High microbiome variability in pediatric tracheostomy cannulas in patients with similar clinical characteristics

Abstract Objectives: To evaluate the bacterial microbiome found in tracheostomy cannulas of a group of children diagnosed with glossoptosis secondary to Robin Sequence (RS), and its clinical implications. Methods: Pediatric patients were enrolled in the study at the time of the cannula change in the hospital. During this procedure, the removed cannula was collected and stored for amplicon sequencing of 16s rRNA. DNA extraction was performed using DNeasy PowerBiofilm Kit (QIAGEN® - Cat nº 24000-50) while sequencing was performed with the S5 (Ion S5™ System, Thermo Fisher Scientific), following Brazilian Microbiome Project (BMP) protocol. Results: All 12 patients included in the study were using tracheostomy uncuffed cannulas of the same brand, had tracheostomy performed for over 1-year and had used the removed cannula for approximately 3-months. Most abundant genera found were Aggregatibacter, Pseudomonas, Haemophilus, Neisseria, Staphylococcus, Fusobacterium, Moraxella, Streptococcus, Alloiococcus, and Capnocytophaga. Individual microbiome of each individual was highly variable, not correlating to any particular clinical characteristic. Conclusion: The microbiome of tracheostomy cannulas is highly variable, even among patients with similar clinical characteristics, making it challenging to determine a standard for normality. © 2022 Associa¸c˜ao Brasileira de Otorrinolaringologia e Cirurgia C´ervico-Facial. Published by Elsevier Editora Ltda. This is an open access article under the CC BY license (https://creativecommons.org/licenses/by/4.0/).

Cultivo versus metagenómica para la identificación bacteriana en pacientes con osteomielitis de pie diabético: una revisión sistemática / Culture and metagenomics as bacterial identification methods in patients with diabetic foot ulcers: a systematic review

BACKGROUND: Diabetic foot osteomyelitis (DFO) is a serious complication of infected ulcers in a diabetic patient. The identification of the infecting microorganisms is generally by culture, which causes a bias. Recently, metagenomics has been used for microbial identification. AIM: To systematically review the scientific literature related to DFO in the last 10 years to evaluate if culture and metagenomics are complementary. MATERIAL AND METHODS: To carry out the systematic review, PRISMA and Rayyan were used for the selection of studies, using three databases, using the keywords diabetes, osteomyelitis, culture and microbiome. Articles in English or Spanish were included, containing information related to bacterial identification in DFO. Characteristics of the technique, patients and frequency of bacterial appearance were collected. RESULTS: Twenty six articles were included, 19 used culture and 7 metagenomics. The patients were predominantly men (68%), with an average age of 61 years, 83% had type 2 diabetes and comorbidities, mainly vascular and neuropathy. The Families with the highest frequency of appearance using the culture technique were Enterobacteriaceae (29.3%) and Staphylococcaceae(28.3%) and with metagenomics Peptoniphilaceae (22.1%) and Staphylococcaceae (9.4%). Peptoniphilaceae were not identified in culture, although they were frequently identified by metagenomics. Methicillin- resistant Staphylococcus aureus, regularly identified by culture, was not identified using metagenomics. CONCLUSIONS: Comparing results, there is a certain complementarity between microbiological culture and sequencing to identify bacteria present in DFO.

Distribution and function of cariogenic bacteria in supragingival plaque in patients with type 2 diabetes mellitus / 口腔疾病防治

Objective@#To investigate the distribution characteristics and functional genes of cariogenic bacteria in oral microorganisms of patients with type 2 diabetes mellitus and to improve the understanding of the relationship between type 2 diabetes mellitus and dental caries.@*Methods@#The experimental group included 10 patients with type 2 diabetes treated in the Department of Endocrinology, the First Affiliated Hospital of Air Force Medical University. The normal control group included healthy oral subjects without type 2 diabetes in the community population (10 cases). Samples of supragingival plaque from patients with type 2 diabetes mellitus and normal controls were collected and sequenced. Bioinformatics and statistical analysis of cariogenic bacteria such as Streptococcus mutans, Lactobacillus, Actinomyces viscosus and Candida albicans were carried out.@*Results@#There were slightly fewer cariogenic bacteria such as Streptococcus mutans, Lactobacillus, Actinomyces viscosus and Candida albicans in supragingival plaque samples of type 2 diabetic patients than in normal controls, but the difference was not statistically significant (P>0.05). The results of KEGG pathway functional metabolic differences showed that the metabolic pathways of D-arginine and D-ornithine metabolism, biofilm formation-Escherichia coli, carolactam degradation and arginine biosynthesis were more abundant in the T2DM group than in the normal control group, while metabolic pathways such as tyrosine metabolism, selenocompound metabolism and pyruvate metabolism showed the opposite trend. @*Conclusion @#There was no significant difference in the content of cariogenic microorganisms between type 2 diabetic patients and normal control group. The differential metabolic pathways of the functional genes indicated that an increase in the arginine metabolic pathway was beneficial to the maintenance of acid-base balance in the oral microecological environment.

