRNA networks and web tools based on single-cell and spatial transcriptomics sequencing data.

We describe LnCeCell 2.0 (http://bio-bigdata.hrbmu.edu.cn/LnCeCell), an updated resource for lncRNA-associated competing endogenous RNA (ceRNA) networks and web tools based on single-cell and spatial transcriptomics sequencing(stRNA-seq)data. We have updated the LnCeCell 2.0 database with significantly expanded data and improved features, including(i) 257 single-cell RNA sequencingandstRNA-seqdatasets across 86 diseases/phenotypes and 80 human normal tissues, (ii) 836581 cell-specific and spatial spot-specific ceRNA interactions and functional networks for 1002988 cells and 367971 spatial spots, (iii) 15489 experimentally supported lncRNA biomarkers related to disease pathology, diagnosis and treatment, (iv) detailed annotation of cell type, cell state, subcellular and extracellular locations of ceRNAs through manual curationand (v) ceRNA expression profiles and follow-up clinical information of 20326 cancer patients. Further, a panel of 24 flexible tools (including 8 comprehensive and 16 mini-analysis tools) was developed to investigate ceRNA-regulated mechanisms at single-cell/spot resolution. The CeCellTraject tool, for example, illustrates the detailed ceRNA distribution of different cell populations and explores the dynamic change of the ceRNA network along the developmental trajectory. LnCeCell 2.0 will facilitate the study of fine-tuned lncRNA-ceRNA networks with single-cell and spatial spot resolution, helping us to understand the regulatory mechanisms behind complex microbial ecosystems.

Does Encapsulation Improve the Bioavailability of Polyphenols in Humans? A Concise Review Based on In Vivo Human Studies.

Polyphenols offer an array of health benefits that can contribute to well-being. Nevertheless, their bioactivity can be compromised due to their low bioavailability. Encapsulation has been explored as a strategy to enhance the stability and bioavailability of polyphenols. During encapsulation, polyphenols are protected from degradation by a wall material that acts as a protective coating. This coating shields the polyphenols from the harsh physiological conditions of digestion, ensuring their delivery to the intestine. However, the majority of evidence, particularly regarding bioavailability after digestion, is derived from in vitro studies. While these studies provide valuable preliminary insights, they cannot definitively confirm the effects in vivo due to their inability to accurately replicate physiological conditions and the complex gut microbial ecosystem. Consequently, this review seeks to evaluate the current evidence from in vivo human studies to elucidate the efficacy of encapsulation in improving polyphenols' bioavailability. Current clinical evidence on the impact of encapsulation on polyphenol bioavailability is primarily focused on polyphenols derived from grape pomace, cocoa, and bilberries, as well as individual polyphenols such as fisetin, hesperidin, and curcumin. Encapsulation has been an effective technique in improving the bioavailability of individual polyphenols like hesperidin, fisetin, and curcumin. However, this approach has not yielded consistent results when applied to groups of polyphenols, such as bilberry anthocyanins or cocoa phenolic acids. Encapsulation by micellization has shown promising results in improving the bioavailability of curcumin in a nutraceutical context. Further studies are needed to explore the bioavailability of encapsulated polyphenols, especially in the functional food context.

One health: the impact of environment, detergents and hygiene on barrier, microbiome and allergy

SummaryA variety of body surfaces, such as skin and mucosal membranes—from the nasopharyngeal area to the lungs, uterus, vaginal area, and digestive tract—contain complex microbial ecosystems that are tailored to the specifics of the respective niche [1].The so-called dysbiosis—a disadvantageous change in the composition of the microbiome—is associated with the pathogenesis of a variety of diseases [2]. Gastrointestinal as well as cardiovascular, metabolic, neurodegenerative, psychological, oncological, and also allergic diseases have been linked to microbial dysbiosis. Susceptibility to allergies can be due to genetic predisposition; in addition, extrinsic factors from today’s lifestyle increasingly contribute to microbiome changes, but also to the disruption of the skin and mucosal barrier and thus to the development of allergies [3].Gisela, a fictional farmer, guides us through this review. She is representative of adults and children of all genders in industrialized countries. During her daily routine, the skin and mucosal microbiome is influenced by a variety of exogenous factors. These include everyday personal hygiene products, detergents for laundry and dishes, food, medication, animal contact, and exposure to various outdoor environments. Gisela’s daily routine will illustrate how the human microbiome and the skin barrier are modified in positive or negative ways, and how this could influence the development of allergies. Furthermore, potential measures for the prevention and management of dysbiosis will be discussed in terms of examples of alternative products and behaviors.

