Modulating the Microbial Landscape

As an important part of ecosystem, microbes are widely distributed in various habitats. In recent years, more and more attention has been paid to the study on gut microbiota. The gut microbiota and their metabolites influence human and animal nutrition processing, metabolic balance, immune function, gastrointestinal development and other physiological activities. With the deepening of studies on human and animal gut microbiota, it has been found that some factors, such as diet, age, gender, and living environment, impacting on the composition of gut microbiota, while the differences among animal species have more significant influence on the gut microbiota composition. In relatively primitive grassland ecosystems, soil microbes interact with human and animal activities. On the one hand, microbes in the soil environment are the driving forces for the transformation and circulation of organic matter and nutrients. The improvement of soil microbial community diversity is beneficial for the soil fertility. On the other hand, human and animal activities will affect the diversity of soil microbial community. Although there are a lot of researches on soil microbiota, animal and human gut microbiota, their differences in diversity and composition within the same environment have not been studied. The advent of sequencing technology provides an effective mean for the accurate and comprehensive understanding of microbes, especially for the study of uncultivable microorganisms. The PacBio single-molecule real-time (SMRT) technology is advantageous in producing long sequence reads with high accuracy. Based on sequencing the full length 16S rRNA genes, the microbiota composition can be identified to the species level. Therefore, it is an effective approach for studying microbial diversity. We collected 56 stool and soil samples from Xilinguole, including 6, 10, 11, 9, and 10 stool samples from human, goat, cattle, horse, and sheep, respectively, as well as 10 soil samples. Genomic DNA was extracted from the samples. After DNA extraction and quality check, the 16S rRNA genes of all samples were amplified from the genomic DNA. The PCR products were sequenced using the PacBio RS II instrument. The QIIME software (V1.7) was used to analyze the sequencing data, and the R software (version 3.5.0) was used to further analyze and visualize the results. Firstly, it was found that the gut microbiota diversity of human was significantly lower than other samples ( P 0.01). The overall composition of the human and animal gut microbiota were dominated by the Firmicutes and Bacteroidetes phyla. However, the soil microbiota was dominated by Proteobacteria and Acidobacteria. At the genus level, the sheep, goat and cattle gut microbiota were dominated by Clostridium , Bacteroides , and Oscillibacter , while the horse gut microbiota was mainly composed of Clostridium , Eubacterium , and Treponema . The soil microbiota was composed mainly of Blastocatella and Bacillus . The human gut microbiota comprised much of Veillonella , Clostridium , Escherichia/Shigella . At the species level, the human gut microbiota mainly contained Escherichia/Shigella , dysenteriae , Streptococcus salivarius . The sheep, goat, cattle, and horse gut microbiota were dominated by Oscillibacter valericigenes and Eubacterium coprostanoligenes . The major species in soil were Blastocatella fastidiosa and Bacillus longiquaesitum . Moreover, principal coordinate analysis (PCoA) and hierarchical clustering analysis showed some differences in the microbiota structure among human gut, animal gut and soil samples. The gut microbiota structure was similar among cattle, goats and sheep. They were more different from the samples collected from human, horse and soil. We classified all samples into four clusters. Cluster 1 only included human samples; cluster 2 comprised the horse samples; cluster 3 was consisted of the sheep, goat, and cattle samples; while cluster 4 contained only the soil samples. Lastly, we identified the discriminatory OTUs and assigned them taxonomically to the species level. In conclusion, there were significant differences between animal gut microbiota and soil microbiota. The soil microbiota was more complex. As an omnivore, human gut microbiota diversity was significantly lower than other herbivorous animal (namely cattle, goat, horse and sheep). Although cattle, sheep, goat and horses are all herbivorous animals, the distinct features of the digestive systems could contribute to the difference in gut microbiota composition of horse from those of sheep, goat and cattle. This study revealed the differences of gut microbiota diversity between human and other animals, as well as from the soil microbial community. This work has laid a theoretical foundation for further studies on microbial diversity in different habitats.

Probiotics ameliorates pulmonary inflammation via modulating gut microbiota and rectifying Th17/Treg imbalance in a rat model of PM2.5 induced lung injury.

