Results analysis of mNGS applied to infectious diseases / 中华预防医学杂志

The application of metagenomic second-generation sequencing (mNGS) is shifting from research to clinical laboratories due to rapid technological advances and significant cost reductions. Although many studies and case reports have confirmed that the success of mNGS in improving the prevention, diagnosis, treatment and tracking of infectious diseases, there are still some obstacles that must be overcome. The results of mNGS show all the possible pathogens in the sample, however, in the face of thousands of microbes that can infect humans, it remains challenging to accurately identify the key pathogens. So far, there is no unified interpretation standard for mNGS in clinical practice. This article reviews the interpretation of mNGS results for pathogen infection in different systems, the clinical interpretation and application regulations of mNGS results, and the challenges of mNGS interpretation in pathogen diagnosis.

Research progress of the application of metagenomics technology in female reproductive tract diseases / 中华预防医学杂志

In recent years, many studies have found that vaginal microbiota is closely related to female reproductive tract diseases. However, traditional microbial culture technology has the defects of long culture cycle and most microorganisms cannot be cultured. The development of metagenomics technique has broken the limitations of culture technology, and has been gradually applied to the study of vaginal microorganisms with the characteristics of high throughput, short time, identification of microbial population structure and gene function. It also provides technical support for elucidating the relationship between vaginal microbiota and female reproductive tract diseases. This article mainly introduces the metagenomics techniques and their applications in prevention, screening and diagnosis of common female reproductive tract diseases, and discusses their promising development and limitations to be overcome.

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.

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.

0ne case report of Chlamydia psittaci pneumonia / 中华劳动卫生职业病杂志

This paper reported a case of severe Chlamydia psittaci pneumonia. The patient had a clear history of contact with sick poultry. The clinical manifestations were dry cough, fever and respiratory failure. Chest CT showed consolidation in the lower lobe of the right lung, and a small amount of exudative ground-glass opacity in the left lung. Chlamydia psittaci was detected in bronchoalveolar lavage fluid (BALF) by metagenomic assay. After treatment with antibiotics such as nitroimidazoles and carbapenems, the patient was discharged with a better health condition.

Application value of metagenomic next-generation sequencing for pathogen detection in childhood agranulocytosis with fever / 中国当代儿科杂志

OBJECTIVES@#To study the application value of metagenomic next-generation sequencing (mNGS) for pathogen detection in childhood agranulocytosis with fever.@*METHODS@#A retrospective analysis was performed on the mNGS results of pathogen detection of 116 children with agranulocytosis with fever who were treated from January 2020 to December 2021. Among these children, 38 children with negative mNGS results were enrolled as the negative group, and 78 children with positive results were divided into a bacteria group (n=22), a fungal group (n=23), and a viral group (n=31). Clinical data were compared between groups.@*RESULTS@#For the 116 children with agranulocytosis and fever, the median age was 8 years at diagnosis, the median turnaround time of mNGS results was 2 days, and the positive rate of mNGS testing was 67.2% (78/116). Compared with the negative group, the bacterial group had a higher procalcitonin level (P<0.05), the fungal group had higher level of C-reactive protein and positive rate of (1,3)-β-D glucan test/galactomannan test (P<0.05), and the fungal group had a longer duration of fever (P<0.05). Among the 22 positive microbial culture specimens, 9 (41%) were consistent with the mNGS results. Among the 17 positive blood culture specimens, 8 (47%) were consistent with the mNGS results. Treatment was adjusted for 28 children (36%) with the mNGS results, among whom 26 were cured and discharged.@*CONCLUSIONS@#The mNGS technique has a shorter turnaround time and a higher sensitivity for pathogen detection and can provide evidence for the pathogenic diagnosis of children with agranulocytosis and fever.