Advancing Aquaculture Sustainability: A Comprehensive Review of Biofloc Technology Trends, Innovative Research Approaches, and Future Prospects

ABSTRACTBiofloc technology (BFT), initially adapted for shrimp farming in the 1970s, represents a sophisticated ecosystem of microorganisms designed to enhance aquaculture productivity and sustainability. Despite its established history, research into BFT is surprisingly still at an early stage globally. This review conducted a bibliometric analysis of 612 articles from major aquaculture journals spanning 2008–2023 to systematically explore the development, trends, and focal points of BFT research. The analysis revealed that the bulk of significant contributions originates from Brazil and China, and highlighting areas of interest can be categorized into four hotspots, such as (1) efficient nitrogen transformation, (2) biofloc microbiology, (3) biofloc's immunostimulant properties, and (4) the evaluation of research methodologies. At the end, the microecology concept was introduced, and the cross‐discipline methods were promoted in the aquaculture field. Notably, much of the BFT research is still at an exploratory phase, with numerous functional bacteria unidentified and optimization strategies for BFT underdeveloped. These gaps present opportunities for enhancing aquaculture through improvements in wastewater management, product quality, safety, and yield. Furthermore, the review notes a growing trend in applying microbiome research and microecological analysis in aquaculture, with high‐throughput sequencing data increasingly used to understand microbial interactions and nitrogen transformation within bioflocs. This direction promises to unlock further insights into the complex microbial ecosystems of bioflocs and their applications in sustainable aquaculture.

463 Cyber-Physical Systems with robots and AI for precision dairy farming

Abstract The emergence of precision livestock farming (PLF) offers a transformative lens through which to prioritize animal welfare. At the heart of this transformation lies the rumen, a complex microbial ecosystem within dairy cows responsible for converting feed into nutrients and impacting cow health, productivity, and environmental footprint. Despite its pivotal role, our understanding of the inner workings of the rumen remains limited due to a lack of real-time monitoring tools. My research leverages AI and robotics in PLF to address this gap, focusing on developing a closed-loop system for continuous, in-vivo rumen monitoring. This system employs cyber-physical systems (CPS) embedded with modular sensors and adaptive algorithms. These sensor modules, powered by AI-based data tracking, autonomously monitor rumen temperature, humidity, pressure, and methane concentration, enabling early detection of imbalances and prompt interventions to maintain optimal rumen health. A key innovation is the self-powered in-vivo robot capable of traversing the rumen’s stratified layers. Guided by AI-powered localization, this robot unlocks unparalleled access to new data, aiding in identifying specific regions associated with conditions like subacute ruminal acidosis (SARA) and methane production. This non-invasive approach eliminates the need for traditional cannulation, minimizing stress on the animal and opening new avenues for animal scientists. The impact of this research extends beyond individual cow health. By optimizing rumen function, we can improve feed efficiency, reduce methane emissions, and promote overall sustainability in dairy farming. Additionally, real-time data insights pave the way for precision nutrition, tailored interventions, and improved disease prevention, directly enhancing animal welfare. This novel approach to rumen monitoring represents a significant step towards realizing the full potential of PLF. By integrating AI and robotics, we can usher in a future where animal welfare and environmental sustainability go hand-in-hand, ultimately contributing to a more responsible and ethical dairy industry.

A streamlined culturomics case study for the human gut microbiota research

Bacterial culturomics is a set of techniques to isolate and identify live bacteria from complex microbial ecosystems. Despite its potential to revolutionize microbiome research, bacterial culturomics has significant challenges when applied to human gut microbiome studies due to its labor-intensive nature. Therefore, we established a streamlined culturomics approach with minimal culture conditions for stool sample preincubation. We evaluated the suitability of non-selective medium candidates for maintaining microbial diversity during a 30-day incubation period based on 16S rRNA gene amplicon analysis. Subsequently, we applied four culture conditions (two preincubation media under an aerobic/anaerobic atmosphere) to isolate gut bacteria on a large scale from eight stool samples of healthy humans. We identified 8141 isolates, classified into 263 bacterial species, including 12 novel species candidates. Our analysis of cultivation efficiency revealed that seven days of aerobic and ten days of anaerobic incubation captured approximately 91% and 95% of the identified species within each condition, respectively, with a synergistic effect confirmed when selected preincubation media were combined. Moreover, our culturomics findings expanded the coverage of gut microbial diversity compared to 16S rRNA gene amplicon sequencing results. In conclusion, this study demonstrated the potential of a streamlined culturomics approach for the efficient isolation of gut bacteria from human stool samples. This approach might pave the way for the broader adoption of culturomics in human gut microbiome studies, ultimately leading to a more comprehensive understanding of this complex microbial ecosystem.