Humans are colonized from birth by bacteria, which form a complex and dynamic consortium of microorganisms known as microbiota. Overall, this complex microbial community outnumbers the somatic and germ cells of the host and collectively contains significantly higher genetic variability than that of the host genome (Backhed et al. 2005). Health-promoting indigenous bacteria, known as probiotic bacteria, represent a significant proportion of the human gut microbiota, whose composition is modulated by several factors including diet (Muegge et al. 2011). Probiotic bacteria are often introduced as live dietary supplements, but they are also present as live microflora in fermented foodstuffs for human consumption. The molecular mechanisms by which probiotics beneficially affect human health include strengthening of the intestinal barrier, modulation of the immune response and antagonism of pathogens through production of antimicrobial compounds or competition for mucosal binding sites (Marco et al. 2006). A significant proportion of the commercialized probiotic bacterial species was originally selected on the basis of their technological stability (e.g., resistance and viability during food processing and storage) or by a variety of easily measurable phenotypes, such as the ability to tolerate bile salts or to survive passage through the gastro-intestinal tract. These features do not necessarily associate with capabilities to provide human health benefits. Regulatory requirements concerning probiotic products are currently undergoing a profound transformation that will require elucidation of the mechanisms by which probiotic microorganisms beneficially influence human health. In order to achieve such fine characterization, the so-called “omics” approaches involving genomics and functional analysis represent an essential tool. In particular, probiogenomics, a recently proposed genomic discipline (Ventura et al. 2009), provides insights into the diversity and the evolution of probiotic microorganisms, thus allowing to clarify the molecular basis of their health-promoting activities. Probiogenomics also includes functional genomics, as well as investigation of microbe–microbe and host-microbe interactions that represent crucial aspects to expand our understanding of the roles of probiotics. The study of probiotic bacteria must necessarily take into account recent advances on the microbial ecology of the human gut. Elucidation of the bacterial biodiversity encompassing such a complex ecosystem is essential to highlight the presence or absence of specific groups of microorganisms (microbial biomarkers) and their association with health/disease conditions. In-depth knowledge of the composition and functionality of the human gut microbiota can also provide molecular criteria to predict individual susceptibility to specific probiotic supplements and could be utilized as a priori criteria for successful probiotic therapy. For all these reasons, we believe that a special issue of Genes & Nutrition devoted to probiotic bacteria and human gut microbiota is extremely appropriate. Two reviews within this special issue deal with the genomics of lactobacilli (Alterman et al.) and bifidobacteria (Pokusaeva et al.), which are considered the golden stars among probiotic bacteria. Probiotics are subject to several stressful conditions during industrial processing as well as in nature, where a fast stress-response is essential for survival (Ventura et al. 2006). Genetic characterization of the molecular players that enable probiotic bacteria to cope with such stressful stimuli are discussed by Ruiz et al. Microbial diversity within the human intestinal community is reported by Gerritsen et al., with special focus on the contribution of the gut microbiota to the health/disease balance. The impact of bacteriophages in modulating gut microbiota, as well as on bacterial survival and thus on the efficacy of probiotic treatments is described by Ventura et al. Prebiotic approaches represent new avenues for manipulating gut microbial composition and host responses to achieve health benefits. Conterno et al. explore the possible relationships between prebiotics and modulation of bifidobacterial and lactobacilli populations in the human gut, as a potential tool for obesity prevention and treatment. The effects of probiotics on human health are further discussed by Taverniti and Guglielmetti, who review the current knowledge on interactions of gut bacteria with the mammalian immune system. Safety is a crucial pre-requisite that probiotic bacteria must possess, and safety validation of probiotics includes exclusion of pathogenic potential. A key food safety issue reviewed by Devirgiliis et al. is the potential presence of horizontally transferable antibiotic resistance genes in probiotic strains naturally present in fermented foods, which can interact with the gut microbiota through the food chain. We wish to thank all authors who provided their manuscripts for this special issue, as well as all reviewers involved in processing the submitted articles. Overall, such a collective effort has provided a clear picture of the rapid progress occurring in the field of biology of probiotic bacteria, with special focus on the health benefits resulting from their interactions with the human host.