Value of metagenomic next-generation sequencing in children with severe infectious diseases / 中国当代儿科杂志

OBJECTIVES@#To study the application value of metagenomic next-generation sequencing (mNGS) in children with severe infectious diseases.@*METHODS@#An analysis was performed on the clinical data and laboratory test results of 29 children with severe infection who were admitted to the Second Affiliated Hospital of Wenzhou Medical University from June 2018 to December 2020. Conventional pathogen culture was performed for the 29 specimens (27 peripheral blood specimens and 2 pleural effusion specimens) from the 29 children, and mNGS pathogen detection was performed at the same time.@*RESULTS@#Among the 29 children, 2 tested positive by conventional pathogen culture with 2 strains of pathogen, and the detection rate was 7% (2/29); however, 20 children tested positive by mNGS with 38 strains of pathogen, and the detection rate was 69% (20/29). The pathogen detection rate of mNGS was significantly higher than that of conventional pathogen culture (P<0.05), and mNGS could detect the viruses, fungi, and other special pathogens that conventional pathogen culture failed to detect, such as Orientia tsutsugamushi. The univariate analysis showed that gender, routine blood test results, C-reactive protein, procalcitonin, D-dimer, radiological findings, and whether antibiotics were used before admission did not affect the results of mNGS (P>0.05).@*CONCLUSIONS@#Compared with conventional pathogen culture, mNGS is more sensitive for pathogen detection, with fewer interference factors. Therefore, it is a better pathogenic diagnosis method for severe infectious diseases in children.

Clinical value of metagenomic next-generation sequencing in complicated infectious diseases / 中国当代儿科杂志

Infectious diseases are commonly seen in clinical practice, and pathogen diagnosis is the key link in diagnosis and treatment; however, conventional pathogen detection methods cannot meet clinical needs due to time-consuming operation and low positive rate. As a new pathogen detection method, metagenomic next-generation sequencing (mNGS) has a wide detection range and can detect bacteria, viruses, fungi, parasites, rare pathogens, and even unknown pathogens. The technique of mNGS is unbiased and can rapidly, efficiently, and accurately obtain all nucleic acid information in test samples, analyze pathogens, and guide clinical diagnosis and treatment, thereby playing an important role in complicated infectious diseases. This article reviews the diagnostic advantages and clinical value of mNGS in bacterial, fungal, viral, and parasitic infections.

Microbiota intestinal y su relación con agentes oportunistas vinculados a las epidemias / Gut microbiota and its relationship with opportunistic agents linked to epidemics

Resumen Existen epidemias silenciosas asociadas al estrés y a los malos hábitos de alimentación, tan importantes como las epidemias tradicionales asociadas a la pobreza, a problemas geográficos y climáticos. Numerosos estudios se suman al importante papel de un patrón estable de la microbiota intestinal que favorece el estado saludable en los seres humanos y por lo tanto, su posible implicación en la incidencia y prevalencia de enfermedades que pueden convertirse en epidémicas. En esta revisión se analiza el estado actual de la relación entre los factores demográficos, geográficos, ambientales, patrones de consumo de alimentos con la microbiota intestinal y la aparición de epidemias de origen microbiano, metabólico e inmunológico. Se apoya la iniciativa promovida internacionalmente para la creación de plataformas metagenómicas que contribuyan al estudio del patrón de la microbiota intestinal, el seguimiento epidemiológico y la prevención de las enfermedades epidémicas asociadas con su alteración, así como el diseño de métodos rápidos y económicos para la complementación de estos estudios.

Abstract Silent epidemics associated with stress and unhealthy eating habits are as important as traditional epidemics related to poverty, geographical and climate problems. Many studies incorporate the important role of a stable pattern of gut microbiota that favours the human health status and therefore, its possible implication in incidence and prevalence of diseases that can become epidemics. In this review, the current state-of-art is analysed in terms of relationship between demographic, geographic, environmental factors, and habits with the gut microbiota pattern and the onset of epidemics of microbial, metabolic and immunological origin. The internationally promoted initiative for the creation of metagenomic platforms contributing to studies of the gut microbiota pattern for the epidemiological monitoring and prevention of epidemic diseases associated with its alteration is fostered, as well as the design of rapid and economic methods to complement these studies.

Resumo Existem epidemias silenciosas associadas ao estresse, maus hábitos alimentares, tão importantes quanto as epidemias tradicionais associadas à pobreza, problemas geográficos e climáticos. Numerosos estudos contribuem para o importante papel de um padrão estável de microbiota intestinal que favorece o estado saudável em seres humanos e, portanto, sua possível comprometimento na incidência e prevalência de doenças que podem se tornar epidêmicas. Esta revisão analisa o estado atual da relação entre fatores demográficos, geográficos, ambientais, padrões de consumo de alimentos com a microbiota intestinal e o aparecimento de epidemias de origem microbiana, metabólica e imunológica. É fornecido apoio à iniciativa promovida internacionalmente para a criação de plataformas metagenômicas que contribuam para o estudo do padrão da microbiota intestinal, monitoramento epidemiológico e prevenção de doenças epidêmicas associadas à sua alteração, bem como o desenho de métodos rápidos e baratos para a complementação desses estudos.

