Recent sets of evidence have described profiles of 16S rDNA sequences in host tissues, notably in fat pads that are significantly overrepresented and can serve as signatures of metabolic disease. However, these recent and original observations need to be further detailed and functionally defined. Here, using state-of-the-art targeted DNA sequencing and discriminant predictive approaches, we describe, from the longitudinal FLORINASH cohort of patients who underwent bariatric surgery, visceral, and subcutaneous fat pad-specific bacterial 16SrRNA signatures. The corresponding Porphyromonadaceae, Campylobacteraceae, Prevotellaceae, Actimomycetaceae, Veillonellaceae, Anaerivoracaceae, Fusobacteriaceae, and the Clostridium family XI 16SrRNA DNA segment profiles are signatures of the subcutaneous adipose depot while Pseudomonadaceae and Micrococcacecae, 16SrRNA DNA sequence profiles characterize the visceral adipose depot. In addition, we have further identified that a specific pre-bariatric surgery adipose tissue bacterial DNA signature predicts the efficacy of body weight loss in obese patients 5-10 years after the surgery. 16SrRNA signatures discriminate (ROC ~ 1) the patients who did not maintain bodyweight loss and those who did. Second, from the 16SrRNA sequences we infer potential pathways suggestive of catabolic biochemical activities that could be signatures of subcutaneous adipose depots that predict body weight loss.

Investigating the microbiota of blood and urine from acute myeloid leukemia (AML) patients is essential to unravel the complex role of microbiota in systemic host-microbe interactions and implications.

We conducted a longitudinal observational study to characterize the temporal dynamics of blood and urine microbiota in 27 AML patients, utilizing metagenomic analysis pipeline for microbial identification to identify disease-associated microbial signatures.

The composition of blood and urine microbiota of AML was dominated by Proteobacteria phylum in blood, Firmicutes phylum in urine. The species and diversity of blood and urine microbiota did not have difference between AML patients and healthy controls. Restitution of alpha and beta diversity of blood microbiota and urine microbiota to resemble that of healthy controls occurred after cessation of treatment. Temporal variation of urine microbiome was higher than blood after treatment which was closely related to pathogenic bacteria and beneficial bacteria measured by coefficient of variation (CV) of alpha diversity. The temporal variability of urine microbiota was significantly correlated with platelet and exposure of levofloxacin. The variation of microbiome of AML patients with infection was found that the relative abundance of Burkholderia significantly enriched in blood and urine which had high accuracy and sensitivity. The correlation between blood microbiota and serum amino acid metabolites was similar to that between gut microbiota and serum metabolites.

This study represents the first comprehensive investigation to quantify the longitudinal variability of blood and urine microbiota in AML patients, revealing distinct patterns compared to gut microbiota and associations with adverse clinical outcomes. Our findings highlight the potential of leveraging stabilizing taxa as a target for microbiome restoration.

Sepsis, a dysregulated host response to infection, severely affects calf health. To date, sepsis diagnosis relies on clinical examination and positive blood culture. Differently, in humans 16S rRNA gene analysis is a valuable adjunct to blood culture as it allows for broader assessment of bacterial DNA in whole blood and its fractions. However, its efficacy in cattle remains unknown. Therefore, this study characterized and compared the bacterial DNA detected in whole blood and its fractions between healthy calves and those showing clinical signs of sepsis. The study sample was 18 Piedmontese calves classified according to their clinical status as suspected septic (S, 8/18) or healthy (H, 10/18). Aseptic blood samples were collected into EDTA tubes for 16S rRNA gene analysis of whole blood (WB), plasma (PL), buffy coat (BC), and red blood cells (RBC). Aseptic samples were additionally taken only from the S calves for blood culture. Clinical and microbiological parameters were compared between the two groups and between the blood fractions within each group. The S calves were diagnosed with pneumonia (3/8, 37.5%), enteritis (3/8, 37.5%), and omphalitis (2/8, 25%). Microbiome analysis revealed significant intra-group differences in α and β diversity indices between PL and the other blood fractions for both groups. Comparison between the S and the H calves showed differences in β diversity indices for PL and WB. DNA of known pathogens (e.g., Escherichia coli) and species not commonly associated with sepsis (e.g., Cutibacterium acnes) were more abundant in the S calves. Moreover, in S calves, 16S rRNA gene sequencing detected E. coli DNA more often (8/8, 100%) than blood culture (2/8, 25%). While the DNA of several bacteria can be detected in calves showing clinical signs of sepsis, further studies are needed to clarify its origin, role, and distribution in blood fractions.

Colorectal cancer (CRC) is the third most common cancer, and it can be prevented by performing early screening. As a hallmark of cancer, the human microbiome plays important roles in the occurrence and development of CRC. Recently, the blood microbiome has been proposed as an effective diagnostic tool for various diseases, yet its performance on CRC deserves further exploration. In this study, 133 human feces and 120 blood samples are collected, including healthy individuals, adenoma patients, and CRC patients. The blood cfDNA and fecal genome are subjected to shotgun metagenome sequencing. After removing human sequences, the microbial sequences in blood are analyzed. Based on the differential microbes and functions, random forest (RF) models are constructed for adenoma and CRC diagnosis. The results show that alterations of blood microbial signatures can be captured under low coverage (even at 3×). RF diagnostic models based on blood microbial markers achieve high area under the curve (AUC) values for adenoma patients (0.8849) and CRC patients (0.9824). When the fragmentation pattern is combined with microbial and KEGG markers, higher AUC values are obtained. Furthermore, compared to the blood microbiome, the fecal microbiome shows a different community composition, whereas their changes in KEGG pathways are similar. Pathogenic bacteria Fusobacterium nucleatum (F. nucleatum) in feces increased gradually from the healthy group to the adenoma and CRC groups. Additionally, F. nucleatum in feces and blood shows a positive correlation in CRC patients. Cumulatively, the integration of blood microbiome and fragmentation pattern is promising for CRC diagnosis.IMPORTANCEThe cell-free DNA of the human microbiome can enter the blood and can be used for cancer diagnosis, whereas its diagnostic potential in colorectal cancer and association with gut microbiome has not been explored. The microbial sequences in blood account for less than 1% of the total sequences. The blood microbial composition, KEGG functions, and fragmentation pattern are different among healthy individuals, adenoma patients, and CRC patients. Machine learning models based on these differential characteristics achieve high diagnostic accuracy, especially when they are integrated with fragmentation patterns. The great difference between fecal and blood microbiomes indicates that microbial sequences in blood may originate from various organs. Therefore, this study provides new insights into the community composition and functions of the blood microbiome of CRC and proposes an effective non-invasive diagnostic tool.