Application of emerging technologies for gut microbiome research

Microbiome is associated with a wide range of diseases. The gut microbiome is also a dynamic reflection of health status, which can be modified, thus representing great potential to exploit the mechanisms that influence human physiology. Recent years have seen a dramatic rise in gut microbiome studies, which has been enabled by the rapidly evolving high-throughput sequencing methods (i.e. 16S rRNA sequencing and shotgun sequencing). As the emerging technologies for microbiome research continue to evolve (i.e. metatranscriptomics, metabolomics, culturomics, synthetic biology), microbiome research has moved beyond phylogenetic descriptions and towards mechanistic analyses. In this review, we highlight different approaches to study the microbiome, in particular, the current limitations and future promise of these techniques. This review aims to provide clinicians with a framework for studying the microbiome, as well as to accelerate the adoption of these techniques in clinical practice.

Microbiome and virome on indoor surfaces of an Antarctic research ship

BACKGROUND Few studies have focused on microbial diversity in indoor environments of ships, as well as the role of the microbiome and its ecological interconnections. In this study, we investigated the microbiome and virome present on the internal surfaces of a polar ship in different stages (beginning, during, and at the end) of the Brazilian Antarctic expedition in order to evaluate abundance of microorganisms in different periods. OBJECTIVES AND METHODS We used shotgun metagenomic analysis on pooled samples from sampling surfaces in the ship's interior to track the microbial diversity. FINDINGS Considering the total fraction of the microbiome, the relative abundance of bacteria, eukaryotes, viruses, and archaea was 83.7%, 16.2%, 0.04%, and 0.002%, respectively. Proteobacteria was the most abundant bacterial phyla, followed by Firmicutes, Actinobacteria, and Bacteroidetes. Concerning the virome, the greatest richness of viral species was identified during the middle of the trip, including ten viral families after de novo assembly: Autographiviridae, Chrysoviridae, Genomoviridae, Herelleviridae, Myoviridae, Partitiviridae, Podoviridae, Potyviridae, Siphoviridae, and Virgaviridae. MAIN CONCLUSIONS This study contributed to the knowledge of microbial diversity in naval transportation facilities, and variations in the abundance of microorganisms probably occurred due to factors such as the number of passengers and activities on the ship.

Consequential study on different levels of C/N ratios used in biofloc-based aquaculture system / Estudo consequente sobre diferentes níveis de proporções C/N utilizadas no sistema de aquicultura à base de biofloc

Biofloc technology is much highlighted these days because of its tremendous effects on aquaculture. Microbes were enriched on cheapest organic carbon source i. e., powdered banana peels and were incorporated in different aquaria rearing grass carp fingerlings under different C/N treatments (10:1, 15:1 and 20:1) and 10% water daily water exchange. The initial growth of fingerlings was recorded. The experiment was settled in triplicates for 60 days and run parallel to control group provided with commercial feed and daily water exchange. Its effect was evaluated by measuring the growth of fingerlings and water parameters of each aquarium. The average % gain in weight and length of fingerlings was obtained significantly highest (28.12 ± 0.30g and 17.29 ± 0.46cm respectively) in aquaria containing pure powdered banana peels with 10% water exchange and C/N ratio was adjusted at 20: 1 (T3) than other treatments and control. Ammonia and other water parameters were also under control in T3 than other experimental and control groups. By all counts, it was concluded that the highest C/N ratio in biofloc system had the potential to increment C. idella growth rate by reducing toxicity and could be used as fish meal substitute.