We investigated the hypothesis that exposure to inhaled diesel exhaust PM can alter the gut microbiome and intestinal integrity, thereby promoting systemic inflammatory response and early CVD risk, which are exacerbated by HF diet. Furthermore, we investigated whether the observed exposure and diet-mediated outcomes could be mitigated through probiotic treatment. We performed an exposure study on C57Bl/6 male mice, placed on either a low fat (LF) diet or a high-fat (HF) diet, and exposed via oropharyngeal aspiration to 35 μg diesel exhaust particles (DEP) suspended in 35 μl of sterile saline or sterile saline controls (CON) twice a week for four weeks. A subset of mice on HF diet were dosed with 0.3 g/day (PRO, ~7.5x108 CFU/day) of probiotic Ecologic® Barrier 849 (Winclove Probiotics) in drinking water during the course of the study. For our first aim, we investigated the alterations in the gut microbiome, measured circulating cytokines and lipopolysaccharide (LPS), and measured CVD biomarkers in the heart. Our results revealed that exposure to inhaled DEP results in gut dysbiosis characterized by expansion of the phyla Verrucomicrobia and Proteobacteria and reduction in Actinobacteria, which was exacerbated by HF diet. Probiotics mitigated the DEP-mediated expansion of Proteobacteria and re-established Actinobacteria in the intestine of HF animals. Furthermore, we determined that exposure to inhaled DEP increases systemic LPS and inflammatory markers IL-1α, IL-3, G-CSF, and TNF-α. Furthermore, we found that inhaled DEP exposure results in increased CVD biomarkers sICAM-1, sP-selectin, and thrombomodulin in the heart. Probiotic treatment was effective in attenuating LPS, inflammatory responses, and CVD biomarkers in HF animals, validating the involvement of the microbiome in mediating inhaled DEP-mediated responses. Considering the effects we observed in the microbiota and systemically of the HF and probiotic treatment animals, we investigated the effects of inhaled DEP on intestinal integrity and inflammation in HF ± PRO animals. Our results showed that inhaled DEP in conjunction with HF diet promotes increased goblet cell and mucin 2 expression, tight junction (TJ) proteins (claudin-3, occludin, and zonula occludens (ZO)-1) expression, matrix metalloproteinase (MMP)-9, toll-like receptor (TLR)-4, and decreased TNF-α and IL-10. Moreover, we found that probiotics promoted intestinal immune response following inhaled DEP exposure characterized by an increase in TNF-α and IL-10 and showed variable expression of TJs in the intestine. In conclusion, we found that inhaled DEP exposure results in changes in gut microbial profiles, altered intestinal integrity, systemic inflammation, and increased CVD biomarkers, which are exacerbated by HF diet. The use of probiotics in this study proved to be pivotal in understanding the microbiome's influences on the regulation of intestinal integrity, intestinal inflammation, systemic inflammation, and cardiovascular system following inhaled DEP exposure with HF diet.

Gut microbiota are suspected to affect brain functions and behavior as well as lowering inflammation status. Therefore, an effect on depression has already been suggested by recent research. The aim of this randomized double-blind controlled trial was to evaluate the effect of probiotic treatment in depressed individuals. Within inpatient care, 82 currently depressed individuals were randomly assigned to either receive a multistrain probiotic plus biotin treatment or biotin plus placebo for 28 days. Clinical symptoms as well as gut microbiome were analyzed at the begin of the study, after one and after four weeks. After 16S rRNA analysis, microbiome samples were bioinformatically explored using QIIME, SPSS, R and Piphillin. Both groups improved significantly regarding psychiatric symptoms. Ruminococcus gauvreauii and Coprococcus 3 were more abundant and β-diversity was higher in the probiotics group after 28 days. KEGG-analysis showed elevated inflammation-regulatory and metabolic pathways in the intervention group. The elevated abundance of potentially beneficial bacteria after probiotic treatment allows speculations on the functionality of probiotic treatment in depressed individuals. Furthermore, the finding of upregulated vitamin B6 and B7 synthesis underlines the connection between the quality of diet, gut microbiota and mental health through the regulation of metabolic functions, anti-inflammatory and anti-apoptotic properties. Concluding, four-week probiotic plus biotin supplementation, in inpatient individuals with a major depressive disorder diagnosis, showed an overall beneficial effect of clinical treatment. However, probiotic intervention compared to placebo only differed in microbial diversity profile, not in clinical outcome measures.

The Intestinal Metabolome: An Intersection Between Microbiota and Host

The gut microbiota, which plays an important role in health and disease processes, is affected by many disease processes, such as cirrhosis, and dysbiosis can lead to the development of numerous liver diseases, including complications of cirrhosis. In this disease group, the intestinal microbiota shifts towards dysbiosis for reasons such as endotoxemia, increased intestinal permeability, and decreased bile acid production. Although weak absorbable antibiotics and lactulose are among the treatment strategies in cirrhosis and its most common complication, hepatic encephalopathy (HE), this may not be the most appropriate treatment option for all patients, in view of its side-effects and high costs. Accordingly, it seems possible that probiotics could be used as an alternative treatment. The use of probiotics in these patient groups has a direct effect on the gut microbiota. Probiotics can also provide treatment with multiple effects through various mechanisms, such as lowering serum ammonia levels, reducing oxidative stress and reducing the intake of other toxins. This review was written to explain the intestinal dysbiosis associated with HE in cirrhotic patients, and the role of probiotics in treatment.