An increasing body of research indicates that the circulating microbiome plays a significant role in cancer initiation and progression and the treatment response. The genomic characteristics of circulating microorganisms may influence the tumor immune microenvironment, thereby affecting cancer progression and therapeutic outcomes. However, whether the circulating microbiome can serve as a prognostic biomarker for cervical cancer patients and its mechanistic role in the tumor immune microenvironment still requires further investigation. Univariate, Lasso, and multivariate Cox regression analyses were utilized to identify the circulating microbial signatures associated with overall survival (OS) in patients with cervical cancer. A circulating Microbial Abundance Prognostic Score (MAPS) model was constructed based on these findings. A nomogram that integrated clinical features and MAPSs was developed to predict the OS rates in patients with cervical cancer. Blood microbiome data were combined with matched tumor RNA-seq data to analyze the differences in the tumor microenvironment between high- and low-MAPS groups, elucidating the impact of the MAPS on the tumor immune microenvironment. Finally, the potential application of the circulating MAPS to predicting the efficacy of immunotherapy and chemotherapy was assessed. The MAPS predictive model, which includes 15 circulating microorganisms, has shown independent prognostic value for patients with cervical cancer. Integrating the MAPS into a nomogram improved the accuracy of the prognostic predictions. Combined microbial and gene analyses revealed potential interactions between prognostic tumor microbiomes and the tumor immune microenvironment. The drug sensitivity analysis indicated the potential of MAPS as a predictor of chemotherapy's efficacy. Our findings suggest that circulating microbial signatures hold promise as novel prognostic biomarkers and may inform personalized treatment strategies in cervical cancer. Further large-scale and multicenter studies are warranted to validate the clinical utility of the MAPS.

Metabolic dysfunction-associated steatotic liver disease (MASLD) is a condition wherein excessive fat accumulates in the liver, leading to inflammation and potential liver damage. In this narrative review, we evaluate the tissue microbiota, how they arise and their constituent microbes, and the role of the intestinal and hepatic microbiota in MASLD. The history of bacteriophages (phages) and their occurrence in the microbiota, their part in the potential causation of MASLD, and conversely, "phage therapy" for antibiotic resistance, obesity, and MASLD, are all described. The microbiota metabolism of bile acids and dietary tryptophan and histidine is defined, together with the impacts of their individual metabolites on MASLD pathogenesis. Both periodontitis and intestinal microbiota dysbiosis may cause MASLD, and how individual microorganisms and their metabolites are involved in these processes is discussed. Novel treatment opportunities for MASLD involving the microbiota exist and include fecal microbiota transplantation, probiotics, prebiotics, synbiotics, tryptophan dietary supplements, intermittent fasting, and phages or their holins and endolysins. Although FDA is yet to approve phage therapy in clinical use, there are multiple FDA-approved clinical trials, and this may represent a new horizon for the future treatment of MASLD.

Fever of unknown origin (FUO) without a respiratory component is a frequent clinical presentation in horses. Multiple pathogens, both tick-borne and enteric, can be involved as etiologic agents. An additional potential mechanism is intestinal barrier dysfunction.

This case-control study aimed to detect and associate microbial taxa in blood with disease state.

Areas known for a high prevalence of tick-borne diseases in humans were chosen to survey horses with FUO, which was defined as fever of 101.5°F or higher with no signs of respiratory illness or other recognisable diseases. Blood samples and clinical parameters were obtained from 52 FUO cases and also from matched controls from the same farms. An additional 23 febrile horses without matched controls were included.

Broadly targeted polymerase chain reaction (PCR) amplification directed at conserved sequence regions of bacterial 16S rRNA, parasite 18S rRNA, coronavirus RdRp and parvovirus NS1 was performed, followed by deep sequencing. To control for contamination and identify taxa unique to the cases, metagenomic sequences from the controls were subtracted from those of the cases, and additional targeted molecular testing was performed. Sera were also tested for antibodies to equine coronavirus.

Over 60% of cases had intestinal microbial DNA circulating in the blood. Nineteen percent of cases were attributed to infection with Anaplasma phagocytophilum, of which two were subtyped as human-associated strains. A novel Erythroparvovirus was detected in two cases and two controls. Serum titres for equine coronavirus were elevated in some cases but not statistically different overall between the cases and controls.

Not all pathogens are expected to circulate in blood, which was the sole focus of this study.

The presence of commensal gut microbes in blood of equine FUO cases is consistent with a compromised intestinal barrier, which is highlighted as a direction for future study.

Recurrent acute pancreatitis (RAP) poses significant clinical challenges, with 32.3% developing to chronic pancreatitis within 5 years. The underlying microbial factors contributing to RAP remain poorly understood. This study aims to identify blood microbial signatures associated with RAP and explore the potential microbial predictors for RAP.

In this prospective cohort, 90 acute pancreatitis patients are classified into non-recurrent acute pancreatitis (NRAP, n=68) and RAP (n=22) groups based on the number of pancreatitis episodes. Microbial composition of blood samples is analyzed using 5-region (5R) 16S rRNA gene sequencing. Key microbial taxa and functional predictions are made. A random forest model is used to assess the predictive value of microbial features for RAP. The impact of Staphylococcus hominis (S. hominis) on RAP is further evaluated in an experimental mouse model.

