A practical guide to amplicon and metagenomic analysis of microbiome data

Advances in high-throughput sequencing (HTS) have fostered rapid developments in the field of microbiome research, and massive microbiome datasets are now being generated. However, the diversity of software tools and the complexity of analysis pipelines make it difficult to access this field. Here, we systematically summarize the advantages and limitations of microbiome methods. Then, we recommend specific pipelines for amplicon and metagenomic analyses, and describe commonly-used software and databases, to help researchers select the appropriate tools. Furthermore, we introduce statistical and visualization methods suitable for microbiome analysis, including alpha- and beta-diversity, taxonomic composition, difference comparisons, correlation, networks, machine learning, evolution, source tracing, and common visualization styles to help researchers make informed choices. Finally, a step-by-step reproducible analysis guide is introduced. We hope this review will allow researchers to carry out data analysis more effectively and to quickly select the appropriate tools in order to efficiently mine the biological significance behind the data.

Clinical characteristics and genetic analysis of two cases of pseudohypoparathyroidism type Ⅰa with early-onset skin nodules as the diagnostic clue / 中华皮肤科杂志

Clinical features of and genetic mutations in two cases of pseudohypoparathyroidism type Ⅰ a(PHP Ⅰ a) with early-onset skin nodules were analyzed.Both of the two patients were males,and their ages at onset were 2 and 3 months respectively.They both presented with early-onset skin nodules as the main clinical manifestation,and were clinically characterized by a round face,short neck and early obesity.Histopathological examination of skin lesions showed subcutaneous ectopic osteogenesis in both patients.The first patient had low blood calcium,high blood phosphorus,high parathyroid hormone (PTH),and gene sequencing showed a heterozygous mutation c.399delT causing a T base deletion at position 399 in exon 5 of the GNAS gene.The second patient had normal blood calcium and phosphorus levels as well as normal PTH levels at early stage,and gene sequencing showed a heterozygous mutation c.939delT causing a T base deletion at position 939 in exon 9 of the GNAS gene.The blood PTH level was found to increase in the second patient after 1-year follow-up.Both the patients were confirmedly diagnosed with PHP Ⅰa.After treatment with vitamin D3,no new skin nodules occurred,and the blood calcium and phosphorus levels returned to normal.

A case of ichthyosis follicularis, atrichia and photophobia syndrome caused by a novel mutation in the MBTPS2 gene / 中华皮肤科杂志

A case of ichthyosis follicularis,alopecia and photophobia syndrome caused by a novel mutation c.1165C＞T in the membrane-bound transcription factor protease site 2 (MBTPS2) gene was firstly reported.The proband presented with dry skin,congenital hairlessness,follicular keratotic papules,photophobia,epilepsy,and mental and motor retardation.Next-generation and Sanger sequencing analysis confirmed that the proband and his mother both had a c.1165C＞T (p.pro389Ser) mutation in exon 9 of the MBTPS2 gene.According to the clinical manifestations of the patient and genetic characteristics of the MBTPS2 gene mutation,the patient was diagnosed with ichthyosis follicularis,alopecia and photophobia syndrome.

A case of multiple carboxylase deficiency presenting with skin lesions as the initial symptom induced by a novel mutation in the holocarboxylase synthetase gene / 中华皮肤科杂志

A male patient, who was aged 3 months and 12 days, presented with well-circumscribed erythema and scales on the scrotum, perineum, buttocks and perianal region at 1 month after birth. The lesions gradually involved the perioral and axillary regions, flexor aspect of the elbow, popliteal fossa and neck. Shortness of breath, crying, dysphoria and vomiting occurred without fever and cough 3 days before hospitalization. Laboratory examinations at admission showed metabolic acidosis, hyperlactacidemia, hyperammonemia and organic aciduria. Second-generation sequencing and Sanger sequencing of the holocarboxylase synthetase gene revealed a known mutation c.1522C>T in exon 9 and a novel mutation c.1796_1814del in exon 11. According to a guideline from the American College of Medical Genetics and Genomics, this novel mutation was ranked as a pathogenic mutation. The patient was diagnosed as multiple carboxylase deficiency. His clinical symptoms were improved after oral biotin treatment, no neurological symptoms or signs were observed.

Mutation analysis of GJB2 gene in a family with Vohwinkel syndrome / 中华皮肤科杂志

ObjectiveTo detect the mutation of GJB2 gene in a Chinese family with Vohwinkel syndrome.MethodsClinical data were collected from 5 patients with Vohwinkel syndrome in a family,and blood samples were obtained from the 5 patients and 4 unaffected individuals in the family as well as from 100 normal human controls.Genomic DNA was extracted and subjected to PCR for the amplification of the entire encoding and flanking sequences of GJB2 gene(1015 bp) followed by bidirectional sequencing with the ABI PRISM 3730 automatic DNA sequencer.Finally,sequence alignment was carried out by using the software Sequencher 4.10.1 Demo.ResultsA heterozygous missense mutation 196G→C in the GJB2 gene,which resulted in the substitution of aspartic acid by histidine at codon 66 (D66H) in the first extracellular domain of the protein,was observed in all the patients of this family,but in none of the 4 unaffected individuals in this family or the 100 normal human controls.ConclusionThe D66H missense mutation in the GJB2 gene may contribute to the occurrence of Vohwinkel syndrome in Chinese Han population.