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Research Square Apr 2024Latent tuberculosis infection (LTBI) is common in people living with HIV (PLHIV) in high TB burden settings. Active TB is associated with specific stool taxa; however,...
BACKGROUND
Latent tuberculosis infection (LTBI) is common in people living with HIV (PLHIV) in high TB burden settings. Active TB is associated with specific stool taxa; however, little is known about the stool microbiota and LTBI, including in PLHIV.
METHOD
Within a parent study that recruited adult females with HIV from Cape Town, South Africa into predefined age categories (18-25, 35-60 years), we characterised the stool microbiota of those with [interferon-γ release assay (IGRA)- and tuberculin skin test (TST)-positive] or without (IGRA- and TST- negative) LTBI (n=25 per group). 16S rRNA DNA sequences were analysed using QIIME2, Dirichlet Multinomial Mixtures, DESeq2 and PICRUSt2.
RESULTS
No α- or β-diversity differences occurred by LTBI status; however, LTBI-positives were depleted. Inferred metagenome data showed LTBI-negative-enriched pathways included several involved in methylglyoxal degradation, L-arginine, putrescine, 4-aminobutanoate degradation and L-arginine and ornithine degradation. Stool from LTBI-positives demonstrated differential taxa abundance based on a quantitative response to antigen stimulation (depletion associated with higher IGRA or TST responses, respectively). In LTBI-positives, older people had different β-diversities than younger people whereas, in LTBI-negatives, no differences occurred across age groups.
CONCLUSION
Amongst female PLHIV, those with LTBI had, vs. those without LTBI, Gemmiger-enriched, which are producers of short chain fatty acids. Taxonomic differences amongst people with LTBI occurred according to quantitative response to antigen stimulation and age. These data enhance our understanding of the microbiome's potential role in LTBI.
PubMed: 38645218
DOI: 10.21203/rs.3.rs-4182285/v1 -
Clinical Nutrition (Edinburgh, Scotland) May 2024Enteral nutrition (EN) involves replacing all or part of a person's habitual diet with a nutritional formula. The impact of varying doses of EN on the gut microbiome...
INTRODUCTION
Enteral nutrition (EN) involves replacing all or part of a person's habitual diet with a nutritional formula. The impact of varying doses of EN on the gut microbiome remains understudied.
METHODS
Healthy adults replaced all (100% EN) or part (85% EN, 50% EN and 20% EN) of their energy requirements with EN for 7 days. Faecal samples were collected before and on day 7 of interventions. Faecal pH, short chain fatty acids (SCFAs), branched-chain fatty acids (BCFAs) and 16S rRNA sequencing were performed. Dietary assessment was performed with 7-day food diaries.
RESULTS
Sixty-one participants (31 females; median (IQR) age: 24.7 (23.0-27.8) years) were recruited. A dose-dependent impact of EN on faecal microbiota, SCFAs, BCFAs) and pH was observed, with changes detectable at EN intakes of at least 50% of energy requirements. 100% and 85% EN reduced the abundance of fibre-fermenting taxa such as Agathobacter, Faecalibaterium, Succinivibrio and Acidaminococcus. In parallel, potentially harmful organisms like Eubacterium, Actinomyces, and Klebsiella increased. In the 50% EN group, adherence to a diet high in fish, vegetables, potatoes, non-alcoholic beverages, and fat spreads, and low in cereal products, milk, and meat negatively correlated with changes in microbiota structure (r = -0.75, P = 0.025). This signal was not observed when using compositional tools for microbiota analysis.
CONCLUSIONS
EN detrimentally influences the faecal microbiota and diet-related bacterial metabolites in a dose-dependent manner, particularly at doses of at least 50%. The findings of this study have implications for the dietary management and counselling of patients receiving high volume EN.
Topics: Humans; Feces; Female; Male; Adult; Gastrointestinal Microbiome; Fatty Acids, Volatile; Enteral Nutrition; Young Adult
PubMed: 38615449
DOI: 10.1016/j.clnu.2024.04.010 -
Frontiers in Psychiatry 2024Schizophrenia is a complex psychiatric disorder, of which molecular pathogenesis remains largely unknown. Accumulating evidence suggest that gut microbiota may affect...
INTRODUCTION
Schizophrenia is a complex psychiatric disorder, of which molecular pathogenesis remains largely unknown. Accumulating evidence suggest that gut microbiota may affect brain function via the complex gut-brain axis, which may be a potential contributor to schizophrenia. However, the alteration of gut microbiota showed high heterogeneity across different studies. Therefore, this study aims to identify the consistently altered gut microbial taxa associated with schizophrenia.