Linear discriminant analysis effect size (LEfSe) analysis highlights significant microbial differences, with Paracoccus aminovorans, Corynebacterium glucuronolyticum and S. hominis being prominent in RAP. Functional predictions indicate enrichment of metabolic pathways in the RAP group. Random forest analysis identifies key microbial taxa with an AUC value of 0.759 for predicting RAP. Experimental validation shows that S. hominis exacerbates pancreatic inflammation in mice.

This study identifies distinct clinical and microbial features associated with RAP, emphasizing the role of specific bacterial taxa in pancreatitis recurrence. The findings suggest that microbial profiling could enhance the diagnosis and management of RAP, paving the way for personalized therapeutic approaches.

In the absence of infection, blood has previously been understood to be free of microbes. However, with advances in sequencing technology this notion has been challenged, prompting new investigations into microbial DNA within the blood of both healthy and diseased individuals. To comprehensively survey microbial DNA in blood, we separated blood into fractions (plasma, red blood cells, and buffy coat) and assessed if the microbial-DNA is cell-free by the addition of DNase to a subset of each fraction. We measured 16S rRNA gene copy number with digital droplet PCR and identified the taxonomic origin of the microbial DNA with synthetic full-length 16S rRNA gene sequencing. As a use case, we examine microbial DNA from the blood of 5 men without prostate cancer (PC), 5 men with low-grade PC, and 5 men with high-grade PC. Our study demonstrates that the majority of microbial DNA is cell-free, indicating that it is not representative of proliferating microbes. Our analyses also revealed buffy coat had the lowest number of 16S rRNA gene copies yet highest number of genera of the fractions (median 23.3 copies/μL and 10 genera) and thus may be a useful fraction to study moving forward. Additionally, microbial DNA in blood may have utility as a biomarker, as we detected disease-associated compositional differences in the plasma and buffy coat fractions. This study lays the groundwork for rigorously studying microbial DNA in blood, however larger studies are needed to confirm our disease-association findings.

This study aimed to establish the human reference microbiome profiles in blood, saliva, and stool of healthy individuals, serving as reference values to identify microbiome alterations in human disease.

The study population consisted of a reference group of healthy adults and a second group consisting of adults with periodontal disease (PD). Blood, saliva, and stool samples were subjected to 16S rRNA sequencing. Reference intervals of alpha diversity indices were calculated. To reduce the effects of inherent limitations of microbiome data, the taxonomic profiles of the reference group were estimated as log-scaled fold change (logFC) in the abundance of microorganisms between two habitats within the subjects.

For stool and saliva microbiomes, differences in the abundances of Firmicutes, Patescibacteria, and Verrucomicrobia distinguished healthy from PD subjects (95% confidence interval (CI) of logFC: [-0.18, 0.31], [-1.19, -0.34], and [-3.68, -2.90], respectively). Differences in the abundances of Cyanobacteria, Fusobacteria, and Tenericutes in stool and blood microbiome of healthy subjects fell within 95% CI of logFC [-0.38, 0.61], [-4.14, -3.01], and [1.66, 2.77], respectively. In saliva and blood, differences in the abundances of Epsilonbacteraeota, Firmicutes, Fusobacteria, and Proteobacteria could be used as reference values (95% CI of logFC: [-3.67, -2.47], [-0.35, 0.49], [-4.59, -3.26], and [-1.20, 0.07], respectively).

As the reference microbiome profiles could discern healthy subjects and individuals with PD, a relatively mild disease state, they can be applied as reference values representing the healthy status of the microbiome and for screening of disease states, preferably in preclinical stages.

Metabolic dysfunction-associated steatotic liver disease (MASLD) encompasses a range of histological findings from the generally benign simple steatosis to steatohepatitis (MASH) which can progress to fibrosis and cirrhosis. Several factors, including the microbiome, may contribute to disease progression.

Here, we demonstrate links between the presence and abundance of specific bacteria in the adipose and liver tissues, inflammatory genes, immune cell responses, and disease severity. Overall, in MASLD patients, we observed a generalized obesity-induced translocation of gut bacteria to hepatic and adipose tissues. We identified microbial patterns unique to more severely diseased tissues. Specifically, Enterococcus, Granulicatella, and Morganellaceae abundance is positively correlated with immune cell counts and inflammatory gene expression levels, and both genera are significantly enriched in MASH patients. Brevibacterium is enriched in adipose tissues of patients with liver fibrosis.

Together, these results provide further insight into the microbial factors that may be driving disease severity. Video Abstract.

African buffalo (Syncerus caffer) is a significant reservoir host for many zoonotic and parasitic infections in Africa. These include a range of viruses and pathogenic bacteria, such as tick-borne rickettsial organisms. Despite the considerations of mammalian blood as a sterile environment, blood microbiome sequencing could become crucial for agnostic biosurveillance. This study investigated the blood microbiome of clinically healthy wild buffaloes in Kenya to determine its applicability in agnostic testing for bacteria in apparently healthy wild animals.

Whole blood and serum samples were collected from 46 wild African buffalos from Meru National Park (30), Buffalo Springs (6) and Shaba (10) National Reserves in upper eastern Kenya. Total deoxyribonucleic acid (DNA) was extracted from these samples and subjected to amplicon-based sequencing targeting the 16 S rRNA gene. The bacteria operational taxonomic units (OTU) were identified to species levels by mapping the generated V12 and V45 regions of 16 S rRNA gene to the SILVA database. These OTU tables were used to infer the microbial abundance in each sample type and at the individual animal level. The sequences for the corresponding OTUs were also used to generate phylogenetic trees and thus infer evolution for the OTUs of interest.

Here, we demonstrate that buffaloes harbor many bacteria in their blood. We also report a diversity of 16 S rRNA gene sequences for Anaplasma and Mycoplasma from individual animals. By sequencing both whole blood and serum in triplicate for each animal, we provide evidence of the differences in detecting bacteria in both sample types.

