Common Operational Taxonomic Units Research Articles

Efficacy of intestinal microorganisms on immunotherapy of non-small cell lung cancer

While the 5-year survival rate of patients with advanced non-small cell lung cancer (NSCLC) has seen some improvement, the majority of NSCLC patients fail to respond to immunotherapy with immune checkpoint inhibitors (ICIs). It is critical to identify effective biomarkers that can enhance the efficacy of immunotherapy. The clinical data in the current study were collected from NSCLC patients treated with ICIs, and two groups were classified according to treatment effect: good group with consistent efficacy, poor group with only progressiveness. Differences in intestinal microbiota between the two groups were analyzed using 16s rRNA sequencing. Beta diversity analysis indicated differences between the two groups that were available for differentiation. Comparison of the number of common or unique operational taxonomic units (OTUs) among different groups suggested that there were 53 unique OTUs in the good group and 51 unique OTUs in the poor group. At the phylum level, there was a difference between the two groups for several bacterial groups with the highest abundance values, among which Firmicutes, Actinobacteria and Fusobacteria were more abundant in the good group. Members of the genera Bifidobacterium and Lactobacillus were abundant in the good group, while the abundance of Bacteroides was low. Biomarkers in the poor group included Bacteroides, Bacteroidetes, Bacteroidia, Bacteroidales, Bacteroidaceae and Veillonellaceae. The intestinal microbiota composition affected the immunotherapy process for NSCLC, which might offer more rational instructions for the clinical application of ICIs in NSCLC patients.

Impact of Parthenium hysterophorus L. invasion on soil fungal communities in the Yellow River Delta

PurposeAs an invasive plant, Parthenium hysterophorus severely impacts the ecological environment of the Yellow River Delta and reduces biodiversity in the invaded areas. The effects of P. hysterophorus invasion on the local environment became increasingly critical, while few information was available for the effects of P. hysterophorus invasion on soil bacteria. The present study aimed to reveal the impacts of hysterophorus on the fungal communities in the Yellow River Delta.MethodsSixteen soil samples including four groups (ROOT group, YRR group, YNR group, and GBS group) were collected. High-throughput methods were used to explore the fungal composition of the P. hysterophorus-invaded surrounding environment and native plant-growed environment.ResultsOur results showed that the ACE (351.97) and Chao1 (351.95) values of the rhizosphere soils of P. hysterophorus (YRR group) were the highest among the four groups, whereas the non-rhizosphere soil samples of P. hysterophorus (YNR group) had the highest Shannon (7.188) and Simpson (0.984) values. The total number of operational taxonomic units (OTUs) obtained from the four groups was 1965, with 161 common OTUs among different groups. At the phylum level, both Ascomycota and Basidiomycota were the dominant fungi, with Ascomycota having the highest abundance. At the genus level, except for the endophytic fungi of P. hysterophorus roots (ROOT group), Fusarium, Mortierella, Comoclathris, and Cladosporium were the dominant fungi in three groups. The fungal communities within the roots of P. hysterophorus were distant from other groups, indicating that the composition of the fungal communities within the roots had a low degree of similarity to the other three groups. LEfSe analysis showed that Ascomycota at the phylum level and Cladosporium, Curvularia, and Alternaria at the genus level play essential roles in the ROOT group, and Comoclathris plays a vital role in the YNR group.ConclusionsThis study explored the effects of P. hysterophorus invasion on the local soil fungal communities by analyzing the fungal communities in P. hysterophorus roots, rhizosphere soil, non-rhizosphere soil, and rhizosphere soil of native plants. Generally, P. hysterophorus rhizosphere fungi specifically affect the surrounding environment.