Crosstalk between gut microbiota and host immune system and its response to traumatic injury.

Millions of microorganisms make up the complex microbial ecosystem found in the human gut. The immune system's interaction with the gut microbiota is essential for preventing inflammation and maintaining intestinal homeostasis. Numerous metabolic products that can cross-talk between immune cells and the gut epithelium are metabolized by the gut microbiota. Traumatic injury elicits a great and multifaceted immune response in the minutes after the initial offense, containing simultaneous pro- and anti-inflammatory responses. The development of innovative therapies that improve patient outcomes depends on the gut microbiota and immunological responses to trauma. The altered makeup of gut microbes, or gut dysbiosis, can also dysregulate immunological responses, resulting in inflammation. Major human diseases may become more common as a result of chronic dysbiosis and the translocation of bacteria and the products of their metabolism beyond the mucosal barrier. In this review, we briefly summarize the interactions between the gut microbiota and the immune system and human disease and their therapeutic probiotic formulations. We also discuss the immune response to traumatic injury.

Influence of the initial microbiota on eggplant shibazuke pickle and eggplant juice fermentation.

The findings shown in this study provide insight into the microbial succession during spontaneous pickle fermentation and the role of Lactiplantibacillus plantarum in eggplant pickle production. Moreover, the novel method of using filter-sterilized vegetable juice with an artificial microbiota to emulate spontaneous fermentation can be applied to other spontaneously fermented products. This approach allows for the evaluation of the effect of specific initial microbiota in the absence of plant-associated bacteria from raw materials potentially promoting a greater understanding of microbial behavior in complex microbial ecosystems during vegetable fermentation.

Tradition unveiled: a comprehensive review of microbiological studies on Portuguese traditional cheeses, merging conventional and OMICs analyses

The microbial communities inhabiting Portuguese traditional cheeses play a fundamental role in shaping their unique flavor, texture, and safety characteristics. This comprehensive review synthesizes findings from both conventional microbiological studies and advanced OMICs analyses to provide a deeper understanding of the microbiota dynamics in these cheeses. We explore the microbial composition, diversity, and functional roles of bacteria, yeasts, and molds across various Protected Designation of Origin (PDO) cheeses, highlighting their contributions to cheese ripening, flavor development, and safety. Additionally, we discuss the potential of OMICs technologies, namely metagenomics, in unraveling the complex microbial ecosystems of Portuguese traditional cheeses. Through this integrative approach, we aim to shed light on the intricate interplay between microorganisms and cheese matrices, unveiling the secrets behind the rich heritage and distinctiveness of Portuguese traditional cheeses.

Actinobacteria diversity associated with sponge Amorphinopsis exacavans from Rancabuaya Beach, Garut, Indonesia

Abstract Sponges are complex marine organisms known for their symbiotic relationships with various bacterial communities, which play structural and functional roles within the sponge holobiont. Actinobacteria have received much attention because of their potential pharmaceutical applications. This study examines Amorphinopsis excavans profile, distinguishing between endosymbionts and ectosymbionts. The microbial grouping was characterized using Next Generation Sequencing (NGS) anchored to the 16S rRNA marker. The results showed that Proteobacteria and Firmicutes dominated both the endosymbiont and ectosymbiont communities at the phylum level. The actinobacterial diversity index at the genus level in both communities was 2.77 and 3.11, indicating moderate to high diversity without a dominant genus. For the genus level, the evenness scores of 0.81 and 0.89 indicated a high population type within the bacterial community. Relative abundance revealed the three most prevalent genera in the endosymbiont community were Rothia, Thermoplyspora, and Thermomonospora. In contrast, Kocuria, Mycobacterium, and Bifidobacterium were the three most common genera of ectosymbionts. Leuconostoc citreum was the first species known to be associated with a sponge. This study is a developing metagenomic assessment of actinobacterial diversity in A. excavans, providing novel insights into the sponge’s complex microbial ecosystem.