A tecnologia Biofloc é muito destacada hoje em dia por causa de seus tremendos efeitos na aquicultura. Os micróbios foram enriquecidos com a fonte de carbono orgânico mais barata, i. e., cascas de banana em pó, e foram incorporadas em diferentes aquários de criação de alevinos de carpa-capim sob diferentes tratamentos C/N (10: 1, 15: 1 e 20: 1) e 10% de troca diária de água. O crescimento inicial dos alevinos foi registrado. O experimento foi resolvido em triplicatas por 60 dias e executado paralelamente ao grupo controle fornecido com ração comercial e troca diária de água. Seu efeito foi avaliado medindo o crescimento dos alevinos e os parâmetros da água de cada aquário. O% de ganho médio em peso e comprimento dos alevinos foi obtido significativamente mais alto (28,12 ± 0,30g e 17,29 ± 0,46 cm respectivamente) em aquários contendo cascas de banana em pó puro com 10% de troca de água e a relação C/N foi ajustada em 20: 1 (T3) do que outros tratamentos e controle. A amônia e outros parâmetros da água também estavam sob controle no T3 mais do que nos outros grupos experimentais e de controle. Por todas as contagens, concluiu-se que a maior razão C/N no sistema de bioflocos tem o potencial de incrementar a taxa de crescimento de C. idella reduzindo a toxicidade e pode ser usada como substituto da farinha de peixe.

Consequential study on different levels of C/N ratios used in biofloc-based aquaculture system

Abstract Biofloc technology is much highlighted these days because of its tremendous effects on aquaculture. Microbes were enriched on cheapest organic carbon source i. e., powdered banana peels and were incorporated in different aquaria rearing grass carp fingerlings under different C/N treatments (10:1, 15:1 and 20:1) and 10% water daily water exchange. The initial growth of fingerlings was recorded. The experiment was settled in triplicates for 60 days and run parallel to control group provided with commercial feed and daily water exchange. Its effect was evaluated by measuring the growth of fingerlings and water parameters of each aquarium. The average % gain in weight and length of fingerlings was obtained significantly highest (28.12 ± 0.30g and 17.29 ± 0.46cm respectively) in aquaria containing pure powdered banana peels with 10% water exchange and C/N ratio was adjusted at 20: 1 (T3) than other treatments and control. Ammonia and other water parameters were also under control in T3 than other experimental and control groups. By all counts, it was concluded that the highest C/N ratio in biofloc system had the potential to increment C. idella growth rate by reducing toxicity and could be used as fish meal substitute.

Resumo A tecnologia Biofloc é muito destacada hoje em dia por causa de seus tremendos efeitos na aquicultura. Os micróbios foram enriquecidos com a fonte de carbono orgânico mais barata, i. e., cascas de banana em pó, e foram incorporadas em diferentes aquários de criação de alevinos de carpa-capim sob diferentes tratamentos C/N (10: 1, 15: 1 e 20: 1) e 10% de troca diária de água. O crescimento inicial dos alevinos foi registrado. O experimento foi resolvido em triplicatas por 60 dias e executado paralelamente ao grupo controle fornecido com ração comercial e troca diária de água. Seu efeito foi avaliado medindo o crescimento dos alevinos e os parâmetros da água de cada aquário. O% de ganho médio em peso e comprimento dos alevinos foi obtido significativamente mais alto (28,12 ± 0,30g e 17,29 ± 0,46 cm respectivamente) em aquários contendo cascas de banana em pó puro com 10% de troca de água e a relação C/N foi ajustada em 20: 1 (T3) do que outros tratamentos e controle. A amônia e outros parâmetros da água também estavam sob controle no T3 mais do que nos outros grupos experimentais e de controle. Por todas as contagens, concluiu-se que a maior razão C/N no sistema de bioflocos tem o potencial de incrementar a taxa de crescimento de C. idella reduzindo a toxicidade e pode ser usada como substituto da farinha de peixe.

Metagenomic Analysis of Environmental Samples from Wildlife Rescue Station at Poyang Lake, China / 生物医学与环境科学（英文）

OBJECTIVE@#To improve the understanding of the virome and bacterial microbiome in the wildlife rescue station of Poyang Lake, China.@*METHODS@#Ten smear samples were collected in March 2019. Metagenomic sequencing was performed to delineate bacterial and viral diversity. Taxonomic analysis was performed using the Kraken2 and Bracken methods. A maximum-likelihood tree was constructed based on the RNA-dependent RNA polymerase (RdRp) region of picornavirus.@*RESULTS@#We identified 363 bacterial and 6 viral families. A significant difference in microbial and viral abundance was found between samples S01-S09 and S10. In S01-S09, members of Flavobacteriia and Gammaproteobacteria were the most prevalent, while in S10, the most prevalent bacteria class was Actinomycetia. Among S01-S09, members of Myoviridae and Herelleviridae were the most prevalent, while the dominant virus family of S10 was Picornaviridae. The full genome of the pigeon mesivirus-like virus (NC-BM-233) was recovered from S10 and contained an open reading frame of 8,124 nt. It showed the best hit to the pigeon mesivirus 2 polyprotein, with 84.10% amino acid identity. Phylogenetic analysis showed that RdRp clustered into Megrivirus B.@*CONCLUSION@#This study provides an initial assessment of the bacteria and viruses in the cage-smeared samples, broadens our knowledge of viral and bacterial diversity, and is a way to discover potential pathogens in wild birds.