Diosgenin reduces bone loss through the regulation of gut microbiota in ovariectomized rats

Diosgenin (DIO) is an aglycone of steroid saponins acquired from plants, including Dioscorea alata, Smilax China, and Trigonella foenum graecum, acting as an anti-osteoporosis, anti-diabetic, anti-hyperlipidemic, anti-inflammatory. Recent studies have demonstrated that DIO reduces bone loss. This study aimed to investigate the effects of DIO on the gut microbiota (GM) of ovariectomized (OVX) osteoporotic rats. Female Sprague-Dawley rats were randomly divided into sham operation (sham + vehicle group) or ovariectomy. For 12 weeks, OVX rats were treated using a vehicle (OVX + vehicle group) and DIO (OVX + DIO group). Subsequently, ELISA was conducted to determine serum estradiol levels, micro-CT scanning was performed to evaluate bone quality, and feces were collected for metagenomics sequencing to examine the structure and function of GM. Raw reads were filtered to remove chimera sequences. Operational taxonomic units (OTUs) were clustered in the filtered reads. A Venn diagram analysis was conducted to study the common and unique OTUs in the sham + vehicle, OVX + vehicle, and OVX + DIO groups. LEfSe analysis was conducted to evaluate the specific GM of the three groups. The GM functions were analyzed using the KEGG and CAZy databases. After a 12-week treatment, DIO administration prevented OVX-induced weight gain and increased the estradiol levels. DIO treatment improved the bone microstructure and structural parameters of rat tibias. Metagenomics sequencing results identified 1139, 1207, and 1235 operational taxonomic units (OTUs) in the sham + vehicle, OVX + vehicle, and OVX + DIO groups, respectively. The percentage of common OTUs was 41.2%. Treatment with DIO restored the composition of GM in OVX rats by increasing the abundance of Coriobacteriia Adlercreutzia, Romboutsia, and Romboutsia_idealis and reducing the abundance of Betaproteobacteria, Gammaproteobacteria, Methanobacteria, Bacteroides, Phocaeicola, Alistipes, Bacteroids_uniformis, Bacteroids_xylanisolvens. The anti-osteoporosis effect of DIO can be regulated through environmental information processing, organismal Systems, Cellular Processes, human diseases, metabolism, and genetic information processing. Meanwhile, treatment with DIO improved GM homeostasis by increasing the metabolism of carbohydrates, other amino acids, and glycans and reducing translation, energy metabolism, and nucleotide metabolism. DIO can reduce bone loss by regulating the structural composition and function of GM, a novel strategy for preventing osteoporosis.

Co-variance between free-living bacteria and Cochlodinium polykrikoides (Dinophyta) harmful algal blooms, South Korea

To understand the co-variance between common free-living bacteria and Cochlodinium polykrikoides harmful algal blooms (HABs) and their metabolic functions, we investigated 110 sampling sites in the Southern Sea of South Korea. These sampling sites were divided into three groups based on environmental factors and phytoplankton data with a similarity of 85% using non-metric multidimensional scaling. One group represented high-severity C. polykrikoides blooms, while the other two represented low-severity or no blooms. In high-severity HABs, inorganic phosphorous and dissolved organic carbon concentrations were strongly correlated with C. polykrikoides density (p < 0.01). This may reflect the changes in biochemical cycling due to inorganic and organic substrates released by HAB cells (or by cell destruction). Furthermore, 88 common bacterial operational taxonomic units (OTUs, with mean relative abundance > 1%) were identified. These included Gammaproteobacteria (36 OTUs), Flavobacteriia (24), Alphaproteobacteria (18), and other taxa (11). When C. polykrikoides blooms intensified, the relative abundances of Gammaproteobacteria also increased. OTU #030 (Flavicella sp., Flavobacteria, 96%) was positively correlated with C. polykrikoides abundance (r = 0.77, p < 0.001). Functional analysis based on the dominant bacterial OTUs revealed that chemoheterotrophy-related functions were more common in high-severity sites of HABs than in other groups. Therefore, the occurrence of HABs highlighted their interactions with bacteria and affected the bacterial community structure and metabolic functions.

Bacterial and fungal communities in indoor aerosols from two Kuwaiti hospitals.