Diverse bacteria, including some potential pathogens, can be found in the blood of clinically healthy wild African buffalo. Agnostic surveillance for such pathogens can be achieved through blood microbiome sequencing. However, considerations for the question being asked for the blood microbiome in wildlife will impact the choice for using whole blood or serum for sequencing.

There is an overlap between the respiratory, blood and gut microbiomes in patients with acute respiratory distress syndrome. Specific taxa in the lungs and blood are associated with an inflammatory response. https://bit.ly/3TdkHd7.

The discoveries of the oncomicrobiome (intratumoral microbiome) and oncomicrobiota (intratumoral microbiota) represent significant advances in tumor research and have rapidly become of key interest to the field. Within tumors, microorganisms such as bacteria, fungi, viruses, and archaea form the oncomicrobiota and are primarily found within tumor cells, immunocytes, and the intercellular matrix. The oncomicrobiome exhibits marked heterogeneity and is associated with tumor initiation, progression, metastasis, and treatment response. Interactions between the oncomicrobiome and the immune system can modulate host antitumor immunity, influencing the efficacy of immunotherapies. Oncomicrobiome research also faces numerous challenges, including overcoming methodological issues such as low target abundance, susceptibility to contamination, and biases in sample handling and analysis methods across different studies. Furthermore, studies of the oncomicrobiome may be confounded by baseline differences in microbiomes among populations driven by both environmental and genetic factors. Most studies to date have revealed associations between the oncomicrobiome and tumors, but very few have established mechanistic links between the two. This review introduces the relevant concepts, detection methods, sources, and characteristics of the oncomicrobiome. We then describe the composition of the oncomicrobiome in common tumors and its role in shaping the tumor microenvironment. We also discuss the current problems and challenges to be overcome in this rapidly progressing field.

Many studies have reported microbial signatures in thrombi at major vascular sites, such as the coronary artery and the middle cerebral artery, which are critical for maintaining proper blood flow and oxygenation. Chronic thromboembolic pulmonary hypertension (CTEPH) is a condition involving non-resolving thrombosis that has not been fully studied. This study explored the microbial taxonomy and functional profiles of both fresh and organized thrombi associated with CTEPH to investigate the role of microbiota in thrombus non-resolving.

In this study, 12 CTEPH fresh thrombi and 12 organized thrombi were collected from 14 patients with CTEPH. Metagenomic sequencing was employed to explore the genomic information of all microorganisms in the thrombus samples.

Our data demonstrated a diverse range of microorganisms in CTEPH thrombi, whether fresh or organized. Notably, a considerable proportion (54.7 %) of sequencing data could not be classified into the relative microbial taxa, highlighting the complexity and novelty of the thrombus ecosystem. Although there were no significant differences in microbial community structure between the two groups, the abundance of dominant microbial species varied. Leuconostoc sp. DORA 2, Staphylococcus aureus, and Aliidongia dinghuensis were common dominant species in CTEPH thrombus. Organized thrombus significantly increased the relative abundance of Staphylococcus aureus, which was confirmed to effectively distinguish between organized and fresh thrombi by LeFSe analysis and random forest analysis. Functional annotation using both the KEGG and eggNOG databases revealed that organized thrombi exhibit stronger metabolic functions, particularly in amino acid metabolism.

Our findings suggest that microbial composition and function may play an important role in thrombus organization. Targeting inflammation to prevent thrombosis presents promising opportunities for further research in this area.

Gut microbiota and associated metabolites have been linked to breast carcinogenesis. Evidences demonstrate blood microbiota primarily originates from the gut and may act as a biomarker for breast cancer. We aimed to characterize the microbiota-gut microbial metabolites cross-talk in blood and develop a composite diagnostic panel for breast cancer. We performed 16S rRNA gene sequencing and metabolomics profiling on blood samples from 107 breast cancer cases and 107 age-paired controls. We found that the alpha diversity of the blood microbiota was decreased in breast cancer compared to controls. There were significantly different profiles of microbiota and gut microbial metabolites in blood between these two groups, with nine bacterial genera and four gut microbial metabolites increased in patients, while thirty-nine bacterial genera and two gut microbial metabolites increased in controls. Some breast cancer-associated gut microbial metabolites were linked to differential blood microbiota, and a composite microbiota-metabolite diagnostic panel was further developed with an area under the curve of 0.963 for breast cancer. This study underscored the pivotal role of microbiota and gut microbial metabolites in blood and their interactions for breast carcinogenesis, as well as the potential of a composite diagnostic panel as a non-invasive biomarker for breast cancer.IMPORTANCEOur integrated analysis demonstrated altered profiles of microbiota and gut microbial metabolites in blood for breast cancer patients. The extensive correlation between microbiota and gut microbial metabolites in blood assisted the understanding of the pathogenesis of breast cancer. The good performance of a composite microbiota-gut microbial metabolites panel in blood suggested a non-invasive approach for breast cancer detection and a novel strategy for better diagnosis and prevention of breast cancer in the future.

Hepatocellular carcinoma (HCC) ranks among the most prevalent types of cancer in the world and its incidence and mortality are increasing year by year, frequently diagnosed at an advanced stage. Traditional treatments such as surgery, chemotherapy, and radiotherapy have limited efficacy, so new diagnostic and treatment strategies are urgently needed. Recent research has discovered that intratumoral microbiota significantly influences the development, progression, and metastasis of HCC by modulating inflammation, immune responses, and cellular signaling pathways. Intratumoral microbiota contributes to the pathologic process of HCC by influencing the tumor microenvironment and altering the function of immune system. This article reviews the mechanism of intratumoral microbiota in HCC and anticipates the future possibilities of intratumoral microbiota-based therapeutic strategies for HCC management. This emerging field provides fresh insights into early diagnosis and personalized approaches for HCC while holding substantial clinical application potential to improve patient outcomes and tailor interventions to individual tumor profiles.