Distribution characteristics of antibiotic resistance genes in the domestic water of residents in Haimen， Jiangsu Province / 上海预防医学

ObjectiveAntibiotic resistance genes （ARGs） have received wide attention all over the world. The purpose of this study was to explore the bacterial community structure， the types and levels of antibiotic resistance genes in a water body in east China， and to compare and analyze the characteristics of microbial species distribution and antibiotic resistance gene distribution in various water environments. MethodsA total of 10 households in Haimen City， Jiangsu Province were selected and their surrounding water environment samples were collected. 21 water samples including river water （4）， Mingou water （9） and well water （8） were collected for metagenomics sequencing， assembled with MetaWRAP， annotated with CARD database， and analyzed with R software. ResultsIn various water bodies， the dominant bacteria phyla was Proteobacteria， the dominant bacteria genera were Deuterostomia， Pseudomonas， Flavobacteriales and Streptomycetaceae. The ARGs annotated were mainly composed of quinolones， aminoglycosides， macrolides and beta-lactams antibiotic resistance genes. The top four relative abundance of resistance genes were macB， RanA， evgS and TxR， The average absolute abundance and expression of resistance genes in well water and Mingou water were higher than those in river water. ConclusionMultiple ARGs are detected to varying degrees in well water， river water， and Mingou water bodies， and the expression of resistance genes in well water and Mingou water bodies is higher than that in river water bodies， possibly due to human production and living activities.

Detection of platelet bacteria based on cultomics and metagenomics / 中国输血杂志

【Objective】 To explore the composition of culturable bacteria in platelets through bacterial culturomics and verify the results of culturomics and metagenomics to improve the detection rate of bacteria in platelets. 【Methods】 Platelet samples from 6 healthy people were collected. Eight kinds of culture media were placed in aerobic conditions and 12 kinds of culture media were placed in anaerobic conditions for large-scale culture and isolation of bacteria in platelets. The isolated single colony was identified by 16S rRNA gene sequencing. The bacterial abundance of healthy human platelet microbiome was analyzed by metagenomic sequencing, and the cultivable bacterial species in platelets was confirmed based on metagenomic and culturomics results. 【Results】 A total of 90 strains of bacteria belonging to 3 phylums, 5 classes, 5 orders, 7 families, 9 genus and 23 species were isolated from 6 platelet samples by culturomics. Among them, the strains with more monoclonal clones at the species level were Brevundimonas aurantiaca (16.7%), Bacillus sp. Y1 (15.6%), Cutibacterium acnes (14.4%) and Brevibacillus brevis (13.3%). The platelet samples sequenced by mNGS showed that the abundance values of Proteobacteria, Firmicutes and Actinobacteria were high. The bacteria detected by both culturomics and metagenomic sequencing methods were as follows: Firmicutes: Bacillus sp. Y1, B. thuringiensis, B. cereus, B. mobilis, B. velezensis, Staphylococcus epidermidis, and Brevibacillus brevis; Actinobacteria: Cutibacterium acnes; Proteobacteria: Escherichia coli and Delftia tsuruhatensis. 【Conclusion】 The mutual validation of culturomics and metagenomics has identified some bacteria, proving that bacteria exist in platelets.

Application and consideration of metagenomic next-generation sequencing technology in the diagnosis of insect-borne diseases / 中华检验医学杂志

Insect-borne diseases are serious life-threatening infectious diseases. Rapid and accurate etiological diagnosis are the premise of timely and effective clinical treatments, reducing mortality and sequelae. Laboratory diagnoses of insect-borne diseases mainly focus on targeted serological detection and polymerase chain reaction, which is difficult to detect rare insect borne pathogens. At present, the metagenomic next-generation sequencing (mNGS) technology has moved from scientific research into clinical application. The detection of nucleic acid sequences of all organisms in infected samples by mNGS exhibited significant advantages in the diagnosis and traceability of rare pathogens. But at the same time, mNGS is also suffered with challenges such as background microbial interference, false results caused by database restrictions, pathogen resistance and host immune status information that are urgently needed for clinical treatments. This article systematically summarized applications of mNGS in the diagnosis of insect-borne pathogens and the challenges and difficulties it faces. With the continuous optimization of mNGS in the detection, it will bring new development and innovation to the etiology diagnosis of clinical infectious diseases.