Metagenomics approach to identify lignocellulose-degrading enzymes in the gut microbiota of the Chinese bamboo rat cecum

BACKGROUND: Lignocellulose is considered a renewable organic material, but the industrial production of biofuel from lignocellulose is challenging because of the lack of highly active hydrolytic enzymes. The guts of herbivores contain many symbiotic microorganisms that have evolved to hydrolyze plant lignocellulose. Chinese bamboo rats mainly consume high-fiber foods, indicating that some members of the intestinal tract microbiota digest lignocellulose, providing these rats with the energy required for growth. RESULTS: Here, we used metagenomics to analyze the diversity and functions of the gut microbiota in Chinese bamboo rats. We identified abundant populations of lignocellulose-degrading bacteria, whose main functions involved carbohydrate, amino acid, and nucleic acid metabolism. We also found 587 carbohydrate-active enzyme genes belonging to different families, including 7 carbohydrate esterase families and 21 glycoside hydrolase families. The glycoside hydrolase 3, glycoside hydrolase 1, glycoside hydrolase 43, carbohydrate esterase 4, carbohydrate esterase 1, and carbohydrate esterase 3 families demonstrated outstanding performance. CONCLUSIONS: The microbes and enzymes identified in our study expand the existing arsenal of proficient degraders and enzymes for lignocellulosic biofuel production. This study also describes a powerful approach for targeting gut microbes and enzymes in numerous industries.

Bacterial communities in fecal samples of myotis chiloensis from Southern, Chile / Comunidades bacterianas presentes en muestras fecales de myotis chiloensis en el sur de Chile

SUMMARY: The insectivorous bat Myotis chiloensis is endemic of South America. Even though potentially pathogenic bacterial species of Mycoplasma have been reported from this species, there are no further studies regarding the bacterial communities they harbor. This may provide important insights for the better understanding of its ecology, diet and implications in cross-species pathogens transmission. Here we report a first survey on bacterial communities of M. chiloensis based on metagenomic analysis of fecal samples. We found that taxonomic profile is dominated by Proteobacteria (23.7 to 57.7 %) and Firmicutes (11.8 to 61.6 %), which main families are represented by Burkholderiaceae- Enterobacteriaceae and Veillonellaceae-Bacillaceae, respectively. Phyla Bacteroidetes, Actinobacteria, Cyanobacteria, Planctomycetes and Acidobacteria were also present with abundance above 1 % of the total reads. Variations among individuals could be observed at genus level and no significant differences were found between sex groups regarding taxonomic profiles and diversity. Potentially pathogenic species were also detected in all the samples, including Staphylococcus aureus and Clostridium perfringens. Our results highlight the significance M. chiloensis as a reservoir of pathogenic bacteria and its microbiota as an interesting ecological model due to its wide distribution. Further metagenomic studies are necessary for a better understanding of M. chiloensis diet and its host-symbiont relationships.

RESUMEN: El murciélago insectívoro Myotis chiloensis es endémico de América del Sur. A pesar de que en esta especie se han reportado bacterias potencialmente patógenas tipo Mycoplasma, no existen estudios sobre sus comunidades bacterianas, lo cual podría proporcionar información importante para una mejor comprensión de su ecología, dieta e implicaciones en la transmisión de patógenos. En el presente trabajo se realiza una descripción de las comunidades bacterianas del murciélago M. chiloensis basada en análisis metagenómico de muestras fecales. El perfil taxonómico encontradofue dominado por Proteobacterias (23,7-57,7 %) y Firmicutes (11,8-61,6 %), cuyas principales familias fueron representadas por Burkholderiaceae-Enterobacteriaceae y Veillonellaceae-Bacillaceae, respectivamente. También se encontraron los filos Bacteroidetes, Actinobacteria, Cyanobacteria, Planctomycetes y Acidobacteria con una abundancia superior al 1 %. Se observaron variaciones entre los individuos a nivel de género, sin diferencias significativas de los perfiles taxonómicos y diversidad según sexo. Se detectaron especies potencialmente patógenas en todas las muestras, entre ellos Staphylococcus aureus y Clostridium perfringens. Nuestros resultados destacan la importancia de M. chiloensis como un reservorio de bacterias patógenas y el estudio de su microbiota como un modelo ecológico debido a su amplia distribución. Más estudios metagenómicos son necesarios para comprender la dieta de M. chiloensis y sus relaciones huésped-simbionte.

