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Human microbiome composition varies by location in the GI tract. Predominant bacterial genera in the oral cavity, esophagus, stomach, small intestine, and colon are delineated in this figure
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The human gastrointestinal (GI) tract contains communities of microbes (bacteria, fungi, viruses) that vary by anatomic location and impact human health. Microbial communities differ in composition based on age, diet, and location in the gastrointestinal tract. Differences in microbial composition have been associated with chronic disease states. I...
Citations
... The metabolites that act on the microbiota are called quorum sensing, and are essential in interbacterial communication, influencing homeostasis, development, death, virulence, and biofilm formation, in addition to allowing biofilm adaptation and changes in the environment (Ruan et al. 2020). Bacterial organisms are known to produce substances that can hinder the growth of other competing bacteria. ...
... Bacterial organisms are known to produce substances that can hinder the growth of other competing bacteria. These substances include proteins known as bacteriocins and small molecules like lactic acid, hydrogen peroxide, and reactive aldehydes (Ruan et al. 2020). As for the metabolites that directly influence host metabolism, evidence suggests that the microbiota produces and metabolizes neurotransmitters such as GABA, tryptophan, polyamines, and histamine (Tremlett et al. 2017;Pellegrini et al. 2018). ...
... The most populous bacterial phyla, constituting more than 90% of the intestinal microbiota, are Bacteriodetes and Firmicutes, with Bacteroidaceae and Prevotellaceae being the most abundant families of Bacteriodetes and Ruminococcuceae of Firmicutes (Kim and Jazwinski 2018). The main genera in the gut microbiota are Bacteroides, Eubacterium, Faecalibacterium, Alistipes, Ruminococcus, Clostridium, Roseburia, and Blautia, with the species Faecalibacterium prausnitzii, Oscillospira guillermondii, and Ruminococcus obeum more observed in adults (Ruan et al. 2020). ...
The aging of populations is a global phenomenon that follows a possible increase in the incidence of neurodegenerative diseases. Alzheimer’s, Parkinson’s, Multiple Sclerosis, Amyotrophic Lateral Sclerosis, and Huntington’s diseases are some neurodegenerative disorders that aging could initiate or aggravate. Recent research has indicated that intestinal microbiota dysbiosis can trigger metabolism and brain functioning, contributing to the etiopathogenesis of those neurodegenerative diseases. The intestinal microbiota and its metabolites show significant functions in various aspects, such as the immune system modulation (development and maturation), the maintenance of the intestinal barrier integrity, the modulation of neuromuscular functions in the intestine, and the facilitation of essential metabolic processes for both the microbiota and humans. The primary evidence supporting the connection between intestinal microbiota and its metabolites with neurodegenerative diseases are epidemiological observations and animal models experimentation. This paper reviews up-to-date evidence on the correlation between the microbiota-gut-brain axis and neurodegenerative diseases, with a specially focus on gut metabolites. Dysbiosis can increase inflammatory cytokines and bacterial metabolites, altering intestinal and blood-brain barrier permeability and causing neuroinflammation, thus facilitating the pathogenesis of neurodegenerative diseases. Clinical data supporting this evidence still needs to be improved. Most of the works found are descriptive and associated with the presence of phyla or species of bacteria with neurodegenerative diseases. Despite the limitations of recent research, the potential for elucidating clinical questions that have thus far eluded clarification within prevailing pathophysiological frameworks of health and disease is promising through investigation of the interplay between the host and microbiota.
... It is interconnected with other microbial communities like the vaginal and oral microbiota, influencing each other's composition and function. The oral cavity, the entry point for food digestion, hosts diverse microbial environments rich in different microbial taxa (Ruan et al., 2020;Hou et al., 2022). Moving through the GI tract, distinct microbiota populations thrive in various segments due to differences in pH, bile content, and nutrient availability, including bacteria belonging to the Bacillales, Steptococcaceae, Enterobacteriaceae, Veillonellaceae, and Pseudomonadaceae, as well as the pathogen Helicobacter pylori (Ruan et al., 2020). ...
... The oral cavity, the entry point for food digestion, hosts diverse microbial environments rich in different microbial taxa (Ruan et al., 2020;Hou et al., 2022). Moving through the GI tract, distinct microbiota populations thrive in various segments due to differences in pH, bile content, and nutrient availability, including bacteria belonging to the Bacillales, Steptococcaceae, Enterobacteriaceae, Veillonellaceae, and Pseudomonadaceae, as well as the pathogen Helicobacter pylori (Ruan et al., 2020). The colon, particularly, houses a complex microbiota responsible for fermenting complex carbohydrates and absorbing water and minerals including microbes shared by all the adults, belonging to the genera Bacteroides, Eubacterium, Faecalibacterium, Alistipes, Ruminococcus, Clostridium, Roseburia, and Blautia. ...