Ureaplasma parvum-induced peritoneal dialysis-associated peritonitis: a case report / 中华肾脏病杂志

Pathogen detection is very important to improve the prognosis of patients with peritoneal dialysis-associated peritonitis. The paper reported a case of peritonitis caused by Ureaplasma parvum diagnosed by metagenomics next-generation sequencing（mNGS）technology. The patient was a middle-aged woman and hospitalized due to abdominal pain and muddy effluent. Anti-infective treatments such as ceftazidime and vancomycin were given but the effect was poor. The result of traditional culture was negative. Ureaplasma parvum was detected by mNGS. After using doxycycline，the patient's inflammation was controlled. It is suggested that mNGS plays an important role in the detection of the pathogens in peritoneal dialysis-associated peritonitis patients with negative culture. Through this case report and literature review，clinical experience is provided for the diagnosis and treatment in such patients.

Etiological diagnosis value of metagenomic next generation sequencing in the patients with spinal infection / 中华传染病杂志

Objective:To investigate the efficacy of metagenomic next generation sequencing (mNGS) in the etiological diagnosis of patients with spinal infection, so as to provide reference for timely diagnosis and treatment.Methods:A total of 40 patients with suspected spinal infection admitted to the Department of Infectious Diseases in Henan Provincial People′s Hospital from January 2020 to July 2022 were included. The results of tissue culture, histopathological examination and tissue mNGS detection were analyzed retrospectively. According to the clinical diagnose, the patients were divided into the spinal infection group (28 cases) and the non-spinal infection group (12 cases). The positive rate, sensitivity and specificity of mNGS and tissue culture in the pathogen detection of patients with spinal infection were compared. McNemar test was used for statistical analysis.Results:There were 23 males and 17 females in 40 patients. The positive rate of mNGS was higher than that of tissue culture (75.0%(30/40) vs 12.5%(5/40)), and the difference was statistically significant ( χ2=0.08, P<0.001). Based on clinical diagnostic criteria, the sensitivity of mNGS in the diagnosis of spinal infection was higher than that of tissue culture (82.1% vs 17.9%), with a statistically significant difference ( χ2=0.02, P<0.001), while the specificity compared to the tissue culture (33.3% vs 100.0%), the difference was not statistically significant ( P>0.05). Conclusions:mNGS has a high pathogen detection rate and sensitivity in the etiological diagnosis of patients with spinal infection, which could provide clinical guidance for the diagnosis and treatment of patients with spinal infection.

Cerebrospinal fluid analysis: current diagnostic methods in central nervous system infectious diseases / Novos métodos diagnósticos liquóricos nas doenças infecciosas do sistema nervoso central

ABSTRACT Cerebrospinal fluid (CSF) analysis is an important diagnostic tool for many conditions affecting the central nervous system (CNS), especially CNS infectious diseases. Despite its low specificity, CSF white blood cell counts, CSF protein levels, CSF serum glucose ratio and CSF lactate measurement are useful in differentiating infections caused by distinct groups of pathogens. CSF direct examination and cultures can identify causative organisms and antibiotic sensitivities as well. Adjunctive tests such as latex agglutination, different immunological assays and molecular reactions have great specificities and increasing sensitivities. In this article, some recent diagnostic methods applied to CSF analysis for frequent CNS infections are presented.

RESUMO A análise do líquido cefalorraquiano (LCR) é uma importante ferramenta diagnóstica para muitas condições que afetam o sistema nervoso central (SNC), especialmente as doenças infecciosas. Apesar da baixa especificidade, a contagem de leucócitos no LCR, a determinação dos níveis de proteína, glicose e lactato podem ser úteis na diferenciação de infecções causadas por diferentes grupos de patógenos. O exame direto e as culturas podem identificar organismos causadores de infecções bem como suas sensibilidades a antibióticos. Testes adjuvantes como aglutinação em látex, diferentes ensaios imunológicos e reações moleculares têm taxas de sensibilidades e especificidades crescentes. Neste artigo, são apresentados alguns métodos diagnósticos mais recentemente aplicados à análise do LCR no diagnóstico das infecções do SNC.