Identification of 3-ketocapnine reductase activity within the human microbiota.

The microbial synthesis of sulfonolipids within the human body is likely involved in maintaining human health or causing diseases. However, the enzymes responsible for their biosynthesis remain largely unknown. In this study, we identified and verified the role of 3-ketocapnine reductase, the third-step enzyme, in the four-step conversion of l-phosphoserine into sulfobacin B both in vivo and in vitro. This finding builds upon our previous research into sulfonolipid biosynthesis, which focused on the vaginal bacterium Chryseobacterium gleum DSM 16776 and the gut bacterium Alistipes finegoldii DSM 17242. Through comprehensive gene mapping, we demonstrate the widespread presence of potential sulfonolipid biosynthetic genes across diverse bacterial species inhabiting various regions of the human body. These findings shed light on the prevalence of sulfonolipid-like metabolites within the human microbiota, suggesting a potential role for these lipid molecules in influencing the intricate biointeractions within the complex microbial ecosystem of the human body.

Idiosyncratic invasion trajectories of human bacterial pathogens facing temperature disturbances in soil microbial communities

Current knowledge about effects of disturbance on the fate of invaders in complex microbial ecosystems is still in its infancy. In order to investigate this issue, we compared the fate of Klebsiella pneumoniae (Kp) and Listeria monocytogenes (Lm) in soil microcosms. We then used environmental disturbances (freeze–thaw or heat cycles) to compare the fate of both invaders and manipulate soil microbial diversity. Population dynamics of the two pathogens was assessed over 50 days of invasion while microbial diversity was measured at times 0, 20 and 40 days. The outcome of invasion was strain-dependent and the response of the two invaders to disturbance differed. Resistance to Kp invasion was higher under the conditions where resident microbial diversity was the highest while a significant drop of diversity was linked to a higher persistence. In contrast, Lm faced stronger resistance to invasion in heat-treated microcosms where diversity was the lowest. Our results show that diversity is not a universal proxy of resistance to microbial invasion, indicating the need to properly assess other intrinsic properties of the invader, such as its metabolic repertoire, or the array of interactions between the invader and resident communities.

Source tracing the bedroom bacteria across different climate zones in China during the heating season

Approximately 1/3 of people's time is spent in bedrooms. Regulating the health implications arising from the bedroom bacterial community demands an in-depth understanding of both the bacterial composition and the influential factors. This study employed high-throughput 16 S rRNA amplicon sequencing to characterize the bacterial community in 23 residential bedrooms across five climate zones in China. Our findings reveal that the bacterial richness and diversity were highest in the Hot-Summer-Cold-Winter (HSCW) zone, possibly due to its lowest indoor temperature during the heating season. Employing an advanced source tracing algorithm, we identified ventilation rate as the dominant factor affecting outdoor bacterial presence, with each additional air change per hour (ACH) increasing the outdoor bacterial abundance by 13.7 %. The integumentary system was the largest contributor to the occupant-associated bacteria, particularly in the residences located in the Severe Cold and Cold zones. Our study provides valuable insights into the diverse bacterial communities in residential bedrooms across various climate zones in China, elucidating the key factors and sources that contribute to shaping these complex microbial ecosystems.

Small Intestinal Bacterial Overgrowth (SIBO) and Twelve Groups of Related Diseases-Current State of Knowledge.

The human gut microbiota creates a complex microbial ecosystem, characterized by its high population density, wide diversity, and complex interactions. Any imbalance of the intestinal microbiome, whether qualitative or quantitative, may have serious consequences for human health, including small intestinal bacterial overgrowth (SIBO). SIBO is defined as an increase in the number of bacteria (103-105 CFU/mL), an alteration in the bacterial composition, or both in the small intestine. The PubMed, Science Direct, Web of Science, EMBASE, and Medline databases were searched for studies on SIBO and related diseases. These diseases were divided into 12 groups: (1) gastrointestinal disorders; (2) autoimmune disease; (3) cardiovascular system disease; (4) metabolic disease; (5) endocrine disorders; (6) nephrological disorders; (7) dermatological diseases; (8) neurological diseases (9); developmental disorders; (10) mental disorders; (11) genetic diseases; and (12) gastrointestinal cancer. The purpose of this comprehensive review is to present the current state of knowledge on the relationships between SIBO and these 12 disease groups, taking into account risk factors and the causal context. This review fills the evidence gap on SIBO and presents a biological-medical approach to the problem, clearly showing the groups and diseases having a proven relationship with SIBO, as well as indicating groups within which research should continue to be expanded.