Prosthetic Joint Infection (PJI) is the most devastating complication of arthroplasty surgery and affects 1-5% of patients. Despite strict adherence to aseptic protocols and preventive measures, infection is the most common reason for revision arthroplasty, and the incidence is increasing. Treatment of PJI is challenging and often requires repeated major surgeries with sequentially poor results. The continued occurrence of PJI, and persistence after treatment, brings into question the current treatment paradigm. Preclinical evidence suggests a link between altered gut health and the risk of PJI in arthroplasty patients. Resistant starches helps to restore gut physiology by enhancing the beneficial microbiome and producing short-chain fatty acids, which have several health-conferring properties. The primary aim of this study is to investigate the effect of a commercially available prebiotic fibre formulation on the gut microbiome in PJI patients planned for a two-stage revision surgery.

A double-blind placebo-controlled trial will assess the effect of 8-week supplementation of a commercially available prebiotic supplement in patients presenting with first-time PJI undergoing two-stage revision surgery. The supplementation phase will start after the first stage revision, and 80 patients will be randomised to receive either a test product (34 g of resistant starch) or a placebo (custard powder) daily for eight weeks. Stool and blood specimens will be collected at baseline, four weeks and eight weeks after the first-stage surgery and once at second-stage surgery. Gut microbiome profile, inflammatory cytokines and gut permeability biomarkers will be measured. Tissue specimens will be collected intra-operatively during first and second-stage surgeries. Baseline dietary patterns and gut symptoms will be recorded using validated questionnaires. Treatment outcomes will be reported for both cohorts using the Delphi criterion at one and two years after second-stage surgery.

This will be the first study to investigate the relationship between gut health optimisation and preventing PJI recurrence in arthroplasty patients. If supplementation with resistant starch improves gut health and reduces systemic inflammation, optimising the gut microbiome will be a recommended preoperative management strategy for arthroplasty patients.

ACTRN12623001273673.

In this review, we tentatively tried to connect the most recent findings on the bat microbiome and to investigate on their microbial communities, that may vary even in conspecific hosts and are influenced by host physiology, feeding behavior and diet, social interactions, but also by habitat diversity and climate change. From a conservation perspective, understanding the potentially negative and indirect effects of habitat destruction on animal microbiota can also play a crucial role in the conservation and management of the host itself. According to the One Health concept, which recognizes an interdependence between humans, animals, and the environment, bat microbiota represents an indicator of host and environmental health, besides allowing for evaluation of the risk of emerging infectious diseases. We noticed that a growing number of studies suggest that animal microbiota may respond in various ways to changes in land use, particularly when such changes lead to altered or deficient food resources. We have highlighted that the current literature is strongly focused on the initial phase of investigating the microbial communities found in Chiroptera from various habitats. However, there are gaps in effectively assessing the impacts of pathogens and microbial communities in general in animal conservation, veterinary, and public health. A deeper understanding of bat microbiomes is paramount to the implementation of correct habitat and host management and to the development of effective surveillance protocols worldwide.

Background: The presence of bacteria in the blood of healthy individuals remains controversial. This study explored the comprehensive bacterial profiles and specific biomarkers in different components of healthy Chinese blood donors. Methods: A total of 5230 whole blood (WB) specimens were collected. Among them, 5200 random samples were pooled into 26 mixed samples for bacterial profile analysis. The remaining 30 random samples were divided into 4 groups based on components: WB, plasma, red blood cells (RBCs), and buffy coat (BC). Subsequently, the amplicons of the bacterial 16S rDNA V3-V4 fragments were sequenced to measure the diversity and composition of the bacteria using next-generation sequencing. Results: The bacterial DNAs in the blood primarily originated from the Proteobacteria phylum. A total of 301 species of bacterial DNA were found in blood specimens, with 46 species being present among all groups. A significantly higher abundance of bacterial DNA was found in the plasma and RBCs compared to those in BC and WB. However, the plasma and RBC groups showed significantly higher species diversity and richness compared to the BC and WB groups. In addition, the WB group had a significantly different community structure and composition compared to the plasma and RBC groups but was similar to the BC group. Conclusion: The presence of bacterial DNA fragments was confirmed in blood from healthy Chinese donors. The bacterial DNA fragments enriched in plasma showed the highest diversity, followed by RBC, WB, and BC. These results provide a foundation for further research on the microbiome in the blood of healthy individuals.

Positive blood cultures have been identified in debilitated, stranded, and deceased green turtles (Chelonia mydas), suggestive of septicemia. Interpretation of these results is often difficult because multiple studies have previously identified bacteremia in clinically healthy reptiles. In this study, paired blood cultures and skin cultures obtained after aseptic preparation of the venipuncture site were collected from 50 immature free-ranging green turtles from Port Canaveral, Florida. Blood culture results were compared with health status (apparently healthy versus unhealthy, based on physical examination findings and appropriate body condition), date of collection, presence of external fibropapillomatosis, healed or unhealed injuries, and presence of barnacles. Weight, body condition score, body condition index, morphometric measures, volume of blood collected, and body temperature were compared between blood culture-positive and blood culture-negative turtles. Positive blood cultures were identified in 14% (7 of 50) of all turtles, including 15.6% (5 of 32) of apparently healthy turtles. Vibrio spp., Bacillus megaterium, Cellulomonas sp., and Staphylococcus pasteuri were isolated in blood culture from apparently healthy individuals. There was a significant association (P = 0.048) between positive skin cultures and positive blood cultures, but isolates obtained were consistently different between paired results. There was no significant association (P > 0.05) between blood culture results and health status, evidence of healed or unhealed injuries, external fibropapillomatosis, or presence of barnacles. Based on the results of this study, positive blood cultures suggestive of nonclinical bacteremia may be present in apparently healthy green turtles. The results of this study will aid the attending clinician in interpretation of blood culture results of apparently healthy or presumed septicemic captive and rehabilitating green turtles as part of the conservation and population recovery of this threatened species.