Modern lifestyle greatly influences human well-being. Indeed, nowadays people are centered in the cities and this trend is growing with the ever-increasing population. The main habitat for modern humans is defined as the built environment (BE). The modulation of life quality in the BE is primarily mediated by a biodiversity of microbes. They derive from different sources, such as soil, water, air, pets, and humans. Humans are the main source and vector of bacterial diversity in the BE leaving a characteristic microbial fingerprint on the surfaces and spaces. This review, focusing on articles published from the early 2000s, delves into bacterial populations present in indoor and outdoor urban environments, exploring the characteristics of primary bacterial niches in the BE and their native habitats. It elucidates bacterial interconnections within this context and among themselves, shedding light on pathways for adaptation and survival across diverse environmental conditions. Given the limitations of culture-based methods, emphasis is placed on culture-independent approaches, particularly high-throughput techniques to elucidate the genetic and -omic features of BE bacteria. By elucidating these microbiota profiles, the review aims to contribute to understanding the implications for human health and the assessment of urban environmental quality in modern cities.
... Embora os avanços no tratamento da RCU tenham sido significativos, desafios persistem, incluindo a variabilidade na resposta ao tratamento, o risco de efeitos adversos, a necessidade de monitoramento regular e a identificação de biomarcadores preditivos de resposta terapêutica. Além disso, questões relacionadas à acessibilidade e custo das terapias emergentes continuam a ser obstáculos para muitos pacientes.Além dos avanços farmacológicos, reconhece-se cada vez mais a importância das intervenções não farmacológicas, incluindo mudanças dietéticas, suplementação probiótica e manejo do estresse, no tratamento complementar da RCU(RUAN et al., 2020). Essas abordagens visam modificar a microbiota intestinal, reduzir a inflamação e melhorar a qualidade de vida dos pacientes. ...
A retocolite ulcerativa (RCU) é uma doença inflamatória intestinal crônica de etiologia complexa, caracterizada por inflamação contínua do cólon e do reto, resultando em sintomas debilitantes e complicações severas. Com isso, o presente artigo apresenta uma revisão dos avanços recentes no tratamento da RCU, destacando estratégias terapêuticas emergentes e sua eficácia clínica. A metodologia empregada consiste em uma revisão sistemática da literatura, na qual foram consultadas bases de dados relevantes e selecionados estudos que abordam os avanços no tratamento da RCU. Os resultados revelam os últimos anos, houve um rápido desenvolvimento de terapias direcionadas, incluindo agentes biológicos e pequenas moléculas, que visam diferentes componentes da cascata inflamatória. Os inibidores de citocinas, tais como os anticorpos monoclonais anti-TNF-α, anti-integrina e anti-interleucina, demonstraram eficácia significativa na indução e manutenção da remissão clínica em pacientes com RCU refratária aos tratamentos convencionais. Além disso, a terapia combinada de múltiplos agentes, como a associação de imunomoduladores e biológicos, tem sido explorada como uma estratégia para melhorar os desfechos clínicos e reduzir a necessidade de cirurgia. O desenvolvimento de biomarcadores preditivos de resposta ao tratamento também tem sido um foco de pesquisa, permitindo uma abordagem mais personalizada e eficaz para a gestão da RCU. No entanto, desafios persistentes, como a variabilidade na resposta ao tratamento e o risco de efeitos adversos, continuam a ser enfrentados na prática clínica. Portanto, são necessários estudos adicionais para otimizar as abordagens terapêuticas existentes e identificar novos alvos terapêuticos que possam proporcionar melhores resultados a longo prazo para os pacientes com RCU.
... However, little is known about the microbial degradation capacity in mammals, probably due to the lack of appropriate high-resolution analytical methods to quantify small MPs and NPs and chemical intermediates in animal and human feces. Similarly, research regarding the microbial degradation of MPs and the human gut microbiota is still scarce; however, numerous plastic-degrading bacteria described in insects or larvae are part of the core of human gut microbiota, particularly, several potentially pathogenic Proteobacteria, such as Enterobacteriaceae, Enterococcaceae, Listeria, Pseudomonas, and Klebsiella, but also Lactococcus [152,153]. ...