Bacterioma en nódulos mamarios y sus efectos morfológicos sobre la línea celular del cáncer de mama / Bacterioma in Mammary Nodules and Their Morphological Effects on Breast Cancer Cell Line

Introducción: En el cáncer de mama no se ha reportado una bacteria como causante, pero sí la presencia de diferentes especies que se relacionan de forma beneficiosa o perjudicial. Objetivo: Identificar la microbiota presente en nódulos mamarios y sus efectos morfológicos sobre la línea celular MCF-7. Métodos: Estudio exploratorio experimental de una población de 57 mujeres con nódulos mamarios, intervenidas para biopsia por punción en un centro de diagnóstico. De estas, se escogieron 17 muestras mediante muestreo no probabilístico para el análisis metagenómico. Se realizó una infección con células MCF-7 y Staphylococcus saprophyticus a MOI de 1:1, 5:1 y 10:1 (48 horas de exposición). Resultados: De las 57 muestras tomadas, solo en 7 pacientes se obtuvo resultado positivo (12,28 por ciento) y en el resto (50) no hubo crecimiento bacteriano. Por metagenómica se obtuvo la microbiota siguiente: Proteobacteria (47 por ciento), Escherichia (9,4 por ciento) y Yokenella (8,2 por ciento), entre otros. Los controles fueron negativos. Solo dos pacientes resultaron positivas para cáncer, entre ellas la especie común fue S. saprophyticus. En la infección, los cambios morfológicos se evidenciaron desde la MOI 5:1. Conclusión: El bacterioma extraído de los nódulos de una población femenina es en su mayoría flora endógena del órgano mamario(AU)

Introduction: No bacterium has been reported as causative of breast cancer, but the presence of different species that are related in a beneficial or detrimental way. Objective: To identify the microbiota present in breast nodules and its morphological effects on the MCF-7 cell line. Methods: Exploratory, experimental study of a population of 57 women with breast nodules, operated for needle biopsy in a diagnostic center. Of these, 17 samples were chosen by non-probabilistic sampling for metagenomic analysis. Infection was performed with MCF-7 cells and Staphylococcus saprophyticus at MOI of 1:1, 5:1 and 10:1 (48 hours of exposure). Results: Of the 57 samples taken, only 7 yielded positive results (12.28 percent) and the rest (50) had no bacterial growth. The following microbiota was obtained by metagenomics: Proteobacteria (47 percent), Escherichia (9.4 percent) and Yokenella (8.2 percent), among others. Controls were negative. Only two patients tested positive for cancer, and S. saprophyticus was the common species. In the infection, morphological changes were evidenced from MOI 5:1. Conclusion: The bacteriome extracted from the nodules of a female population is mostly endogenous flora of the mammary glands(AU)

Gut microbiome in neuropsychiatric disorders / O microbioma intestinal nas doenças neuropsiquiátricas

ABSTRACT Background: Neuropsychiatric disorders are a significant cause of death and disability worldwide. The mechanisms underlying these disorders include a constellation of structural, infectious, immunological, metabolic, and genetic etiologies. Advances in next-generation sequencing techniques have demonstrated that the composition of the enteric microbiome is dynamic and plays a pivotal role in host homeostasis and several diseases. The enteric microbiome acts as a key mediator in neuronal signaling via metabolic, neuroimmune, and neuroendocrine pathways. Objective: In this review, we aim to present and discuss the most current knowledge regarding the putative influence of the gut microbiome in neuropsychiatric disorders. Methods: We examined some of the preclinical and clinical evidence and therapeutic strategies associated with the manipulation of the gut microbiome. Results: targeted taxa were described and grouped from major studies to each disease. Conclusions: Understanding the complexity of these ecological interactions and their association with susceptibility and progression of acute and chronic disorders could lead to novel diagnostic biomarkers based on molecular targets. Moreover, research on the microbiome can also improve some emerging treatment choices, such as fecal transplantation, personalized probiotics, and dietary interventions, which could be used to reduce the impact of specific neuropsychiatric disorders. We expect that this knowledge will help physicians caring for patients with neuropsychiatric disorders.