METHODS
We conducted a systematic search and synthesis of the up-to-date human gut microbiome studies on schizophrenia, and performed vote counting analyses to identify consistently changed microbiota. Further, we investigated the effects of potential confounders on the alteration of gut microbiota.
RESULTS
We obtained 30 available clinical studies, and found that there was no strong evidence to support significant differences in α-diversity and β-diversity between schizophrenic patients and healthy controls. Among 428 differential gut microbial taxa collected from original studies, we found that 8 gut microbial taxa were consistently up-regulated in schizophrenic patients, including Proteobacteria, Gammaproteobacteria, , , , , and . While 5 taxa were consistently down-regulated in schizophrenia, including , , , and .
DISCUSSION
These findings suggested that gut microbial changes in patients with schizophrenia were characterized by the depletion of anti-inflammatory butyrate-producing genera, and the enrichment of certain opportunistic bacteria genera and probiotics. This study contributes to further understanding the role of gut microbiota in schizophrenia, and developing microbiota-based diagnosis and therapy for schizophrenia.
PubMed: 38596637
DOI: 10.3389/fpsyt.2024.1366311 -
Applied Microbiology and Biotechnology Apr 2024The rumen microbiota is important for energy and nutrient acquisition in cattle, and therefore its composition may also affect carcass merit and meat quality attributes....
The rumen microbiota is important for energy and nutrient acquisition in cattle, and therefore its composition may also affect carcass merit and meat quality attributes. In this study, we examined the associations between archaeal and bacterial taxa in the rumen microbiota of beef cattle and 12 different attributes, including hot carcass weight (HCW), dressing percentage, ribeye area (REA), intramuscular fat content, marbling score, fat thickness, yield grade, moisture content, purge loss, and shear force. There were significant correlations between the relative abundance of certain archaeal and bacterial genera and these attributes. Notably, Selenomonas spp. were positively correlated with live weight and HCW, while also being negatively correlated with purge loss. Members of the Christensenellaceae R-7, Moryella, and Prevotella genera exhibited positive and significant correlations with various attributes, such as dressing percentage and intramuscular fat content. Ruminococcaceae UCG-001 was negatively correlated with live weight, HCW, and dressing percentage, while Acidaminococcus and Succinivibrionaceae UCG-001 were negatively correlated with intramuscular fat content, moisture content, and marbling score. Overall, our findings suggest that specific changes in the rumen microbiota could be a valuable tool to improve beef carcass merit and meat quality attributes. Additional research is required to better understand the relationship between the rumen microbiota and these attributes, with the potential to develop microbiome-targeted strategies for enhancing beef production. KEY POINTS: • Certain rumen bacteria were associated with carcass merit and meat quality • Moryella was positively correlated with intramuscular fat in beef carcasses • Acidaminococcus spp. was negatively correlated with marbling and intramuscular fat.
Topics: Cattle; Animals; Body Composition; Rumen; Meat; Microbiota; Bacteria; Archaea
PubMed: 38581592
DOI: 10.1007/s00253-024-13126-1 -
Animal Bioscience Apr 2024This study investigated the effects of Apidaecin Api-PR19 as feed additive on growth performance, intestinal health, and small intestinal microbiota of broilers.
OBJECTIVE
This study investigated the effects of Apidaecin Api-PR19 as feed additive on growth performance, intestinal health, and small intestinal microbiota of broilers.
METHODS
A total of 360 1-d-old Arbor Acres broilers were randomly assigned to 3 groups with 6 replicates including control group with basal diet (CON), antibiotic growth promotor group with basal plus 10 mg/kg colistin sulfate and 50mg/kg roxarsone (AGP), and antibacterial peptide group with basal diet plus 330 mg/kg Apidaecin Api-PR19 (ABP). The trial lasted 35 d.
RESULTS
Results showed that dietary Api-PR19 addition increased (p<0.05) the average daily feed intake (ADFI), average daily gain (ADG) and decreased (p<0.05) feed conversion ratio (FCR) during 1 to 21 d compared with the CON group. The digestibility of dry matter and crude protein were higher in AGP and ABP groups (p<0.05) where greater trypsin activity was detected in duodenum (p<0.05). The ratio of villus height to crypt depth (V/R) in duodenum and jejunum was increased at 35 d when broilers were given diets with ABP or AGP (p<0.05). Besides, ABP treatments up-regulated (p<0.05) the mRNA expression of EAAT3, GLUT2, ZO-1 and Claudin-1 in duodenum of broilers at 35 d of age. The results of immunohistochemistry showed that ABP treatment significantly increased (p<0.05) duodenal sIgA content. In addition, 16S rRNA gene sequencing revealed that there were differences in the intestinal microbiota diversity and composition among three groups. Notably, the linear discriminant analysis effect size (LEfSe) showed that p_Firmicutes, g_Enterococcus, g_Carnobacterium, g_Kitasatospora and g_Acidaminococcus were dominant in ABP group. Redundancy analysis showed that these changes in gut microbiota in ABP group had correlation with growth performance, intestinal morphology, and content of sIgA.