Microplastics and nanoplastics (MNPs) are becoming an increasingly severe global problem due to their widespread distribution and complex impact on living organisms. Apart from their environmental impact, the effects of MNPs on living organisms have also continued to attract attention. The harmful impact of MNPs has been extensively documented in marine invertebrates and larger marine vertebrates like fish. However, the research on the toxicity of these particles on mammals is still limited, and their possible effects on humans are poorly understood. Considering that MNPs are commonly found in food or food packaging, humans are primarily exposed to them through ingestion. It would be valuable to investigate the potential harmful effects of these particles on gut health. This review focuses on recent research exploring the toxicological impacts of micro- and nanoplastics on the gut, as observed in human cell lines and mammalian models. Available data from various studies indicate that the accumulation of MNPs in mammalian models and human cells may result in adverse consequences, in terms of epithelial toxicity, immune toxicity, and the disruption of the gut microbiota. The paper also discusses the current research limitations and prospects in this field, aiming to provide a scientific basis and reference for further studies on the toxic mechanisms of micro- and nanoplastics.
... However, little is known about microbial degradation capacity in mammals, probably due to lack of appropriate high-resolution analytical methods to quantify small MPs and NPs and chemical intermediates in animal and human feces. Similarly, research regarding microbial degradation of MPs and human gut microbiota is still scarce; however, numerous plastic-degrading bacteria described in insects or larvae are part of the core of human gut microbiota: particularly, several potentially pathogenic Proteobacteria, such as Enterobacteriaceae, Enterococcaceae, Listeria, Pseudomonas e Klebsiella, but also Lactococcus [157,158]. ...
: Microplastics and nanoplastics (MNPs) are becoming an increasingly severe global problem due to their widespread distribution and complex impact on living organisms. Apart from their environmental impact, the effects of MNPs on living organisms have also continued to attract attention. The harmful impact of MNPs has been extensively documented in marine invertebrates and larger marine vertebrates like fish. However, the research on the toxicity of these particles on mammals is still limited, and their possible effects on humans are poorly understood. Considering that MNPs are commonly found in food or food packaging, humans are primarily exposed to them through ingestion. It would be valuable to investigate the potential harmful effects of these particles on gut health. This review focuses on recent research exploring the toxicological impacts of micro- and nanoplastics on the gut, as observed in human cell lines and mammalian models. Available data from various studies indicate that the accumulation of MNPs in mammalian models and human cells may result in adverse consequences, in terms of epithelial toxicity, immune toxicity, and disruption of gut microbiota. The paper also discusses the current research limitations and prospects in this field, aiming to provide a scientific basis and reference for further studies on the toxic mechanisms of micro- and nanoplastics.
... Despite the diverse causes of COPD, current diagnostic and therapeutic approaches are limited, highlighting the need for a deeper understanding of its underlying mechanisms. 2 In recent years, there has been growing interest in the role of the gut microbiota, which has been found to influence various aspects of human health, including immune regulation and systemic inflammation. 3 Accumulating evidence suggests a potential link between the dysbiosis of the gut microbiota and the development of COPD. 4,5 Observational studies have identified gut microbiome dysbiosis in COPD patients, and rodent models have demonstrated its contribution to COPD development. ...
Background
Chronic obstructive pulmonary disease (COPD) is a respiratory disorder with a complex etiology involving genetic and environmental factors. The dysbiosis of gut microbiota has been implicated in COPD. Mendelian Randomization (MR) provides a tool to investigate causal links using genetic variants as instrumental variables. This study aims to employ MR analysis to explore the causal relationship between gut microbiota, lung function, and COPD.
Methods
We utilized genome-wide association study (GWAS) data from MiBioGen, UK Biobank and FinnGen, which were related to gut microbial taxa, lung function parameters including forced vital capacity in one second (FEV1), forced vital capacity (FVC), and percentage of predicted FEV1 (FEV1%pred), as well as GWAS data for COPD. MR analysis was conducted to assess the causal effects of gut microbiota on lung function and the risk of COPD. Sensitivity analysis was utilized to examine the stability of the causal relationships. Multiple testing and reverse analysis were employed to evaluate the robustness of these relationships.