Chapter 12 - Human microbiome and genito-urinary disorders

Diets rich in whole grains are associated with improved health and a lower risk of non-communicable diseases, but the mechanisms through which these health benefits are conveyed are uncertain. One mechanism may be improvements in the gut environment by the delivery of fermentable substrates and associated phytochemicals to the lower gut and modification of the gut microbiome. Quinoa is included in the whole-grain category because of its structural similarities to cereals but the effects of its consumption on the gut microbiome have not been investigated to date. Our aim was to examine the impact of daily quinoa consumption on the gut microbiome in a 4-week randomised cross-over intervention separated by a 4-week wash-out period involving 28 adult males. Participants consumed either a quinoa-enriched wheat-bread roll providing 20 g quinoa flour each day, or a control wheat-only bread roll. Stool samples were collected in sterile collection tubes immediately before and at the end of each intervention period. DNA was then extracted, and the 16S rRNA V4 region of extracted DNA was amplified and sequenced. For both the control and quinoa bread periods, there were no changes at the phyla or genus level between baseline and week 4 (all p > 0.05). Diversity in the microbiome profile was not different from baseline after either intervention arms. The results show that small changes in the type of cereal consumed-substituting 20 g of refined wheat flour with whole-grain quinoa flour-was not able to significantly modulate the gut microbiome. Further studies with higher levels of quinoa or longer exposure periods are needed to ascertain if there is a dose-response effect of quinoa, and if these effects are able to translate into clinical outcomes.

Enzymes containing tungsten rather than the ubiquitous and analogous element molybdenum are prevalent in the human gut microbiome, especifically in microbes that contribute to overall gut health. Eubacterium limosum is a dominant human gut organism whose production of beneficial short-chain fatty acids (SCFAs) from lactate involves tungstoenzymes. Here, we characterized E. limosum Tub, a tungsten storage protein. Tub has a sub-nanomolar affinity for tungstate and contains a single TOBE domain first characterized in a molybdate storage protein. Crystal structures revealed Tub assembles as a hexamer composed of a trimer of dimers, capable of binding eight tungstate oxyanions at two distinct binding sites located at inter-subunit interfaces. Tungstate-saturated Tub exhibited unusually high thermal and chemical stability. Glucose-grown E. limosum accumulates tungsten in Tub and has low levels of two tungstoenzymes, termed WOR1 and FDH, which oxidize aldehydes and formate, respectively. Lactate-grown cells contain high concentrations of these two tungstoenzymes where WOR1 and FDH are involved in converting lactate to SCFAs. Glucose-grown cells appear to accumulate tungstate in Tub in preparation for lactate availability in the human gut. Tub and other TOBE-containing proteins are widespread in the human gut microbiome, and gene co-occurrence analysis predicts that there are comparable numbers of TOBE-containing proteins involved in the storage of tungstate as there are that bind molybdate. The results with E. limosum represent an important step for understanding tungsten storage mechanisms for tungstoenzymes within human gut microbes in general.IMPORTANCETungsten metabolism was found to be prevalent in the human gut microbiome, which is involved in the detoxification of food and antimicrobial aldehydes, as well as in the production of beneficial SCFAs. In this study, we characterized a protein in the human gut microbe, Eubacterium limosum, that stores tungstate in preparation for its use in enzymes involved in SCFA generation. This revealed several families of tungstate binding proteins that are also involved in tungstate transport and tungstate-dependent regulation and are widely distributed in the human gut microbiome. Elucidating how tungsten is stored and transported in the human gut microbes contributes to our understanding of the human gut microbiome and its impact on human health.

