Indoor microbiome and risk of lower respiratory tract infections among children under-five years: A meta-analysis

We investigated whether exposure to microbiome within the indoor environment is associated with risk of lower respiratory tract infections (LRTI) among children under 5 years of age. Electronic scientific repositories; PubMed, Scopus, Web of Science, GreenFILE, EMBASE, and Cochrane library were searched and screened through July 2019 for published reports for inclusion in the meta-analysis. Studies were eligible for inclusion if they reported an adjusted measure of risk for LRTI associated with IM exposure, including the relative risk (RR) or odds ratio (OR) and confidence interval (CI). The pooled OR was computed using the inverse of variance method for weighting. Sensitivity analysis was used to evaluate the effect of individual studies, while heterogeneity was evaluated by I² statistics using RevMan 5.3. Seven studies were eligible for inclusion in our meta-analysis. Exposure to a higher concentration of IM was associated with an increased risk of LRTI [OR:1.20 (1.11, 1.33), P < .0001]. The risk was stronger with exposure to total fungal concentration [OR:1.27 (1.13, 1.44), P < .0001] than visible molds [OR:1.20 (1.07, 1.34, P = .001]. Under-five children exposed to higher IM concentration are likely at increased risk of LRTI. Interventions addressing IM exposure should be considered in the management of LRTI among under-five children.     

Bridging the Gap: Plant-Endophyte Interactions as a Roadmap to Understanding Small-Molecule Communication in Marine Microbiomes

Probing the composition of the microbiome and its association with health and disease states is more accessible than ever due to the rise of affordable sequencing technology. Despite advances in our ability to identify members of symbiont communities, untangling the chemical signaling that they use to communicate with host organisms remains challenging. In order to gain a greater mechanistic understanding of how the microbiome impacts health, and how chemical ecology can be leveraged to advance small-molecule drug discovery from microorganisms, the principals governing communication between host and symbiont must be elucidated. Herein, we review common modes of interkingdom small-molecule communication in terrestrial and marine environments, describe the differences between these environments, and detail the advantages and disadvantages for studies focused on the marine environment. Finally, we propose the use of plant-endophyte interactions as a stepping stone to a greater understanding of similar interactions in marine invertebrates, and ultimately in humans.     

Significance of Inulin Fructans in the Human Diet

This paper reviews the physicochemical properties and nutritional significance of inulin fructans (oligofructose and inulin). These compounds are naturally present in a large number of food crops and serve in our diet as dietary fiber. Inulin fructans can be isolated and purified from the chicory root and used as ingredients in a large range of foods to improve structure and/or taste and to increase the intake of dietary fiber. Inulin fructans have a low caloric value, are safe, and generally well tolerated up to a level of 20 g/d. They exert a range of effects, which can be differentiated into direct effects on the gut and the intestinal flora and indirect systemic effects. Direct effects on the gut include prebiotic (bifidogenic) effects, improvement of bowel habits and bowel function in constipated subjects, increased colonic absorption of minerals (Ca and Mg), and secretion of satiety hormones. Indirect effects are on blood lipids, bone mineral content, the immune system, and energy homeostasis. These issues are discussed and it is argued that promising avenues for research are particularly in the areas of energy homeostasis and systemic low‐grade inflammation in relation to changes in the composition of the intestinal microbiota.     

老年人肠道乳酸菌的分离与鉴定及其来源发酵乳杆菌的遗传进化分析

首先对湖北襄阳和恩施地区的健康老年人肠道乳酸菌进行分离与鉴定，然后从中选择发酵乳杆菌（Lactobacillus fermentum）进行多位点序列分型（multilocus sequence typing，MLST）分析。结果显示，基于可培养方法，湖北襄阳与恩施地区老年人肠道乳酸菌可以鉴定为以乳杆菌属（Lactobacillus）为主的5 个菌属，15 个种。总的来说，发酵乳杆菌和唾液乳杆菌（L. salivarius）占老年人肠道源乳酸菌分离株总量的55%左右，表明人体肠道可以作为发酵乳杆菌的重要分离来源。基于8 个持家基因的MLST分析表明，25 株来源于肠道的发酵乳杆菌可以划分为25 个序列型，具有极高的遗传多样性；基于选择压力分析与phi-test，选用的8 个持家基因均受到纯化选择作用，且其中仅基因rpoB显著经历了基因重组事件；另外，基于Prim’s和goeBURST的进化分析表明，一半左右的肠道源发酵乳杆菌倾向于形成单独的分支，表明它们具有一定的宿主特异性，可能的原因是为适应肠道环境，这些发酵乳杆菌经历了有异于发酵食品生境的进化历程。     

Shotgun metagenomics of dust microbiome from flight deck and cabin in civil aviation aircraft