The airborne transmission of COVID-19 has drawn immense attention to bioaerosols. The topic is highly relevant in the indoor hospital environment where vulnerable patients are treated and healthcare workers are exposed to various pathogenic and non-pathogenic microbes. Knowledge of the microbial communities in such settings will enable precautionary measures to prevent any hospital-mediated outbreak and better assess occupational exposure of the healthcare workers. This study presents a baseline of the bacterial and fungal population of two major hospitals in Kuwait dealing with COVID patients, and in a non-hospital setting through targeted amplicon sequencing. The predominant bacteria of bioaerosols were Variovorax (9.44%), Parvibaculum (8.27%), Pseudonocardia (8.04%), Taonella (5.74%), Arthrospira (4.58%), Comamonas (3.84%), Methylibium (3.13%), Sphingobium (4.46%), Zoogloea (2.20%), and Sphingopyxis (2.56%). ESKAPEE pathogens, such as Pseudomonas, Acinetobacter, Staphylococcus, Enterococcus, and Escherichia, were also found in lower abundances. The fungi were represented by Wilcoxinia rehmii (64.38%), Aspergillus ruber (9.11%), Penicillium desertorum (3.89%), Leptobacillium leptobactrum (3.20%), Humicola grisea (2.99%), Ganoderma sichuanense (1.42%), Malassezia restricta (0.74%), Heterophoma sylvatica (0.49%), Fusarium proliferatum (0.46%), and Saccharomyces cerevisiae (0.23%). Some common and unique operational taxonomic units (OTUs) of bacteria and fungi were also recorded at each site; this inter-site variability shows that exhaled air can be a source of this variation. The alpha-diversity indices suggested variance in species richness and abundance in hospitals than in non-hospital sites. The community structure of bacteria varied spatially (ANOSIM r2 = 0.181–0.243; p < 0.05) between the hospital and non-hospital sites, whereas fungi were more or less homogenous. Key taxa specific to the hospitals were Defluvicoccales, fungi, Ganodermataceae, Heterophoma, and H. sylvatica compared to Actinobacteria, Leptobacillium, L. leptobacillium, and Cordycipitaceae at the non-hospital site (LefSe, FDR q ≤ 0.05). The hospital/non-hospital MD index > 1 indicated shifts in the microbial communities of indoor air in hospitals. These findings highlight the need for regular surveillance of indoor hospital environments to prevent future outbreaks.

Differential Effects of Natural Grazing and Feedlot Feeding on Yak Fecal Microbiota.

Variation in food and diet shapes the diversity of the gut microbiota of ruminants. The present study investigated the microbial diversity in the fecal microbiota of yaks reared under natural grazing and feedlot system. A total of 48 domestic yaks with an average age of 7.5 years were selected from two different grazing habitats: one group grazed on natural pasture (grazing yaks—GY) while the other group was fed fodder and concentrate (feedlot yaks—FY). Crude protein, non-fiber carbohydrate, hemicelluloses, and digestible dry matter contents of natural pastures were higher than those in the feedlot. The lower insoluble fiber contents were found in grazing land. The 16S rRNA gene sequencing revealed 675 and 348 unique operational taxonomic units (OTUs) in the GY and FY, respectively, in addition to 1,778 common OTUs. Overall, a total of 9,891 OTUs were identified as a whole, of which 6,160 OTUs were from GY and 3,731 were from FY. Shannon index analysis revealed a higher bacterial diversity in GY than FY. At the phylum level, Firmicutes were dominant bacterial taxa in both groups. The relative abundance of Firmicutes in GY (56% ± 0.05) was higher than in FY (41% ± 0.08). At the family level, GY had a significantly higher abundance of Ruminococcaceae (p < 0.001) and Rikenellaceae (p < 0.001) than FY, but FY had a significantly higher abundance of Prevotellaceae than GY (p < 0.001). At the genus level, abundances of Faecalibacterium, Alloprevotella, and Succinivibrio were higher in FY than in GY. This study presents novel information on fecal bacterial composition and diversity in yaks reared under two different production systems.

Lung microbiota features of stage III and IV non-small cell lung cancer patients without lung infection.