Linkages between plant rhizosphere and animal gut environments: Interaction effects of pesticides with their microbiomes

BackgroundSulfoquinovose (SQ) is a green-diet-derived sulfonated glucose and a selective substrate for a limited number of human gut bacteria. Complete anaerobic SQ degradation via interspecies metabolite transfer to sulfonate-respiring bacteria produces hydrogen sulfide, which has dose- and context-dependent health effects. Here, we studied potential SQ degradation by the mammalian host and the impact of SQ supplementation on human and murine gut microbiota diversity and metabolism.Results13CO2 breath tests with germ-free C57BL/6 mice gavaged with 13C-SQ were negative. Also, SQ was not degraded by human intestinal cells in vitro, indicating that SQ is not directly metabolized by mice and humans. Addition of increasing SQ concentrations to human fecal microcosms revealed dose-dependent responses of the microbiota and corroborated the relevance of Agathobacter rectalis and Bilophila wadsworthia in cooperative degradation of SQ to hydrogen sulfide via interspecies transfer of 2,3-dihydroxy-1-propanesulfonate (DHPS). Similar to the human gut microbiome, the genetic capacity for SQ or DHPS degradation is sparsely distributed among bacterial species in the gut of conventional laboratory mice. Escherichia coli and Enterocloster clostridioformis were identified as primary SQ degraders in the mouse gut. SQ and DHPS supplementation experiments with conventional laboratory mice and their intestinal contents showed that SQ was incompletely catabolized to DHPS. Although some E. clostridioformis genomes encode an extended sulfoglycolytic pathway for both SQ and DHPS fermentation, SQ was only degraded to DHPS by a mouse-derived E. clostridioformis strain.ConclusionsOur findings suggest that SQ is solely a nutrient for the gut microbiota and not for mice and humans, emphasizing its potential as a prebiotic. SQ degradation by the microbiota of conventional laboratory mice differs from the human gut microbiota by absence of DHPS degradation activity. Hence, the microbiota of conventional laboratory mice does not fully represent the SQ metabolism in humans, indicating the need for alternative model systems to assess the impact of SQ on human health. This study advances our understanding of how individual dietary compounds shape the microbial community structure and metabolism in the gut and thereby potentially influence host health.Video Supplementary InformationThe online version contains supplementary material available at 10.1186/s40168-025-02175-x.

The gut microbiota, made up of trillions of microorganisms that inhabit the gastrointestinal tract, plays a fundamental role in human health, influencing immunological and metabolic processes and even wound healing. Recently, studies have shown that the gut microbiota can also significantly impact post-operative recovery. This emerging field of research is revealing new insights into how the composition and function of the microbiota can affect the recovery of patients after surgery and the effectiveness of wound healing. Understanding these interactions paves the way for the development of innovative therapies that can improve surgical outcomes and promote faster and more efficient recovery. This review seeks to explore the new insights into the impact of gut microbiota on postoperative recovery and wound healing, highlighting the emerging therapies and scientific advances that are shaping this field. By investigating the current literature and evaluating recent clinical studies, we aim to provide a comprehensive overview of the interactions between the microbiota and healing processes, as well as discussing the therapeutic implications of these findings for clinical practice. This literature review aims to investigate the relationship between the gut microbiota and various aspects of health and disease, using a selected set of landmark studies. To this end, high-impact publications were selected that address topics related to the gut microbiota, its functions, benefits and implications for human health. Post-operative recovery and wound healing are complex processes that involve a series of biological responses, including inflammation, tissue remodeling and cell regeneration. The gut microbiota influences these processes in a number of ways, starting with the modulation of the immune system. Studies have shown that a healthy microbiota can promote a balanced inflammatory response, which is crucial for proper wound healing and surgical recovery. Imbalances in the microbiota, known as dysbiosis, can lead to exacerbated or insufficient inflammatory responses, impairing healing and increasing the risk of post-operative complications. The two-way communication between the gut and other organs, known as the gut-organ axis, is fundamental to understanding how the gut microbiota can influence post-operative recovery. Metabolites produced by the microbiota, such as short-chain fatty acids (SCFA), have anti-inflammatory and immunomodulatory effects that can favor wound healing. In addition, the intestinal microbiota can influence the integrity of the intestinal barrier, preventing bacterial translocation and consequent systemic infection, a common complication after surgery. Based on these insights, several emerging therapies are being developed to modulate the gut microbiota and improve post-operative outcomes. One of the promising approaches is the use of probiotics and prebiotics. Probiotics are live microorganisms that, when administered in adequate amounts, confer health benefits on the host, while prebiotics are substrates that promote the growth and activity of beneficial bacteria in the gut. Clinical studies have shown that supplementation with specific probiotics can reduce the incidence of post-operative infections and improve wound healing. Another innovative approach is fecal microbiota transplantation (FMT), which involves transferring microbiota from a healthy donor to a patient with dysbiosis. FMT has shown promising results in restoring the intestinal microbiota and improving post-operative outcomes in patients undergoing major surgery. In addition, diet and nutrition play a crucial role in modulating the microbiota. Diets rich in fiber and bioactive compounds, such as polyphenols, can promote a healthy microbiota and consequently improve postoperative recovery and wound healing. It is concluded that the impact of gut microbiota on postoperative recovery and wound healing is a rapidly evolving field of research with significant potential to transform clinical practices. New insights are revealing how the microbiota influences inflammatory and immunological processes essential for surgical recovery. Emerging therapies, such as probiotics, prebiotics and fecal microbiota transplantation, are showing promising results in improving postoperative outcomes. Modulation of the gut microbiota represents an innovative and effective approach to optimizing patient recovery and promoting faster and more efficient healing. With further research and the integration of this knowledge into clinical practice, it is hoped that microbiota intestinal becomes a key component in post-operative management and wound care, significantly improving patients’ quality of life.