Microbial exposure is related to the health of passengers on commercial aircraft, but no studies characterized the microbial composition at the species level and identified their ecological determinants. We collected vacuum dust from floor and seat surfaces in flight decks and cabins of 18 aircraft, and amplification-free shotgun metagenomics was conducted to characterize the microbial composition. In total, 7437 microbial taxa were identified. The relative abundance for bacteria, eukaryote, viruses, and archaea was 96.9%, 1.8%, 0.3%, and 0.03%, respectively. The top bacterial species mainly derived from outdoor air and human skin included Sphingomonas, Corynebacterium, Micrococcus luteus, Variovorax paradoxus, Paracoccus dentrificans, and Propionibacterium acnes. The abundance of NIAID-defined pathogens was low, accounted for only 0.23% of total microbes. The microbial species and functional composition were structured by the indoor surface type (R² = 0.38, Adonis), followed by the manufacturer of the aircraft (R² = 0.12) and flight duration (R² = 0.07). Indoor surfaces affected species derived from different habitats; the abundance of dry skin and desiccated species was higher on textile surfaces, whereas the abundance of moist and oily skin species was higher on leather surfaces. The growth rates for most microbes were stopped and almost stopped.     

Alterations in ruminal bacterial populations at induction and recovery from diet-induced milk fat depression in dairy cows

Ten ruminally cannulated Holstein cows were used in a crossover design that investigated changes in ruminal bacterial populations in response to induction and recovery from diet-induced milk fat depression (MFD). Further, the effect on the ruminal microbiota of the cows with diet-induced milk fat depression inoculated with rumen contents from non-milk fat-depressed donor cows was evaluated. Milk fat depression was induced during the first 10 d of each period by feeding a low-fiber, high-starch, and high-polyunsaturated fatty acid diet (26.1% neutral detergent fiber, 28.1% starch, 5.8% total fatty acids, and 1.9% C18:2), resulting in a 30% decrease in milk fat yield. Induction was followed by a recovery phase, where all cows were switched to a high-fiber, low-starch, and low-polyunsaturated fatty acid diet (31.8% neutral detergent fiber, 23% starch, 4.2% total fatty acids, and 1.2% C18:2) and were allocated to (1) control (no inoculation) or (2) ruminal inoculation with donor cow digesta (8 kg/d for 6 d). Ruminal samples were collected at the end of induction (d 10) and during recovery (d 13, 16, and 28), separated to solid and liquid fractions, extracted for DNA, PCR- amplified for the V1-V2 region of the 16S rRNA gene, and analyzed for bacterial diversity. Results indicated that bacterial communities were different between fractions. In each fraction, differences were significant between the induction (d 10) and recovery (d 13, 16, and 28) periods; however, differences were less apparent with time during the recovery period. The MFD (d 10) was typified by a reduction in the relative sequence abundance of Bacteroidetes and an increase in the relative sequence abundance of Firmicutes and Actinobacteria across both fractions. At the genus level, relative sequence abundance of unclassified Lachnospiraceae, Butyrivibrio, Bulleidia, and Coriobacteriaceae were higher on d 10 and were positively correlated with trans-10,cis-12 CLA and the trans-10 isomer, suggesting their potential role in altered biohydrogenation reactions. A switch to the recovery diet resulted in a sharp increase in the Bacteroidetes lineages and a decrease in Firmicutes members on d 13; however, this shift appears to stabilize by d 28, indicating the restoration process for ruminal bacteria from an altered state is gradual and complex. Inoculation of 10% of rumen contents from non-MFD donor cows to MFD cows revealed this procedure had transient effects on only a few bacterial populations, and such effects disappeared after d 16 following cessation of inoculation. It can be concluded that alterations in milk FA profiles at induction are preceded by microbial alterations in the rumen driven by dietary changes.     

Altered mucosa-associated microbiota in the ileum and colon of neonatal calves in response to delayed first colostrum feeding

The present study investigated whether delaying the first feeding of colostrum affected ileum and colon mucosa-associated microbiota in calves. Twenty-seven male Holstein calves were randomly assigned to 1 of 3 groups, fed colostrum at 45 min, 6 h, and 12 h after birth, respectively. Ileum and colon mucosa were collected at 51 h after birth, and their associated microbial profiles were assessed using amplicon sequencing. Both ileum and colon mucosa-associated microbiota were predominated by genus Escherichia-Shigella. The negative correlation between the molar proportion of short-chain fatty acids (SCFA) and ileum mucosa-associated opportunistic pathogens, and the positive correlation between the molar proportion of SCFA and colon mucosa-associated beneficial bacteria, suggest that SCFA might play an important role in maintaining the gut health of 2-d-old calves. A higher relative abundance of ileum mucosa-associated Enterococcus and Streptococcus was detected when the first colostrum feeding was delayed for 12 h. The relative abundance of colon mucosa-associated Lactobacillus tended to be lower in calves fed colostrum 12 h than those under the other 2 treatments, whereas that of Faecalibacterium tended to be lower in calves fed colostrum immediately after birth than those fed colostrum 6 and 12 h after birth, respectively. Our findings suggest that delayed first colostrum feeding affects the establishment of ileum and colon mucosa-associated bacteria, which may have long-term effects on gut health of calves.