BackgroundThe microbial community affects the occurrence, development, metastasis and treatment response of cancers. But the detailed role and characteristics of lung microbiota (LM) in non-small cell lung cancer (NSCLC) are not fully known. For NSCLC associated microbiota analysis, it is valuable to combine multiple levels of detection, e.g., tumor, blood plasma, and bronchoalveolar fluid (BALF), but not single tissues.MethodsThis study collected above three sample types from NSCLC patients free from lung infection and aimed to describe their LM features using sequencing techniques. All patients diagnosed at the Department of Oncology in Shijiazhuang People’s Hospital with stage III or IV NSCLC from May 2019 to April 2020 were enrolled. All 37 pieces of tumor tissues and 6 blood samples were sent for pathogen targeted sequencing; for the BALF samples, 4 were used for pathogen targeted sequencing and 2 were sent for 16S ribosomal DNA (rDNA) sequencing.ResultsWe detected 49 pathogenic microorganisms (PMs) in the 37 tumor samples, 28 PMs in the 4 BALF samples, and 14 PMs in the 6 plasma samples. Overall, there were 5 common PMs in 3 types of samples. Between the tumor and BALF samples, there were another 11 common elements. In the 5 tumor-plasma pairs, the presence of a specific PM in blood was not necessarily consistent with that in the tumor. In the tumor-BALF pairs, the PM diversity was dramatically higher in the BALF than in the tumor. The PMs detected in the BALF could largely cover the PMs in the tumor. In the BALF 16S rDNA sequencing, there were 82 common operational taxonomic units (OTUs), and the microbiota in the BALF of advanced NSCLC patients exhibited some similarity.ConclusionsThis study showed the unique features of LM. The amount of intra-tumoral PMs was not necessarily consistent with that in the blood, but there was an obvious correlation between the intra-tumoral microbiota and that in the BALF. It is convenient and non-invasive to obtain BALF. Detection of LM classification and abundance in the BALF may help evaluate the severity of NSCLC.

Endolichenic Fungal Community Analysis by Pure Culture Isolation and Metabarcoding: A Case Study of Parmotrema tinctorum

Lichen is a symbiotic mutualism of mycobiont and photobiont that harbors diverse organisms including endolichenic fungi (ELF). Despite the taxonomic and ecological significance of ELF, no comparative investigation of an ELF community involving isolation of a pure culture and high-throughput sequencing has been conducted. Thus, we analyzed the ELF community in Parmotrema tinctorum by culture and metabarcoding. Alpha diversity of the ELF community was notably greater in metabarcoding than in culture-based analysis. Taxonomic proportions of the ELF community estimated by metabarcoding and by culture analyses showed remarkable differences: Sordariomycetes was the most dominant fungal class in culture-based analysis, while Dothideomycetes was the most abundant in metabarcoding analysis. Thirty-seven operational taxonomic units (OTUs) were commonly observed by culture- and metabarcoding-based analyses but relative abundances differed: most of common OTUs were underrepresented in metabarcoding. The ELF community differed in lichen segments and thalli in metabarcoding analysis. Dissimilarity of ELF community intra lichen thallus increased with thallus segment distance; inter-thallus ELF community dissimilarity was significantly greater than intra-thallus ELF community dissimilarity. Finally, we tested how many fungal sequence reads would be needed to ELF diversity with relationship assays between numbers of lichen segments and saturation patterns of OTU richness and sample coverage. At least 6000 sequence reads per lichen thallus were sufficient for prediction of overall ELF community diversity and 50,000 reads per thallus were enough to observe rare taxa of ELF.

Metagenomic analysis of lichen-associated bacterial community profiling in Roccella montagnei.

A lichen is a composite organism formed of algae or cyanobacteria that live in a mutually advantageous symbiotic relationship with the filaments (hyphae) of fungus. Three lichen samples were obtained from diverse sites at a terrestrial habitat located in Coimbatore and coastal habitats located in Kanyakumari and Nagapattinam districts of Tamil Nadu. Amplification and sequencing of 16S rRNA V3-V4 regions were used for metagenomic study. Aside from the Next-Generation Sequencing data (NGS), distinct types of lichen microbiome profiles were clearly revealed. The bacterial diversity in the lichen genera of Roccella montagnei growing in coastal and terrestrial environments was further investigated using common and unique operational taxonomic units (OTUs) and the QIIME pipeline (1.9.1). Using similarity clustering, the heat map analysis depicts the abundance information of chosen OTUs as well as the similarity and difference between OTUs and lichen samples. Using multiple methods, the alpha and beta diversity analysis revealed that there were differences in all of the samples. However, UPGMA tree inference of comparable bacterial community in coastal habitat lichen samples compared to terrestrial habitat validates their evolutionary lineage. As a result, the bacterial population associated with corticolous lichen is dependent on geographic locations, growth substrate, and climatic circumstances of similar lichen genera produced in different habitats and tree substrates.