CONCLUSION
In general, these results indicated that dietary 330 mg/kg Apidaecin Api-PR19 supplementation promoted growth performance of broilers by improving intestinal development, nutrients absorption, immune function and modulating intestinal microbiota.
PubMed: 38575128
DOI: 10.5713/ab.23.0357 -
Journal of Molecular Biology May 2024The class 2 CRISPR-Cas9 and CRISPR-Cas12a systems, originally described as adaptive immune systems of bacteria and archaea, have emerged as versatile tools for...
The class 2 CRISPR-Cas9 and CRISPR-Cas12a systems, originally described as adaptive immune systems of bacteria and archaea, have emerged as versatile tools for genome-editing, with applications in biotechnology and medicine. However, significantly less is known about their substrate specificity, but such knowledge may provide instructive insights into their off-target cleavage and previously unrecognized mechanism of action. Here, we document that the Acidaminococcus sp. Cas12a (AsCas12a) binds preferentially, and independently of crRNA, to a suite of branched DNA structures, such as the Holliday junction (HJ), replication fork and D-loops, compared with single- or double-stranded DNA, and promotes their degradation. Further, our study revealed that AsCas12a binds to the HJ, specifically at the crossover region, protects it from DNase I cleavage and renders a pair of thymine residues in the HJ homologous core hypersensitive to KMnO oxidation, suggesting DNA melting and/or distortion. Notably, these structural changes enabled AsCas12a to resolve HJ into nonligatable intermediates, and subsequently their complete degradation. We further demonstrate that crRNA impedes HJ cleavage by AsCas12a, and that of Lachnospiraceae bacterium Cas12a, without affecting their DNA-binding ability. We identified a separation-of-function variant, which uncouples DNA-binding and DNA cleavage activities of AsCas12a. Importantly, we found robust evidence that AsCas12a endonuclease also has 3'-to-5' and 5'-to-3' exonuclease activity, and that these two activities synergistically promote degradation of DNA, yielding di- and mononucleotides. Collectively, this study significantly advances knowledge about the substrate specificity of AsCas12a and provides important insights into the degradation of different types of DNA substrates.
Topics: Acidaminococcus; Bacterial Proteins; CRISPR-Associated Proteins; CRISPR-Cas Systems; DNA, Cruciform; Endodeoxyribonucleases; Substrate Specificity
PubMed: 38575054
DOI: 10.1016/j.jmb.2024.168550 -
BioRxiv : the Preprint Server For... May 2024Somatic genome editing in mouse models has increased our understanding of the effects of genetic alterations in areas ranging from neuroscience to cancer biology and...
Somatic genome editing in mouse models has increased our understanding of the effects of genetic alterations in areas ranging from neuroscience to cancer biology and beyond. However, existing models are limited in their ability to create multiple targeted edits. Thus, our understanding of the complex genetic interactions that underlie development, homeostasis, and disease remains incomplete. Cas12a is an RNA-guided endonuclease with unique attributes that enable simple targeting of multiple genes with crRNA arrays containing tandem guides. To accelerate and expand the generation of complex genotypes in somatic cells, we generated transgenic mice with Cre-regulated and constitutive expression of enhanced Cas12a (enAsCas12a). In these mice, enAsCas12a-mediated somatic genome editing robustly generated compound genotypes, as exemplified by the initiation of diverse cancer types driven by homozygous inactivation of trios of tumor suppressor genes. We further integrated these modular crRNA arrays with clonal barcoding to quantify the size and number of tumors with each array, as well as the efficiency of each crRNA. These Cas12a alleles will enable the rapid generation of disease models and broadly facilitate the high-throughput investigation of coincident genomic alterations in somatic cells .
PubMed: 38496463
DOI: 10.1101/2024.03.07.583774 -
Journal of Gastroenterology Apr 2024Alterations in gut microbiota are associated with the pathogenesis of metabolic diseases, including metabolic-associated fatty liver disease (MAFLD). The aim of this...
BACKGROUND/AIM
Alterations in gut microbiota are associated with the pathogenesis of metabolic diseases, including metabolic-associated fatty liver disease (MAFLD). The aim of this study was to evaluate gut microbiota composition and functionality in patients with morbid obesity with different degrees of MAFLD, as assessed by biopsy.
SUBJECTS/METHODS
110 patients with morbid obesity were evaluated by biopsy obtained during bariatric surgery for MAFLD. Stool samples were collected prior to surgery for microbiota analysis.