Investigation of the Microbiome of Industrial PDO Sfela Cheese and Its Artisanal Variants Using 16S rDNA Amplicon Sequencing and Shotgun Metagenomics.

Sfela is a white brined Greek cheese of protected designation of origin (PDO) produced in the Peloponnese region from ovine, caprine milk, or a mixture of the two. Despite the PDO status of Sfela, very few studies have addressed its properties, including its microbiology. For this reason, we decided to investigate the microbiome of two PDO industrial Sfela cheese samples along with two non-PDO variants, namely Sfela touloumotiri and Xerosfeli. Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS), 16S rDNA amplicon sequencing and shotgun metagenomics analysis were used to identify the microbiome of these traditional cheeses. Cultured-based analysis showed that the most frequent species that could be isolated from Sfela cheese were Enterococcus faecium, Lactiplantibacillus plantarum, Levilactobacillus brevis, Pediococcus pentosaceus and Streptococcus thermophilus. Shotgun analysis suggested that in industrial Sfela 1, Str. thermophilus dominated, while industrial Sfela 2 contained high levels of Lactococcus lactis. The two artisanal samples, Sfela touloumotiri and Xerosfeli, were dominated by Tetragenococcus halophilus and Str. thermophilus, respectively. Debaryomyces hansenii was the only yeast species with abundance > 1% present exclusively in the Sfela touloumotiri sample. Identifying additional yeast species in the shotgun data was challenging, possibly due to their low abundance. Sfela cheese appears to contain a rather complex microbial ecosystem and thus needs to be further studied and understood. This might be crucial for improving and standardizing both its production and safety measures.

Digestion and importance of starch in ruminants

Ruminants have a unique digestive physiology that heavily relies on microbial fermentation specifically in the rumen. This review explores the complex mechanisms of starch digestion in ruminants and highlights its crucial role in shaping their nutritional landscape. The rumen, a complex microbial ecosystem, is the primary site for starch digestion. Enzymatic hydrolysis and microbial fermentation of starch in this compartment produce important byproducts, such as volatile fatty acids (VFAs) and microbial proteins. These byproducts are crucial sources of energy and protein, which affect the overall metabolic dynamics of ruminants. It is essential to have a comprehensive understanding of the factors that influence starch digestion rates to optimize ruminant nutrition. This review examines the various factors involved in starch digestion, including feed composition, microbial populations, and enzymatic activity, and how they contribute to the digestive process. Additionally, identifying and characterizing starch fractions in concentrated feed sources is crucial for formulating well-balanced rations. In conclusion, this review synthesizes current knowledge on starch digestion in ruminants, offering insights into the complexities of the process. The collected information not only contributes to our academic understanding but also has practical implications for optimizing feeding strategies, enhancing nutrient utilization, and promoting the overall well-being of ruminants.

An integrated approach to explore the microbial biodiversity of natural milk cultures for cheesemaking

The use of natural milk culture (NMC) represents a key factor in PDO Montasio cheeses, contributing to its distinctive sensory profile. The complex microbial ecosystem of NMCs is the result of heat treatment and incubation conditions, which can vary considerably among different production plants. In this study, the microbiota of NMCs collected from 10 PDO Montasio cheese dairies was investigated employing colony counts and metagenomic analysis. Furthermore, residual sugars, organic acids, and volatile profiles were quantitatively investigated. Results showed that Streptococcus thermophilus was the dominant species in all NMCs, and a subdominant population made of other streptococci and L. salivarius was also present. The incubation temperature appeared to be the main driver of biodiversity in NMCs. Metagenomics allowed us to evidence the presence of minor species involving safety (e.g., Staph. aureus) as well as possible functional aspects (Next Generation Probiotics). Statistical analysis based on residual sugars, organic acids, and volatiles' content allowed to correlate the presence of specific microbial groups with metabolites of great technological and sensory relevance, which can contribute to giving value to the artisanal production procedures of NMCs and clarify their role in the creation of the characteristics of PDO Montasio cheese.

