MicroNiche: an R package for assessing microbial niche breadth and overlap from amplicon sequencing data.

Niche is a fundamental concept in ecology. It integrates the sum of biotic and abiotic environmental requirements that determines a taxon's distribution. Microbiologists currently lack quantitative approaches to address niche-related hypotheses. We tested four approaches for the quantification of niche breadth and overlap of taxa in amplicon sequencing datasets, with the goal of determining generalists, specialists and environmental-dependent distributions of community members. We applied these indices to in silico training datasets first, and then to real human gut and desert biological soil crust (biocrust) case studies, assessing the agreement of the indices with previous findings. Implementation of each approach successfully identified a priori conditions within in silico training data, and we found that by including a limit of quantification based on species rank, one could identify taxa falsely classified as specialists because of their low, sparse counts. Analysis of the human gut study offered quantitative support for Bacilli, Gammaproteobacteria and Fusobacteria specialists enriched after bariatric surgery. We could quantitatively characterise differential niche distributions of cyanobacterial taxa with respect to precipitation gradients in biocrusts. We conclude that these approaches, made publicly available as an R package (MicroNiche), represent useful tools to assess microbial environment-taxon and taxon-taxon relationships in a quantitative manner.

Persistent strongyloidiasis in an immunodeficient patient.

A 56-year-old woman with acquired, common variable immunodeficiency was found to have persistent gastrointestinal as well as pulmonary infection with Strongyloides stercoralis. Repeated courses of treatment with thiabendazole led to marked reduction or loss of Strongyloides stercoralis larvae, but cessation of treatment always led to recurrence of Strongyloides infection. Several small bowel biopsies showed normal villous architecture and little inflammatory response to presence of larvae. Interestingly, no definite symptomatology could be attributed to the Strongyloides infection. It was postulated that the lack of signs and symptoms of strongyloidiasis, as well as poor response to treatment, was related to the immunodeficiency state. With low-dose, long-term interrupted courses of thiabendazole treatment, the Strongyloides infection finally seemed to be cured.

Legionnaires' disease: clinical features of the epidemic in Philadelphia.

A review of the medical records of 123 persons with Legionnaires' disease hospitalized in the 1976 Philadelphia epidemic showed that the manifestations of infection ranged from mild grippe to a severe pneumonia that also involved other organ systems. Early in the illness, constitutional symptoms predominated. Fever, malaise, myalgia, rigors, confusion, headache, and diarrhea were usually followed by nonproductive cough and dyspnea. Physical examination showed few abnormalities other than rales. Moderate leukocytosis with left shift, elevated erythrocyte sedimentation rate, elevation of serum levels of liver enzymes, and hematuria and proteinuria were characteristic. Chest radiograph showed patchy, often nodular, areas of consolidation. Progression of pneumonia led to respiratory failure and the need for mechanical ventilatory assistance for 19 patients; renal failure, primarily after shock, occurred in 18 persons. Twenty-six patients died. Treatment with erythromycin or tetracycline resulted in the lowest case-fatality ratios, but the associations were not statistically significant.