RESULTS
Gut microbiota from patients with steatosis and non-alcoholic steatohepatitis (NASH) were characterized by an enrichment in Enterobacteriaceae (an ethanol-producing bacteria), Acidaminococcus and Megasphaera and the depletion of Eggerthellaceae and Ruminococcaceae (SCFA-producing bacteria). MAFLD was also associated with enrichment of pathways related to proteinogenic amino acid degradation, succinate production, menaquinol-7 (K2-vitamin) biosynthesis, and saccharolytic and proteolytic fermentation. Basic histological hepatic alterations (steatosis, necroinflammatory activity, or fibrosis) were associated with specific changes in microbiota patterns. Overall, the core microbiome related to basic histological alterations in MAFLD showed an increase in Enterobacteriaceae and a decrease in Ruminococcaceae. Specifically, Escherichia coli was associated with steatosis and necroinflammatory activity, whilst Escherichia-shigella was associated with fibrosis and necroinflammatory activity.
CONCLUSIONS
We established a link between gut microbiota alterations and histological injury in liver diagnosis using biopsy. Harmful products such as ethanol or succinate may be involved in the pathogenesis and progression of MAFLD. Thus, these alterations in gut microbiota patterns and their possible metabolic pathways could add information to the classical predictors of MAFLD severity and suggest novel metabolic targets.
Topics: Humans; Non-alcoholic Fatty Liver Disease; Gastrointestinal Microbiome; Obesity, Morbid; Ethanol; Fibrosis; Succinates
PubMed: 38265508
DOI: 10.1007/s00535-023-02075-7 -
International Journal of Molecular... Jan 2024The CRISPR-Cas12a platform has attracted interest in the genome editing community because the prototypical Acidaminococcus Cas12a generates a staggered DNA double-strand...
The CRISPR-Cas12a platform has attracted interest in the genome editing community because the prototypical Acidaminococcus Cas12a generates a staggered DNA double-strand break upon binding to an AT-rich protospacer-adjacent motif (PAM, 5'-TTTV). The broad application of the platform in primary human cells was enabled by the development of an engineered version of the natural Cas12a protein, called Cas12a Ultra. In this study, we confirmed that CRISPR-Cas12a Ultra ribonucleoprotein complexes enabled allelic gene disruption frequencies of over 90% at multiple target sites in human T cells, hematopoietic stem and progenitor cells (HSPCs), and induced pluripotent stem cells (iPSCs). In addition, we demonstrated, for the first time, the efficient knock-in potential of the platform in human iPSCs and achieved targeted integration of a marker gene into the safe harbor site and a super-exon into in up to 90% of alleles without selection. Clonal analysis revealed bi-allelic integration in >50% of the screened iPSC clones without compromising their pluripotency and genomic integrity. Thus, in combination with the adeno-associated virus vector system, CRISPR-Cas12a Ultra provides a highly efficient genome editing platform for performing targeted knock-ins in human iPSCs.
Topics: Humans; CRISPR-Cas Systems; Pluripotent Stem Cells; Induced Pluripotent Stem Cells; Hematopoietic Stem Cells; Alleles
PubMed: 38256061
DOI: 10.3390/ijms25020985 -
Frontiers in Physiology 2023Liver transplantation (LTx) is the most effective treatment for end-stage liver diseases. Gut microorganisms influence the host physiology. We aim to profile the...
Liver transplantation (LTx) is the most effective treatment for end-stage liver diseases. Gut microorganisms influence the host physiology. We aim to profile the dynamics of gut microbiota in the perioperative period and a 1-year follow-up of LTx recipients in Northeast China. A total of 257 fecal samples were longitudinally collected from 85 LTx patients using anal swabs from pre-LTx to 1-year post-LTx. A total of 48 fecal samples from end-stage liver disease patients without LTx served as the control. 16S rRNA sequencing was used to analyze gut microbiota diversity, bacterial genera, phenotype classification, and metabolic pathways. The diversity of gut microbiota decreased significantly after transplantation, accompanied by a profound change in the microbial structure, which is characterized by increased abundance of facultative anaerobic bacteria dominated by g_ and reduced anaerobic bacteria composition. Predicted functional analysis also revealed disturbances in the metabolic pathway of the gut microbiota. After LTx, the diversity of microbiota gradually recovered but to a less preoperative level after 1 year of recovery. Compared with pre-transplantation, the microbiome structure was characterized by an increase in and after 1 year of transplantation. LTx and perioperative treatment triggered gut microbial dysbiosis. The gut microbiota was restructured after LTx to near to but significantly differed from that of pre-LTx.
PubMed: 38187130
DOI: 10.3389/fphys.2023.1266635