Metagenomic next-generation sequencing (mNGS) for diagnostically challenging infectious diseases in patients with acute leukemia

ABSTRACT This report shows the contribution of next-generation metagenomic sequencing (mNGS) as an alternative to challenging diagnostic infection in immunosuppressed individuals. Herein, we report three acute leukemia patients who developed severe invasive infections due to different etiologies: fungi, viruses, and protozoa. mNGS improved the diagnosis of the infections and provided the opportunity for adequate therapy. The mNGS is a hypothesis-free diagnostic platform, increasing potential in challenging diseases in hematological patients due to the extended diagnostic panel and the expedite access to the result.

Distribution of bacteria infected by metagenomic sequencing technology in maxillofacial space / 华西口腔医学杂志

OBJECTIVES@#This study aimed to compare and analyze the consistency and difference between metageno-mic next-generation sequencing (mNGS) and conventional bacterial culture in the detection of pathogenic microorganisms in maxillofacial space infection, as well as to provide a new detection method for the early clinical identification of pathogenic bacteria in maxillofacial space infection.@*METHODS@#The clinical data of 16 patients with oral and maxillofacial space infections in the First Affiliated Hospital of Zhengzhou University from March 2020 to June 2020 were collected. mNGS and conventional bacterial culture methods were used to detect pus. We then analyzed and compared the test results of the two methods, including the test cycle, positive detection rate, anaerobic bacteria, facultative anaerobes and aerobic bacteria detection rates, distribution of pathogenic bacteria, relative species abundance, and resistance genes.@*RESULTS@#The average inspection period of mNGS was (18.81±3.73) h, and the average inspection period of bacterial culture was (83.25±11.64) h, the former was shorter than the latter (@*CONCLUSIONS@#Compared with conventional bacterial culture, mNGS has the characteristics of short test time, high sensitivity, and high accuracy. Thus, it is a new detection method for the early identification of pathogenic bacteria in maxillofacial space infection and is beneficial to the early clinical diagnosis and treatment of the disease.

Metagenomic analysis of the diversity of microbes in the Napahai plateau wetland and their carbon and nitrogen metabolisms / 生物工程学报

Due to the special geographical location and the complex ecosystem types, plateau wetlands play important ecological roles in water supply, greenhouse gas regulation and biodiversity preservation. Napahai plateau wetland is a special wetland type with low latitude and high altitude, and its microbial diversity was rarely studied. The diversity of microbial communities in the Napahai plateau wetland was analyzed using metagenomics method. Among the microbes detected, 184 phyla, 3 262 genera and 24 260 species belong to the bacterial domain, 13 phyla and 32 genera belong to the archaeal domain, and 13 phyla and 47 genera belong to the fungal domain. Significant differences in species diversity between soil and water were observed. Acidobacteria, Proteobacteria and Actinobacteria were dominant phyla in soil, while Proteobacteria and Bacteroides were dominant phyla in water. Since the carbon and nitrogen metabolism genes were abundant, the pathways of carbon fixation and nitrogen metabolism were analyzed. Calvin cycle, reductive tricarboxylic acid cycle and 3-hydroxypropionic acid cycle were the main carbon fixation pathways, while Proteobacteria, Chloroflexi, and Crenarchaeota were the main carbon-fixing bacteria group. As for the nitrogen cycle, nitrogen fixation and dissimilatory nitrate reduction were dominant in water, while nitrification and denitrification were dominant in soil. Proteobacteria, Nitrospirae, Verrucomicrobia, Actinobacteria, Thaumarchaeota and Euryarchaeota contributed to the nitrogen cycle. The study on microbial diversity of Napahai plateau wetlands provides new knowledge for the comprehensive management and protection of wetland environment in China.