Plant growth-promoting abilities and community structure of culturable endophytic bacteria from the fruit of an invasive plant Xanthium italicum.

Diversity of endophytic bacterial communities of capsular fruit, upper and lower seeds of an invasive plant Xanthium italicum growing in Xinjiang, China, was investigated. All isolates from the seed capsules, the upper seeds, and the lower seeds were identified by 16S rRNA gene sequencing, and sequences were compared to bacterial databases to define operational taxonomic units (OTUs). Finally, we obtained 316 endophytic isolates corresponding to 58 OTUs based on 16S rRNA gene sequences. The most common OTU corresponded most closely to Bacillus zhangzhouensis and comprised 9.49% of all bacterial isolates. The richness and diversity of endophytes in lower seeds were higher than that of the upper seeds; moreover, the Chao estimator and Shannon index of endophytes in the lower seeds were approximate to that in the seed capsules. Bacillus and Staphylococcus were found as the common taxa in three different tissues that were investigated (OTUs belong to these genera constituted > 70% of the total community). The bacterial endophytic communities differed significantly among these three fruit tissues, especially Bacillus strains, which have been reported to contribute to plant growth promotion and stress resilience to their hosts in harsh environment; abundance of Bacillus species was in the following order: capsules (78 OTUs) > lower seeds (55 OTUs) > upper seeds (40 OTUs). The lower seeds harboring more Bacillus species might be responsible for their earlier seed germination compared with the upper seeds.

First Insights into the Microbiology of Three Antarctic Briny Systems of the Northern Victoria Land

Different polar environments (lakes and glaciers), also in Antarctica, encapsulate brine pools characterized by a unique combination of extreme conditions, mainly in terms of high salinity and low temperature. Since 2014, we have been focusing our attention on the microbiology of brine pockets from three lakes in the Northern Victoria Land (NVL), lying in the Tarn Flat (TF) and Boulder Clay (BC) areas. The microbial communities have been analyzed for community structure by next generation sequencing, extracellular enzyme activities, metabolic potentials, and microbial abundances. In this study, we aim at reconsidering all available data to analyze the influence exerted by environmental parameters on the community composition and activities. Additionally, the prediction of metabolic functions was attempted by the phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt2) tool, highlighting that prokaryotic communities were presumably involved in methane metabolism, aromatic compound biodegradation, and organic compound (proteins, polysaccharides, and phosphates) decomposition. The analyzed cryoenvironments were different in terms of prokaryotic diversity, abundance, and retrieved metabolic pathways. By the analysis of DNA sequences, common operational taxonomic units ranged from 2.2% to 22.0%. The bacterial community was dominated by Bacteroidetes. In both BC and TF brines, sequences of the most thermally tolerant and methanogenic Archaea were detected, some of them related to hyperthermophiles.

Dynamic Observation of the Effect of Maternal Caries on the Oral Microbiota of Infants Aged 12-24 Months.

AimTo provide a dynamic description of the oral microbial composition in mothers with and without dental caries and their children aging 12-24 months.MethodologyA total of 20 pairs of mothers and their children aged 12 months were included and followed up at 18 and 24 months of age. Ten mothers with dental caries(MEG) and their children(CEG) were in the exposure group, and ten caries-free mothers(MCG) and their children(CCG)in control group. Supragingival plaque biofilm samples were collected and DNA was extracted for bacterial 16S rRNA gene sequencing.ResultsA total of 18 pairs completed follow-ups. At a 3% divergence level, the number of common operational taxonomic units found between the mothers and children increased as the children aged. Proteobacteria, Bacteroidetes, Firmicutes, Fusobacteria, and Actinobacteria accounted for more than 80% phyla of each group. A microbial community structure analysis showed that the differences between mothers and children were significant in all groups except for the MEG24 and CEG24 groups.ConclusionsOral microbiota of children was more like their mothers’ with increasing age, regardless of whether the mothers had dental caries. Mothers with dental caries may have a greater influence on the oral microbiota of children’s than those without dental caries as children age.