The secondary metabolites produced by fungi known as mycotoxins, are capable of causing mycotoxicosis (diseases and death) in human and animals. Contamination of feedstuffs as well as food commodities by fungi occurs frequently in a natural manner and is accompanied by the presence of mycotoxins. The occurrence of mycotoxins' contamination is further stimulated by the on-going global warming as reflected in some findings. This review comprehensively discussed the role of mycotoxins (trichothecenes, zearalenone, fumonisins, ochratoxins, and aflatoxins) toward gut health and gut microbiota. Certainly, mycotoxins cause perturbation in the gut, particularly in the intestinal epithelial. Recent insights have generated an entirely new perspective where there is a bi-directional relationship exists between mycotoxins and gut microbiota, thus suggesting that our gut microbiota might be involved in the development of mycotoxicosis. The bacteria–xenobiotic interplay for the host is highlighted in this review article. It is now well established that a healthy gut microbiota is largely responsible for the overall health of the host. Findings revealed that the gut microbiota is capable of eliminating mycotoxin from the host naturally, provided that the host is healthy with a balance gut microbiota. Moreover, mycotoxins have been demonstrated for modulation of gut microbiota composition, and such alteration in gut microbiota can be observed up to species level in some of the studies. Most, if not all, of the reported effects of mycotoxins, are negative in terms of intestinal health, where beneficial bacteria are eliminated accompanied by an increase of the gut pathogen. The interactions between gut microbiota and mycotoxins have a significant role in the development of mycotoxicosis, particularly hepatocellular carcinoma. Such knowledge potentially drives the development of novel and innovative strategies for the prevention and therapy of mycotoxin contamination and mycotoxicosis.

Nonalcoholic fatty liver disease (NAFLD) is a common chronic liver disease. The present study explores the clinical efficacy of probiotics in the treatment of patients with NAFLD by conducting a systematic search of relevant databases. The RevMan 5.4 software was used to evaluate the effects of probiotics on liver function (i.e. alanine aminotransferase [ALT], aspartate aminotransferase [AST], gamma-glutamyl transferase [GGT], lipid metabolism, blood glucose, inflammatory factors [e.g. tumor necrosis factor-α, TNF-α] and body mass index [BMI]) in patients with NAFLD. A total of 18 high-quality studies were included in the final meta-analysis. The results of the meta-analysis showed that the use of probiotics in the adjuvant treatment of patients with NAFLD improved liver function and reduced ALT levels (mean difference [MD]: −0.07; 95% confidence interval [CI]: −12.95, −7.19), AST levels (MD: −11.90; 95% CI: −16.55, −7.25) and GGT levels (MD: −8.61; 95% CI: −14.74, −2.48); additionally, the treatment effect was more obvious when the treatment time exceeded 12 weeks. Probiotic therapy reduced patients’ triglyceride levels (MD: −9.71; 95% CI: −18.39, −1.03) and total cholesterol levels (MD: −22.31; 95% CI: −25.41, −19.21). Probiotic treatment improved patients’ levels of fasting blood (MD: −8.22; 95% CI: −12.25, −4.20), insulin (MD: −2.68; 95% CI: −4.94, −0.41) and insulin resistance (MD: −0.72; 95% CI: −1.21, −0.24). Probiotic adjuvant therapy for patients with NAFLD reduced their BMI by approximately 1.67 (95% CI: −2.93, −0.41) and TNF-α levels. The adjuvant treatment of NAFLD with probiotics has a positive clinical effect, which is influenced by treatment time.