Oral_voting_transfer: classification of oral microorganisms' function proteins with voting transfer model.

The oral microbial group typically represents the human body's highly complex microbial group ecosystem. Oral microorganisms take part in human diseases, including Oral cavity inflammation, mucosal disease, periodontal disease, tooth decay, and oral cancer. On the other hand, oral microbes can also cause endocrine disorders, digestive function, and nerve function disorders, such as diabetes, digestive system diseases, and Alzheimer's disease. It was noted that the proteins of oral microbes play significant roles in these serious diseases. Having a good knowledge of oral microbes can be helpful in analyzing the procession of related diseases. Moreover, the high-dimensional features and imbalanced data lead to the complexity of oral microbial issues, which can hardly be solved with traditional experimental methods. To deal with these challenges, we proposed a novel method, which is oral_voting_transfer, to deal with such classification issues in the field of oral microorganisms. Such a method employed three features to classify the five oral microorganisms, including Streptococcus mutans, Staphylococcus aureus, abiotrophy adjacent, bifidobacterial, and Capnocytophaga. Firstly, we utilized the highly effective model, which successfully classifies the organelle's proteins and transfers to deal with the oral microorganisms. And then, some classification methods can be treated as the local classifiers in this work. Finally, the results are voting from the transfer classifiers and the voting ones. The proposed method achieved the well performances in the five oral microorganisms. The oral_voting_transfer is a standalone tool, and all its source codes are publicly available at https://github.com/baowz12345/voting_transfer.

A comprehensive guide to assess gut mycobiome and its role in pathogenesis and treatment of inflammatory bowel disease.

Inflammatory bowel disease (IBD) is an immune mediated chronic inflammatory disorder of gastrointestinal tract, which has underlying multifactorial pathogenic determinants such as environmental factors, susceptibility genes, gut microbial dysbiosis and a dysregulated immune response. Human gut is a frequent inhabitant of complex microbial ecosystem encompassing bacteria, viruses, parasites, fungi and other microorganisms that have an undisputable role in maintaining balanced homeostasis. All of these microbes interact with immune system and affect human gut physiology either directly or indirectly with interaction of each other. Intestinal fungi represent a smaller but crucial component of the human gut microbiome. Besides interaction with bacteriome and virome, it helps in balancing homoeostasis between pathophysiological and physiological processes, which is often dysregulated in patients with IBD. Understanding of gut mycobiome and its clinical implications are still in in its infancy as opposed to bacterial component of gut microbiome, which is more often focused. Modulation of gut mycobiome represents a novel and promising strategy in the management of patients with IBD. Emerging mycobiome-based therapies such as diet interventions, fecal microbiota transplantation (FMT), probiotics (both fungal and bacterial strains) and antifungals exhibit substantial effects in calibrating the gut mycobiome and restoring dysbalanced immune homeostasis by restoring the core gut mycobiome. In this review, we summarized compositional and functional diversity of the gut mycobiome in healthy individuals and patients with IBD, gut mycobiome dysbiosis in patients with IBD, host immune-fungal interactions and therapeutic role of modulation of intestinal fungi in patients with IBD.

The Effect of Cross-Sex Fecal Microbiota Transplantation on Metabolism and Hormonal Status in Adult Rats.

Increasing evidence of sexual dimorphism in the pathophysiology of metabolic complications caused by sex steroids is under investigation. The gut microbiota represents a complex microbial ecosystem involved in energy metabolism, immune response, nutrition acquisition, and the health of host organisms. Gender-specific differences in composition are present between females and males. The purpose of this study was to use cross-sex fecal microbiota transplantation (FMT) for the detection of sex-dependent metabolic, hormonal, and gut microbiota changes in female and male recipients. Healthy non-obese female and male Wistar rats were divided into donor, same-sex, and cross-sex recipient groups. After a 30-day period of FMT administration, biochemical markers (glucose and lipid metabolism) and sex hormones were measured, and the gut microbiota was analyzed. The cross-sex male recipients displayed a significantly lower testosterone concentration compared to the males that received same-sex FMT. Sex-dependent changes caused by cross-sex FMT were detected, while several bacterial taxa correlated with plasma testosterone levels. This study represents the first to study the effect of cross-sex changes in the gut microbiome concerning metabolic and hormonal changes/status in adult non-obese Wistar rats. Herein, we present cross-sex FMT as a potential tool to modify sex-specific pathologies.