Microbiota perinatal: Revisión de su importancia en la salud del recién nacido / Perinatal microbiota: review of its importance in newborn health

La metagenómica en el estudio de los ecosistemas bacterianos intestinales ha permitido definir un perfil genético funcional estándar en el recién nacido, de forma que un ecosistema bacteriano será tanto más "normal" cuanto más se parezca su perfil genético funcional a un estándar. El desarrollo de determinado enterotipo funcional en los primeros días de vida tras el parto es fundamental para que tenga lugar el cebado del sistema inmunológico con determinados antígenos bacterianos. Independientemente de si las primeras bacterias intestinales se adquieren antes o justo después del parto, la microbiota del recién nacido va a ser el resultado de una situación de simbiosis con la flora microbiana de su entorno, en especial, con la flora bacteriana de su madre. El tipo de parto, la administración de antibióticos perinatales, el entorno y la exposición nutricional, en especial, la lactancia materna, han demostrado relacionarse de forma importante con el microbioma intestinal predominante

The use of metagenomics in the study of gut bacterial ecosystems has helped to define a standard, functional genetic profile in newborn infants, so that a bacterial ecosystem will be deemed more "normal" the more similar its functional genetic profile is to a standard. The development of a specific functional enterotype in the first days of life after birth is critical for the priming of the immune system with certain bacterial antigens.Regardless of whether the first gut bacteria are acquired before or just after birth, the newborn microbiota will result from the symbiosis with the environmental microbial flora, especially with the bacterial flora of the mother. The type of delivery, the administration of perinatal antibiotics, the environment, and nutritional exposure, especially breastfeeding, have demonstrated an important relationship with the prevalent gut microbiome

Next generation sequencing and microbiome's taxonomical characterization of frozen soil of north western Himalayas of Jammu and Kashmir, India

BACKGROUND: Traditionally, microbial genome sequencing has been restrained to the species grown in pure culture. The development of culture-independent techniques over the last decade allows scientists to sequence microbial communities directly from environmental samples. Metagenomics is the study of complex genome by the isolation of DNA of the whole community. Next generation sequencing (NGS) of metagenomic DNA gives information about the microbial and taxonomical characterization of a particular niche. The objective of the present research is to study the microbial and taxonomical characterization of the metagenomic DNA, isolated from the frozen soil sample of a glacier in the north western Himalayas through NGS. RESULTS: The glacier community comprised of 16 phyla with the representation of members belonging to Proteobacteria and Acidobacteria. The number of genes annotated through the Kyoto Encyclopedia of Genes and Genomes (KEGG), GO, Pfam, Clusters of Orthologous Groups of proteins (COGs), and FIG databases were generated by COGNIZER. The annotation of genes assigned in each group from the metagenomics data through COG database and the number of genes annotated in different pathways through KEGG database were reported. CONCLUSION: Results indicate that the glacier soil taken in the present study, harbors taxonomically and metabolically diverse communities. The major bacterial group present in the niche is Proteobacteria followed by Acidobacteria, and Actinobacteria, etc. Different genes were annotated through COG and KEGG databases that integrate genomic, chemical, and systemic functional information.

Investigación traslacional en microbioma (InTraMic): un área de interés común y creciente en el IMTIB, Hospital Italiano e Instituto Universitario / Translational research in microbiome (InTraMic): an area of common and growing interest at IMTIB, Hospital Italiano and Instituto Universitario