As investigations of low-biomass microbial communities have become more common, so too has the recognition of major challenges affecting these analyses. These challenges have been shown to compromise biological conclusions and have contributed to several controversies. Here, we review some of the most common and influential challenges in low-biomass microbiome research. We highlight key approaches to alleviate these potential pitfalls, combining experimental planning strategies and data analysis methods.

Intestinal dysbiosis is a major contributor to colorectal cancer (CRC) development, leading to bacterial translocation into the bloodstream. This study aimed to evaluate the presence of circulated bacterial DNA (cbDNA) in CRC patients (n = 75) and healthy individuals (n = 25). DNA extracted from peripheral blood was analyzed using PCR, with specific primers targeting 16S rRNA, Escherichia coli (E. coli), and Fusobacterium nucleatum (F. nucleatum). High 16S rRNA and E. coli detections were observed in all patients and controls. Only the detection of F. nucleatum was significantly higher in metastatic non-excised CRC, compared to controls (p < 0.001), non-metastatic excised CRC (p = 0.023), and metastatic excised CRC (p = 0.023). This effect was mainly attributed to the presence of the primary tumor (p = 0.006) but not the presence of distant metastases (p = 0.217). The association of cbDNA with other clinical parameters or co-morbidities was also evaluated, revealing a higher detection of E. coli in CRC patients with diabetes (p = 0.004). These results highlighted the importance of bacterial translocation in CRC patients and the potential role of F. nucleatum as an intratumoral oncomicrobe in CRC.

The association between human metabolites and the environmental microbiome has primarily been investigated in relation to disease. In this study, the associations between environmental conditions and microbial communities on the surface of bloodstains were analyzed from a forensic science approach. The composition of microbial communities can be affected by numerous variables. After exposing bloodstains to two different environments with limited airflow and human interference, the microbial communities of the bloodstain surfaces were subjected to longitudinal analysis. Various microbes showed increasing or decreasing trends at the phylum and species level. The microbes identified in this study are usually found in soil, freshwater, and seawater and are known to exhibit unique properties, such as sporulation. Longitudinal variation in temperature and humidity were associated with various changes and correlations with the blood surface microbial community. Understanding these changes could introduce a new perspective to forensic science and could be used to develop a forensic tool used at crime scenes to analyze blood stains in more detail.

Recent studies highlight the presence of bacterial sequences in the human blood, suggesting potential clinical significance for circulating microbial signatures. These sequences could presumably serve in the diagnosis, prediction, or monitoring of various health conditions. Ensuring the similarity of samples before bacterial analysis is crucial, especially when combining samples from different biobanks prepared under varying conditions (such as different DNA extraction kits, centrifugation conditions, blood collection tubes, etc.). In this study, we aimed to analyze the impact of different sample collection and nucleic acid extraction criteria (blood collection tube, centrifugation, input volume, and DNA extraction kit) on circulating bacterial composition. Blood samples from four healthy individuals were collected into three different sample collection tubes: K2EDTA plasma tube, sodium citrate plasma tube, and gel tube for blood serum. Tubes were centrifugated at standard and double centrifugation conditions. DNA extraction was performed using 100, 200, and 500 μL plasma/serum input volumes. DNA extraction was performed using three different isolation kits: Norgen plasma/serum cell-free circulating DNA purification micro kit, Applied Biosystems MagMAX cell-free DNA isolation kit, and Qiagen QIAamp MinElute cell-free circulating DNA mini kit. All samples were subjected to 16S rRNA V1-V2 library preparation and sequencing. In total, 216 DNA and 18 water control samples were included in the study. According to PERMANOVA, PCoA, Mann-Whitney, and FDR tests the effect of the DNA extraction kit on the microbiota composition was the greatest, whereas the type of blood collection tube, centrifugation type, and sample input volume for the extraction had minor effects. Samples extracted with the Norgen DNA extraction kit were enriched with Gram-negative bacteria, whereas samples extracted with the Qiagen and MagMAX kits were enriched with Gram-positive bacteria. Bacterial profiles of samples prepared with the Qiagen and MagMAX DNA extraction kits were more similar, whereas samples prepared with the Norgen DNA extraction kit were significantly different from other groups.

In healthy conditions, blood was considered a sterile environment until the development of new analytical approaches that allowed for the detection of circulating bacterial ribosomal DNA. Currently, debate exists on the origin of the blood microbiota. According to advanced research using dark field microscopy, fluorescent in situ hybridization, flow cytometry, and electron microscopy, so-called microbiota have been detected in the blood. Conversely, others have reported no evidence of a common blood microbiota. Then, it was hypothesized that blood microbiota may derive from distant sites, e.g., the gut or external contamination of blood samples. Alteration of the blood microbiota's equilibrium may lead to dysbiosis and, in certain cases, disease. Cardiovascular, respiratory, hepatic, kidney, neoplastic, and immune diseases have been associated with the presence of Gram-positive and Gram-negative bacteria and/or their products in the blood. For instance, lipopolysaccharides (LPSs) and endotoxins may contribute to tissue damage, fueling chronic inflammation. Blood bacteria can interact with immune cells, especially with monocytes that engulf microorganisms and T lymphocytes via spontaneous binding to their membranes. Moreover, LPSs, extracellular vesicles, and outer membrane vesicles interact with red blood cells and immune cells, reaching distant organs. This review aims to describe the composition of blood microbiota in healthy individuals and those with disease conditions. Furthermore, special emphasis is placed on the interaction of blood microbiota with host cells to better understand disease mechanisms.