Results
Using the IVW method, 64 causal correlations were identified. Through conducting sensitivity analysis, multiple testing, and reverse analysis, we identified 14 robust and stable causal relationships. The bacterial taxa that showed a positive association with lung function included Desulfovibrionaceae, Erysipelotrichales, Desulfovibrionales, Clostridiales, Clostridia, Deltaproteobacteria and Erysipelotrichia, while Selenomonadales and Negativicutes showed a negative association with lung function. The abundance of Holdemanella were positively correlated with the risk of COPD, while FamilyXIII exhibited a negative correlation with the risk of COPD.
Conclusion
Several microbial taxa were discovered to have a positive causal correlation with lung function, offering potential insights into the development of probiotics. The presence of microbial taxa negatively correlated with lung function and positively correlated with COPD emphasized the potential impact of gut microbiota dysbiosis on respiratory health.
... The microbiota produces metabolites and these metabolites influence the physiological functions of the host through their metabolic activity [31]. The analysis showed that 960 metabolites were quantitatively altered among the groups, of which 124 metabolites were involved in amino acid, carbohydrate, lipid, nucleotide, and vitamin metabolism (Fig. 5). ...
... Microbial metabolic pathways and compounds facilitate digestion and absorption of nutrients from food while promoting maturation and proper immune system function [31]. As the taxonomic richness and diversity in the diarrhoea groups were low compared to the healthy controls, we sought to understand the metabolite composition in children with and without diarrhoea. ...
Background
While the gut microbiome modulates the pathogenesis of enteric viruses, how infections caused by rotavirus A (RVA), with or without diarrhoea, alter the gut microbiota has been sparsely studied.
Methods
From a cohort of 224 vaccine naïve Gabonese children with and without diarrhoea (n = 177 and n = 67, respectively), 48 stool samples were analysed: (i) RVA with diarrhoea (n = 12); (ii) RVA without diarrhoea (n = 12); (iii) diarrhoea without RVA (n = 12); (iv) healthy controls without diarrhoea and RVA (n = 12). The 16S rRNA metabarcoding using Oxford Nanopore sequencing data was analysed for taxonomic composition, abundance, alpha and beta diversity, and metabolic pathways.
Findings
Alpha diversity showed that children with acute diarrhoea (with and without RVA infection), and children with acute diarrhoea without RVA had low microbial diversity compared to healthy children (p = 0.001 and p = 0.006, respectively). No significant differences observed when comparing children with RVA with or without diarrhoea. Beta diversity revealed high microbial heterogeneity in children without diarrhoea. Proteobacteria (68%) and Firmicutes (69%) were most common in the diarrhoea and non-diarrhoea groups, respectively. Proteobacteria (53%) were most common in children without RVA, while Firmicutes (55%) were most common with RVA. At the genus level, Escherichia (21%), Klebsiella (10%) and Salmonella (4%) were abundant in children with diarrhoea, while Blautia (11%), Clostridium (8%), Lachnoclostridium (6%) and Ruminococcus (5%) were abundant in children without diarrhoea. Metabolites involved in amino acid, carbohydrate, lipid, nucleotide, and vitamin metabolism were quantitatively altered.
Interpretation
Although host physiology dictates the intestinal milieu, diarrhoea per se can alter a balanced gut microbiota, whereas infectious diarrhoea disrupts the gut microbiome and reduces its diversity.
... A dense and diverse consortium of bacteria, archaea, fungi, protozoa, and viruses inhabit the human colon, constituting the resident gut microbiota [1][2][3][4]. Bacteria are by far the most abundant and studied community within the microbiome, to the point that the bacteriome has been identified with the microbiome itself for decades. Recently, increasing information on the abundance and diversity of microbes other than bacteria have been accumulating as well, even though the role in the ecology of the gut ecosystem, the interaction with other microbes and with the host, and the effects on human health of other microbial groups remain largely unexplored. ...
Archaea are an understudied component of the human microbiome. In this study, the gut archaeome and bacteriome of 60 healthy adults from different region were analyzed by whole-genome shotgun sequencing. Archaea were ubiquitously found in a wide range of abundances, reaching up to 7.2 %. The dominant archaeal phylum was Methanobacteriota, specifically the family Methanobacteriaceae, encompassing more than 50 % of Archaea in 50 samples. The previously underestimated Thermoplasmatota, mostly composed of Methanomassiliicoccaceae, dominated in 10 subjects (>50 %) and was present in all others except one. Halobacteriota, the sole other archaeal phylum, occurred in negligible concentration, except for two samples (4.6–4.8 %). This finding confirmed that the human gut archaeome is primarily composed of methanogenic organisms and among the known methanogenic pathway: i) hydrogenotrophic reduction of CO2 is the predominant, being the genus Methanobrevibacter and the species Methanobrevibacter smithii the most abundant in the majority of the samples; ii) the second pathway, that involved Methanomassiliicoccales, was the hydrogenotrophic reduction of methyl-compounds; iii) dismutation of acetate or methyl-compounds seemed to be absent. Co-occurrence analysis allowed to unravel correlations between Archaea and Bacteria that shapes the overall structure of the microbial community, allowing to depict a clearer picture of the human gut archaeome.
