Background: There is mounting evidence that individuals with kidney disease and kidney stones have an abnormal gut microbiota composition. No studies to date have summarised the evidence to categorise how the gut microbiota profile of these individuals may differ from controls. Synthesis of this evidence is essential to inform future clinical trials. This systematic review aims to characterise differences of the gut microbial community in adults with kidney disease and kidney stones, as well as to describe the functional capacity of the gut microbiota and reporting of diet as a confounder in these studies. Methods: Included studies were those that investigated the gut microbial community in adults with kidney disease or kidney stones and compared this to the profile of controls. Six scientific databases (CINHAL, Medline, PubMed, Scopus, Web of Science and Cochrane Library), as well as selected grey literature sources, were searched. Quality assessment was undertaken independently by three authors. The system of evidence level criteria was employed to quantitatively evaluate the alteration of microbiota by strictly considering the number, methodological quality and consistency of the findings. Additional findings relating to altered functions of the gut microbiota, dietary intakes and dietary methodologies used were qualitatively summarised. Results: Twenty-five articles met the eligibility criteria and included data from a total of 892 adults with kidney disease or kidney stones and 1400 controls. Compared to controls, adults with kidney disease had increased abundances of several microbes including Enterobacteriaceae, Streptococcaceae, Streptococcus and decreased abundances of Prevotellaceae, Prevotella, Prevotella 9 and Roseburia among other taxa. Adults with kidney stones also had an altered microbial composition with variations to Bacteroides, Lachnospiraceae NK4A136 group, Ruminiclostridium 5 group, Dorea, Enterobacter, Christensenellaceae and its genus Christensenellaceae R7 group. Differences in the functional potential of the microbial community between controls and adults with kidney disease or kidney stones were also identified. Only three of the 25 articles presented dietary data, and of these studies, only two used a valid dietary assessment method.

There is increasing evidence linking the gut microbiota to various aspects of human health. Nuts are a food rich in prebiotic fibre and polyphenols, food components which have been shown to have beneficial effects on the gut microbiota. This systematic review aimed to synthesise the evidence regarding the effect of nut consumption on the human gut microbiota. A systematic search of the databases MEDLINE, PubMed, Cochrane CENTRAL, and CINAHL was performed until November 28, 2019. Eligible studies were those that investigated the effects of nut consumption in humans (aged over three years old), utilising next-generation sequencing technology. Primary outcome measures were between-group differences in α− and β−diversity metrics and gut microbial composition. A total of eight studies were included in the review. Included studies assessed the effects of either almonds, walnuts, hazelnuts or pistachios on the gut microbiota. Overall, nut consumption had a modest impact on gut microbiota diversity, with two studies reporting a significant shift in a α−diversity and four reporting a significant shift in β−diversity. Walnuts, in particular, appeared to more frequently explain shifts in β−diversity, which may be a result of their unique nutritional composition. Some shifts in bacterial composition (including an increase in genera capable of producing short-chain fatty acids: Clostridium, Roseburia, Lachnospira and Dialister) were reported following the consumption of nuts. Nut intake may yield a modulatory effect on the gut microbiota, however results were inconsistent across studies, which may be explained by variations in trial design, methodological limitations and inter-individual microbiota.

No abstract