Alzheimer's disease (AD) is characterized by cognitive decline and neuropathology including amyloid beta (Aβ) plaques and neurofibrillary tangles (tau). Factors initiating or driving these pathologies remain unclear, though microbes have been increasingly implicated. Our data and others' findings indicate that microbes may be common constituents of the brain. It is notable that Aβ and tau have antimicrobial properties, suggesting a response to microbes in the brain. We used 16S rRNA sequencing to compare major bacterial phyla in post-mortem tissues from individuals exhibiting a range of neuropathology and cognitive status in two brain regions variably affected in AD. Our data indicate that strong regional differences exist, driven in part by the varied presence of Proteobacteria and Firmicutes. We confirmed our data using ELISA of bacterial lipopolysaccharide (LPS) and lipoteichoic acid in the same brain tissue. We identified a potential association between the composition of phyla and the presence of neuropathology but not cognitive status. Declining cognition and increasing pathology correlated closely with serum LPS, but not brain levels of LPS, although brain LPS showed a strong negative correlation with cerebral amyloid angiopathy. Collectively, our data suggest a region-specific heterogeneity of microbial populations in brain tissue potentially associated with neurodegenerative pathology.

Although the impact of the gut microbiome on health and disease is well established, there is controversy regarding the presence of microorganisms such as bacteria and their products in organs and tissues. However, recent contamination-aware findings of tissue-resident microbial signatures provide accumulating evidence in support of bacterial translocation in cardiometabolic disease. The latter provides a distinct paradigm for the link between microbial colonizers of mucosal surfaces and host metabolism. In this Perspective, we re-evaluate the concept of tissue-resident bacteria including their role in metabolic low-grade tissue and systemic inflammation. We examine the limitations and challenges associated with studying low bacterial biomass samples and propose experimental and analytical strategies to overcome these issues. Our Perspective aims to encourage further investigation of the mechanisms linking tissue-resident bacteria to host metabolism and their potentially actionable health implications for prevention and treatment.

The cell is the basic unit of life. It is composed of organelles and various organic and inorganic biomolecules. Recent 16S ribosomal ribonucleic acid (16S rRNA) gene sequencing studies have revealed the presence of tissue bacteria in both tumor and normal tissues. Recently, we found that the liver microbiome resided in hepatocytes. Here, we further report on the cellular microbiome in the parenchymal cells of visceral organs as inherent inhabitants. We performed 16S rRNA gene sequencing on visceral organs of male adult Sprague Dawley (SD) rats, pregnant rats, newborn rats, and fetuses and placentas; then, we performed fluorescence in situ hybridization and immunofluorescence in visceral organs. Furthermore, we performed Western blotting on nuclear and cytoplasmic extractions of visceral organs of SD rats and cell lines HepG2, Huh-7, Hepa1-6, and HSC-T6. A high abundance of 16S rRNA gene was detected in the visceral organs of male adult, pregnant, newborn, and fetal rats as well as their placentas. The number of operational taxonomic units (OTUs) of visceral bacteria was higher than that of the feces and ileum bacteria. Bacterial 16S rRNA, lipopolysaccharide (LPS), and lipoteichoic acid (LTA) were found in the parenchymal cells of visceral organs, as well as in HepG2, Huh-7, HSC-T6, and Hepa1-6 cells. LPS consistently appeared in the nucleus of cells, while LTA was mainly found in the cytoplasm. In conclusion, the cellular microbiome is an intrinsic component of cells. Gram-negative bacteria are located in the nucleus, and Gram-positive bacteria are located in the cytoplasm. This differs from the gut microbiome and may be inherited.

The etiology of pediatric acute lymphatic leukemia (ALL) is still unclear. Whole-metagenome shotgun sequencing of bone marrow samples in patients with treatment-naïve ALL (n=6) was performed for untargeted investigation of bacterial and viral DNA. The control group consisted of healthy children (n=4) and children with non-oncologic diseases (n=2) undergoing bone marrow sampling. Peripheral blood of all participants was investigated at the same time. After bioinformatical elimination of potential contaminants by comparison with the employed controls, no significant amounts of microbial or viral DNA were identified.

In recent years several experimental observations demonstrated that the gut microbiome plays a role in regulating positively or negatively metabolic homeostasis. Indole-3-propionic acid (IPA), a Tryptophan catabolic product mainly produced by C. Sporogenes, has been recently shown to exert either favorable or unfavorable effects in the context of metabolic and cardiovascular diseases. We performed a study to delineate clinical and multiomics characteristics of human subjects characterized by low and high IPA levels. Subjects with low IPA blood levels showed insulin resistance, overweight, low-grade inflammation, and features of metabolic syndrome compared to those with high IPA. Metabolomics analysis revealed that IPA was negatively correlated with leucine, isoleucine, and valine metabolism. Transcriptomics analysis in colon tissue revealed the enrichment of several signaling, regulatory, and metabolic processes. Metagenomics revealed several OTU of ruminococcus, alistipes, blautia, butyrivibrio and akkermansia were significantly enriched in highIPA group while in lowIPA group Escherichia-Shigella, megasphera, and Desulfovibrio genus were more abundant. Next, we tested the hypothesis that treatment with IPA in a mouse model may recapitulate the observations of human subjects, at least in part. We found that a short treatment with IPA (4 days at 20/mg/kg) improved glucose tolerance and Akt phosphorylation in the skeletal muscle level, while regulating blood BCAA levels and gene expression in colon tissue, all consistent with results observed in human subjects stratified for IPA levels. Our results suggest that treatment with IPA may be considered a potential strategy to improve insulin resistance in subjects with dysbiosis.