... They can also increase the reabsorption of harmful substances in the intestines, resulting in slow intestinal peristalsis and colonization by pathogenic bacteria easier, such as It also produces metabolites, such as short-chain fatty acids (SCFAs), to provide various vitamins and essential amino acids to the body and reduces the accumulation of body toxins [34][35][36]. The human intestinal flora undergoes a dynamic colonization and development process at different stages of life, and its composition is affected by anatomical location, time, and personal health status [37][38]. The gene pool of the microbial inhabitants is considerably diverse and almost 100 times larger than the gene pool of the host. ...
Type 1 diabetes (T1D) is a specific autoimmune disease related to genetic and autoimmune factors. Recent studies have found that the intestinal flora is one of the important environmental factors in the development of T1D. The gut microbiota is the largest microbiota in the human body and has a significant impact on material and energy metabolism. Related studies have found that the intestinal floras of T1D patients are unbalanced. Compared with normal patients, the abundance of beneficial bacteria is reduced, and various pathogenic bacteria are significantly increased, affecting the occurrence and development of diabetes. Medicinal and food homologous traditional Chinese medicine (TCM) has a multicomponent, multitarget, and biphasic regulatory effect. Its chemical composition can increase the abundance of beneficial bacteria, improve the diversity of the intestinal flora, reduce blood sugar, and achieve the purpose of preventing and treating T1D by regulating the intestinal flora and its metabolites. Therefore, based on a review of T1D, intestinal flora, and TCM derived from medicine and food, this review describes the relationship between T1D and the intestinal flora, as well as the research progress of TCM interventions for T1D through regulation of the intestinal flora. Medicine and food homologous TCM has certain advantages in treating diabetes and regulating the intestinal flora. It can be seen that there is still great research space and broad development prospects for the treatment of diabetes by regulating the intestinal flora with drug and food homologous TCM.
... Currently, increasing evidence indicates that the pathogenesis of type 2 diabetes mellitus (T2DM) is closely related to the gut microbiota of the host in addition to obesity, genetic, and environmental factors [6]. The gut microbiota is referred as "microbial organs" in the human body, which participates in the body's energy metabolism [7]. The gut microbiota is in a relatively upstream position in the progression of pre-diabetes, diabetes to diabetic complications, and mediates insulin resistance [8,9], oxidative stress [10] and chronic inflammation [11] mechanisms throughout the process. ...
Background:
Gut microbiota is closely related to the occurrence and development of diabetes and affects the prognosis of diabetic complications, and the underlying mechanisms are only partially understood. We aimed to explore the possible link between the gut microbiota and vascular inflammation of diabetic mice.
Methods:
The db/db diabetic and wild-type (WT) mice were used in this study. We profiled gut microbiota and examined the and vascular function in both db/db group and WT group. Gut microbiota was analyzed by 16s rRNA sequencing. Vascular function was examined by ultrasonographic hemodynamics and histological staining. Clostridium butyricum (CB) was orally administered to diabetic mice by intragastric gavage every 2 days for 2 consecutive months. Reactive oxygen species (ROS) and expression of nuclear factor erythroid-derived 2-related factor 2 (Nrf2) and heme oxygenase-1 (HO-1) were detected by fluorescence microscopy. The mRNA expression of inflammatory cytokines was tested by quantitative polymerase chain reaction.
Results:
Compared with WT mice, CB abundance was significantly decreased in the gut of db/db mice, together with compromised vascular function and activated inflammation in the arterial tissue. Meanwhile, ROS in the vascular tissue of db/db mice was also significantly increased. Oral administration of CB restored the protective microbiota, and protected the vascular function in the db/db mice via activating the Nrf2/HO-1 pathway.
Conclusion:
This study identified the potential link between decreased CB abundance in gut microbiota and vascular inflammation in diabetes. Therapeutic delivery of CB by gut transplantation alleviates the vascular lesions of diabetes mellitus by activating the Nrf2/HO-1 pathway.