Se estima que aproximadamente 100 trillones de microorganismos (incluidos bacterias, virus y hongos) residen en el intestino humano adulto y que el total del material genético del microbioma es 100 veces superior al del genoma humano. Esta comunidad, conocida como microbioma se adquiere al momento del nacimiento a través de la flora comensal de la piel, vagina y heces de la madre y se mantiene relativamente estable a partir de los dos años desempeñando un papel crítico tanto en el estado de salud como en la enfermedad. El desarrollo de nuevas tecnologías, como los secuenciadores de próxima generación (NGS), permiten actualmente realizar un estudio mucho más preciso de ella que en décadas pasadas cuando se limitaba a su cultivo. Si bien esto ha llevado a un crecimiento exponencial en las publicaciones, los datos sobre las poblaciones Latinoamérica son casi inexistentes. La investigación traslacional en microbioma (InTraMic) es una de las líneas que se desarrollan en el Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB). Esta se inició en 2018 con la línea de cáncer colorrectal (CCR) en una colaboración con el Colorectal Cancer Research Group del Leeds Institute of Medical Research en el proyecto Large bowel microbiome disease network: Creation of a proof of principle exemplar in colorectal cancer across three continents. A fines de 2019 se cumplió el objetivo de comprobar la factibilidad de la recolección, envío y análisis de muestras de MBF en 5 continentes, incluyendo muestras provenientes de la Argentina, Chile, India y Vietnam. Luego de haber participado de capacitaciones en Inglaterra, se ha cumplido con el objetivo de la etapa piloto, logrando efectivizar la recolección, envío y análisis metagenómico a partir de la secuenciación de la región V4 del ARNr 16S. En 2019, la línea de enfermedad de hígado graso no alcohólico se sumó a la InTraMic iniciando una caracterización piloto en el marco de una colaboración con el laboratorio Novartis. Los resultados de ese estudio, así como el de cáncer colorrectal, están siendo enviados a publicación. En 2020, con la incorporación de la línea de trasplante alogénico de células progenitoras hematopoyéticas, fue presentado un proyecto para un subsidio del CONICET que ha superado la primera etapa de evaluación. En el presente artículo se brinda una actualización sobre la caracterización taxonómica de microbioma y se describen las líneas de investigación en curso. (AU)

It is estimated that approximately 100 trillion microorganisms (including bacteria, viruses, and fungi) reside in the adult human intestine, and that the total genetic material of the microbiome is 100 times greater than that of the human genome. This community, known as the microbiome, is acquired at birth through the commensal flora of the mother's skin, vagina, and feces and remains relatively stable after two years, playing a critical role in both the state of health and in disease. The development of new technologies, such as next-generation sequencers (NGS), currently allow for a much more precise study of it than in past decades when it was limited to cultivation. Although this has led to exponential growth in publications, data on Latin American populations is almost non-existent. Translational research in microbiome (InTraMic) is one of the lines developed at the Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB). This started in 2018 with the Colorectal Cancer Line (CRC) in a collaboration with the Colorectal Cancer Research Group of the Leeds Institute of Medical Research in the project "Large bowel microbiome disease network: Creation of a proof of principle exemplar in colorectal cancer across three continents". At the end of 2019, the objective of verifying the feasibility of collecting, sending and analyzing MBF samples on 5 continents, including samples from Argentina, Chile, India and Vietnam, was met. After having participated in training in England, the objective of the pilot stage has been met, achieving the collection, delivery and metagenomic analysis from the sequencing of the V4 region of the 16S rRNA. In 2019, the non-alcoholic fatty liver disease line joined InTraMic, initiating a pilot characterization in the framework of a collaboration with the Novartis laboratory. The results of that study, as well as that of colorectal cancer, are being published. In 2020, with the incorporation of the allogeneic hematopoietic stem cell transplantation line, a project was presented for a grant from the CONICET that has passed the first stage of evaluation. This article provides an update on the taxonomic characterization of the microbiome and describes the lines of ongoing research. (AU)

Research progress and applications of strain analysis based on metagenomic data / 生物工程学报

Strain is the fundamental unit in microbial taxonomy. The functional diversity among strains has great influence on host phenotypes. With the development of microbiome research, knowing the composition and functional capacities of complex microbial communities at the strain level has become increasingly valuable in scientific research and clinical applications. This review introduces the principles of bioinformatics algorithms for strain analysis based on metagenomic data, the applications in microbiome research and directions of future development.

Challenges and considerations on quality control and evaluation of pathogen metagenomic next-generation sequencing / 生物工程学报

Metagenomic next-generation sequencing (mNGS) could be used for pathogen detection from nearly all types of clinical samples. Especially, the unique diagnostic capability of pathogen mNGS detecting unknown causative agent of infectious diseases makes this method become an importation complement and irreplaceable component for conventional routine laboratory test. However, the complexity of the testing process, the rapid product update, and the insufficiency in quality control and evaluation methods that all make clinical transformation, industry development, and regulation of this technology full of challenge and uncertainty. This review briefly introduces the technical advantages and challenges, and describes the general workflow and quality control steps in details. Finally, it focuses on current considerations regarding quality evaluation methods and standards for pathogen mNGS.