In this study, it was aimed to investigate bacterial contamination in apheresis platelet suspensions (APS) by automated blood culture system and flow cytometry method (FCM).33 spiked APS each using 11 bacterial strains (5 standard strains, 6 clinical isolates), were prepared in three different dilutions (1-10, 10-50, 50-100 cfu/mL), incubated in two different temperatures (35-37 °C and 22-24 °C) and different incubation times (18-96 h) evaluated by FCM. This three different dilutions were also inoculated into special platelet culture bottles (BacT/ALERT® BPA) and loaded into the blood culture system. Additionally 80 APSs routinely prepared in the Transfusion Center were evaluated by both FCM and the blood culture system. Platelets were lysed by freeze-thaw method.All spiked samples were positive with BacT/ALERT® BPA in 12-18 h. In 96 h incubation at 22-24 °C, the presence of bacteria was detected by FCM in all other samples (31/33) except low dilutions (1-10 and 10-100 CFU/ml) of K.pneumoniae standard strain. In the 35-37 °C, the presence of bacteria was detected by FCM in all samples (33/33) after 48 h of incubation. In routine APS one sample detected as positive (Bacillus simplex) with BacT/ALERT® BPA and no positivity was detected by FCM.The freeze-thaw method, which we have optimized for the lysis of platelets, is very practical and can be easily applied. The BacT/ALERT® system has been found to be very sensitive in detecting bacterial contamination in PSs. Flow cytometry method has been found to be successful, fast, easy to use and low cost in detecting bacterial contamination in PSs.

This study aimed to evaluate the blood bacterial microbiota in healthy and febrile cats. High-quality sequencing reads from the 16S rRNA gene variable region V3-V4 were obtained from genomic blood DNA belonging to 145 healthy cats, and 140 febrile cats. Comparisons between the blood microbiota of healthy and febrile cats revealed dominant presence of Actinobacteria, followed by Firmicutes and Proteobacteria, and a lower relative abundance of Bacteroidetes. Upon lower taxonomic levels, the bacterial composition was significantly different between healthy and febrile cats. The families Faecalibacterium and Kineothrix (Firmicutes), and Phyllobacterium (Proteobacteria) experienced increased abundance in febrile samples. Whereas Thioprofundum (Proteobacteria) demonstrated a significant decrease in abundance in febrile. The bacterial composition and beta diversity within febrile cats was different according to the affected body system (Oral/GI, systemic, skin, and respiratory) at both family and genus levels. Sex and age were not significant factors affecting the blood microbiota of febrile cats nor healthy ones. Age was different between young adult and mature adult healthy cats. Alpha diversity was unaffected by any factors. Overall, the findings suggest that age, health status and nature of disease are significant factors affecting blood microbiota diversity and composition in cats, but sex is not.

Strenuous exercise can result in disruption of intestinal barrier function and occurrence of gastrointestinal symptoms. The aim of this exploratory study was to elucidate systemic effects of increased intestinal permeability after high-intensity exercise. Forty-one endurance-trained subjects performed a 60-min treadmill run at 80% VO2max. Small intestinal permeability was measured as urinary excretion ratio of lactulose/rhamnose (L/R). Blood, saliva and feces were analyzed for gut barrier and immune-related biomarkers. The exercise challenge increased several markers of intestinal barrier disruption, immune function and oxidative stress. We found a negative correlation between L/R ratio and uric acid (r = -0.480), as well as a positive correlation between the L/R ratio and fecal chromogranin A in male participants (r = 0.555). No significant correlations were found between any of the markers and gastrointestinal symptoms, however, perceived exertion correlated with the combination of IL-6, IL-10 and salivary cortisol (r = 0.492). The lack of correlation between intestinal permeability and gastrointestinal symptoms could be due to minor symptoms experienced in lab settings compared to real-life competitions. The correlation between L/R ratio and uric acid might imply a barrier-protective effect of uric acid, and inflammatory processes due to strenuous exercise seem to play an important role regarding physical exhaustion.

Sepsis is a life-threatening illness caused by the dysregulated host response to infection. Nevertheless, our current knowledge of the microbial landscape in the blood of septic patients is still limited. Next-generation sequencing (NGS) is a sensitive method to quantitatively characterize microbiomes at various sites of the human body. In this study, we analyzed the blood microbial DNA of 22 adult patients with sepsis and 3 healthy subjects. The presence of non-human DNA was identified in both healthy and septic subjects. Septic patients had a markedly altered microbial DNA profile compared to healthy subjects over α- and β-diversity. Unexpectedly, the patients could be further divided into two subgroups (C1 and C2) based on β-diversity analysis. C1 patients showed much higher bacteria, viruses, fungi, and archaea abundance, and a higher level of α-diversity (Chao1, Observed and Shannon index) than both C2 patients and healthy subjects. The most striking difference was seen in the case of Streptomyces violaceusniger, Phenylobacterium sp. HYN0004, Caulobacter flavus, Streptomyces sp. 11-1-2, and Phenylobacterium zucineum, the abundance of which was the highest in the C1 group. Notably, C1 patients had a significantly poorer outcome than C2 patients. Moreover, by analyzing the patterns of microbe-microbe interactions in healthy and septic subjects, we revealed that C1 and C2 patients exhibited distinct co-occurrence and co-exclusion relationships. Together, our study uncovered two distinct microbial signatures in the blood of septic patients. Compositional and ecological analysis of blood microbial DNA may thus be useful in predicting mortality of septic patients.

Perovskite quantum dots (PQDs) are novel nanomaterials wherein perovskites are used to formulate quantum dots (QDs). The present study utilizes the excellent fluorescence quantum yields of these nanomaterials to detect 16S rRNA of circulating microbiome for risk assessment of cardiovascular diseases (CVDs). A long short-term memory (LSTM) deep learning model was used to find the association of the circulating bacterial species with CVD risk, which showed the abundance of three different bacterial species (Bauldia litoralis (BL), Hymenobacter properus (HYM), and Virgisporangium myanmarense (VIG)). The observations suggested that the developed nano-sensor provides high sensitivity, selectivity, and applicability. The observed sensitivities for Bauldia litoralis, Hymenobacter properus, and Virgisporangium myanmarense were 0.606, 0.300, and 0.281 fg, respectively. The developed sensor eliminates the need for labelling, amplification, quantification, and biochemical assessments, which are more labour-intensive, time-consuming, and less reliable. Due to the rapid detection time, user-friendly nature, and stability, the proposed method has a significant advantage in facilitating point-of-care testing of CVDs in the future. This may also facilitate easy integration of the approach into various healthcare settings, making it accessible and valuable for resource-constrained environments.