RESUMO Antecedentes: Os transtornos neuropsiquiátricos são uma importante causa de morte e invalidez no mundo. Os mecanismos subjacentes a esses transtornos incluem uma constelação de etiologias estruturais, infecciosas, imunológicas, metabólicas e genéticas. Avanços nas técnicas de sequenciamento do DNA têm demonstrado que a composição do microbioma entérico é dinâmica e desempenha um papel fundamental não apenas na homeostase do hospedeiro, mas também em várias doenças. O microbioma entérico atua como mediador na sinalização das vias metabólica, neuroimune e neuroendócrina. Objetivo: Apresentar os estudos mais recentes sobre a possível influência do microbioma intestinal nas diversas doenças neuropsiquiátricas e discutir tanto os resultados quanto a eficácia dos tratamentos que envolvem a manipulação do microbioma intestinal. Métodos: foram examinadas algumas das evidências pré-clínicas e clínicas e estratégias terapêuticas associadas à manipulação do microbioma intestinal. Resultados: os táxons-alvo foram descritos e agrupados a partir dos principais estudos para cada doença. Conclusões: Entender a fundo a complexidade das interações ecológicas no intestino e sua associação com a suscetibilidade a certas doenças agudas e crônicas pode levar ao desenvolvimento de novos biomarcadores diagnósticos com base em alvos moleculares. Além disso, o estudo do microbioma intestinal pode auxiliar na otimização de tratamentos não farmacológicos emergentes, tais como o transplante de microbiota fecal, o uso de probióticos e intervenções nutricionais personalizadas. Dessa forma, terapias alternativas poderiam ser usadas para reduzir o impacto dos transtornos neuropsiquiátricos na saúde pública. Esperamos que esse conhecimento seja útil para médicos que cuidam de pacientes com diversos transtornos neuropsiquiátricos.

Bacterial diversity in high Andean grassland soils disturbed with Lepidium meyenii crops evaluated by metagenomics / Diversidade bacteriana em solos de prados andinos elevados perturbados por culturas de Lepidium meyenii avaliadas por metagenômica

Soil quality is usually determined by its physical-chemical characteristics without taking into account the bacterial communities that play a fundamental role in the chemical decomposition of plant nutrients. In this context, the objective of the study was to evaluate bacterial diversity in high Andean grassland soils disturbed with Lepidium meyenii cultivation under different gradients of use (first, second and third use) and crop development (pre-sowing, hypocotyl development and post-harvest). The sampling was carried out in the Bombón plateau in the central Andes of Peru, during the rainy and low water seasons, by the systematic method based on a specific pattern assigned in a geometric rectangular shape at a depth of 0 - 20 cm. The characterization of the bacterial communities was carried out through the metagenomic sequencing of the 16S rRNA. 376 families of bacteria were reported, of which it was determined that there was a significant change in bacterial composition and distribution in relation to use pressure. There were no major changes due to the development of Lepidium meyenii. The families most sensitive to use pressure and soil poverty indicators were Verrucomicrobiaceae, Acidobacteraceae and Aakkermansiaceae.

A qualidade do solo é normalmente determinada pelas suas características físico-químicas sem ter em conta as comunidades bacterianas que desempenham um papel fundamental na decomposição química dos nutrientes das plantas. Neste contexto, o objetivo do estudo foi avaliar a diversidade bacteriana em solos de prados andinos elevados perturbados pelo cultivo de Lepidium meyenii sob diferentes gradientes de utilização (primeira, segunda e terceira utilizações) e desenvolvimento das culturas (pré-semeadura, desenvolvimento do hipocótilo e póscolheita). A amostragem foi realizada no planalto de Bombón, nos Andes centrais do Peru, durante as estações das chuvas e das águas baixas, pelo método sistemático baseado num padrão específico atribuído em forma geométrica retangular a uma profundidade de 0 - 20 cm. A caracterização das comunidades bacterianas foi realizada através da sequenciação metagenômica do rRNA 16S. Foram relatadas 376 famílias de bactérias, das quais se verificou uma alteração significativa na composição e distribuição bacteriana em relação à pressão de utilização. Não se registaram grandes alterações devido ao desenvolvimento do Lepidium meyenii. As famílias mais sensíveis à utilização de indicadores de pressão e pobreza do solo foram as Verrucomicrobiaceae, Acidobacteraceae e Aakkermansiaceae.

Application and development of metagenomics next-generation sequencing technology in diagnosis of bone infection / 国际外科学杂志

Bone infection is a serious infectious disease in clinical practice due to its difficult treatment and poor prognosis. Therefore, early accurate diagnosis of bone infection is the key for successful treatment. The traditional detection methods is time consuming with lower positive rate. Therefore, it is urgent to find better detection techniques to identify the pathogenic microorganisms of bone infection. In recent years, metagenomic second-generation sequencing technology has been widely used in the diagnosis of clinical infectious diseases because of its advantages of accurate, rapid, efficient and comprehensive diagnosis of pathogenic microorganisms, and can be used as an effective tool for the diagnosis of bone infections. This paper mainly reviews the advantages, disadvantages and development direction of metagenomics next-generation sequencing technology in the diagnosis of bone infection.

Metagenomic characterization of the culturable bacterial community structure of Tapuy, a Philippine indigenous rice wine, reveals significant presence of potential probiotic bacteria

Background@#Tapuy is an indigenous fermented rice wine produced in the Northern areas of the Philippines. Fermented foods and drinks have gained interest due to their associated health benefits, attributable to probiotic bacteria in the food items. However, pathogenic bacteria may also be present in fermented food and pose health risks, signifying a need for standardization. Currently, there is limited knowledge on the bacterial content of tapuy. @*Objectives@#This study aimed to characterize the bacterial diversity and community structure of culturable bacteria in traditionally fermented tapuy samples, to perform standardization of tapuy fermentation, and to compare the bacterial diversity and community structure of culturable bacteria in laboratory fermented tapuy with that of the traditional samples. @*Methods@#Tapuy samples were obtained from four municipalities in Benguet, Philippines. Laboratory fermentation of tapuy was performed simultaneously with the fermentation in the sampling site using a standardized protocol. Samples were plated on de Man, Rogosa, and Sharpe (MRS) agar and NA, and the colonies were harvested for DNA extraction. DNA samples were sent for 16S rDNA metagenomic sequencing. Results. Metagenomic analysis revealed the presence of many bacterial species that were previously unreported in tapuy. Traditional tapuy samples were composed primarily of members of the genera Bacillus and Lactobacillus in varying proportions. Potential probiotic bacteria were abundant in Kapangan (97.42%) and Sablan (99.89%) field samples. B. wiedmannii was present in all samples and was identified as a harmful species. Laboratory fermentation increased the abundance of potential probiotic bacteria in Itogon and La Trinidad samples (differences of 75.36% and 78.36%, respectively). It decreased the quantity of B. wiedmannii in La Trinidad (a difference of 97.1%). Laboratory fermented samples generally exhibited higher bacterial diversity and species richness compared to field samples. @*Conclusions@#Traditionally fermented tapuy samples contained a significant proportion of potential probiotic bacteria belonging to the genera Bacillus and Lactobacillus. Laboratory fermented samples were found to have higher bacterial diversity and richness compared to field samples. The significant presence of potential probiotic bacteria suggests that tapuy is a good candidate for development into functional food and a good source of likely probiotic species that could be explored for health applications. The presence of harmful bacteria suggests the need for possible standardization of fermentation practices.

Identification of microbial agents in culture-negative brain abscess samples by 16S/18S rRNA gene PCR and sequencing

@#Despite clinical suspicion of an infection, brain abscess samples are often culture-negative in routine microbiological testing. Direct PCR of such samples enables the identification of microbes that may be fastidious, non-viable, or unculturable. Brain abscess samples (n = 217) from neurosurgical patients were subjected to broad range 16S rRNA gene PCR and sequencing for bacteria. All these samples and seven formalin-fixed paraffin-embedded tissue (FFPE) samples were subjected to species-specific 18S rRNA PCR for neurotropic free-living amoeba that harbour pathogenic bacteria. The concordance between smear and/or culture and PCR was 69%. One-third of the samples were smear- and culture-negative for bacterial agents. However, 88% of these culture-negative samples showed the presence of bacterial 16S rRNA by PCR. Sanger sequencing of 27 selected samples showed anaerobic/fastidious gram negative bacteria (GNB, 38%), facultative Streptococci (35%), and aerobic GNB (27%). Targeted metagenomics sequencing of three samples showed multiple bacterial species, including anaerobic and non-culturable bacteria. One FFPE tissue revealed the presence of Acanthamoeba 18S rRNA. None of the frozen brain abscess samples tested was positive for 18S rRNA of Acanthamoeba or Balamuthia mandrillaris. The microbial 16/18S rRNA PCR and sequencing outperformed culture in detecting anaerobes, facultative Streptococci and FLA in brain abscess samples. Genetic analyses of 16S/18S sequences, either through Sanger or metagenomic sequencing, will be an essential diagnostic technology to be included for diagnosing culture-negative brain abscess samples. Characterizing the microbiome of culture-negative brain abscess samples by molecular methods could enable detection and/or treatment of the source of infection.