Effects of black carbon-based thin-layer capping for nitrogen-overloaded sediment remediation on microbial community assembly

Black carbon is considered as a promising material for thin-layer capping for sediment remediation. However, the effects of black carbon-based thin-layer capping on microbial communities have not been thoroughly studied. Here, the preparation conditions of capping material were optimized, and the interaction and assembly mechanisms of the microbial community in sediment under black carbon capping were studied. The results showed that concentration of NH4+-N in the overlying water was stably lower than 0.5 mg/L after capping. The abundance of key genes related to nitrogen transformation in the sediment was increased. Denitrification was the dominant nitrogen removal pathway under coarse granule capping, while aromatic compound degradation was dominant under fine granule capping and dissimilatory N reduction to ammonium was regarded as the dominant nitrogen removal pathway. Community assembly was mainly driven by deterministic processes (≥ 80%). Interactions between rare and common operational taxonomic units were most frequent. The functional zoning of nitrogen transformation in the vertical aerobic, hypoxic, and anaerobic zones of the sediment was strengthened because of black carbon capping. Overall, these results expand our current understanding of the ecological significance of black carbon capping for remediating contaminated sediment.

Microbiota Diversity in Pearl Oyster Pinctada fucata martensii Intestine and Its Aquaculture Environment

Environmental microbiota plays a vital role in the intestinal microbiota of aquatic organisms. However, data concerning the association between the intestinal microbiota of pearl oyster Pinctada fucata martensii and the surrounding seawater are limited. The existing bacterial communities in pearl oyster intestine and surrounding water from two sites (D and H, within Liusha Bay in Guangdong, China) were investigated using 16S rRNA-based sequencing to explore the relationship among the two. D located in the inner bay, and H located in the open sea area outside bay. Results revealed the richness and diversity of pearl oyster intestinal microbiota to be less than those of the surrounding water, with 38 phyla and 272 genera observed as a result of the classifiable sequence. The microbiota compositions in the intestine and the surrounding water were diversified at the phylum and genus levels, with the sequencing data being statistically significant. However, the functional prediction of microbiota emphasized the overall similarity in the functional profile of the surrounding seawater and intestinal microbiomes. This profile was associated with metabolism of cofactors and vitamin, carbohydrates metabolism, amino acids metabolism, metabolism of terpenoids, and polyketides, metabolism of other amino acids, lipids metabolism, and energy metabolism. Seven common operational taxonomic units (OTUs), which belonged to phyla Tenericutes, Cyanobacteria, and Planctomycetes, were noted in the intestines of pearl oysters from two different sites. These OTUs may be affiliates to the core microbiome of pearl oyster. Significantly different bacterial taxa in the intestines of pearl oysters from two different sites were found at the phylum and genus levels. This finding suggested that the bacterial communities in pearl oyster intestines may exhibit some plasticity to adapt to changes in the surrounding water-cultured environment. This study generally offers constructive discoveries associated with pearl oyster intestinal microbiota and provides guidance for sustainable aquaculture.

Hawaiian Fungal Amplicon Sequence Variants Reveal Otherwise Hidden Biogeography.

To study biogeography and other ecological patterns of microorganisms, including fungi, scientists have been using operational taxonomic units (OTUs) as representations of species or species hypotheses. However, when defined by 97% sequence similarity cutoff at an accepted barcode locus such as 16S in bacteria or ITS in fungi, these OTUs can obscure biogeographic patterns, mask taxonomic diversity, and hinder meta-analyses. Amplicon sequence variants (ASVs) have been proposed to alleviate all of these issues and have been shown to do so in bacteria. Analyzing ASVs is just emerging as a common practice among fungal studies, and it is unclear whether the benefits found in bacterial studies of using such an approach carryover to fungi. Here, we conducted a meta-analysis of Hawaiian fungi by analyzing ITS1 amplicon sequencing data as ASVs and exploring ecological patterns. These surveys spanned three island groups and five ecosystems combined into the first comprehensive Hawaiian Mycobiome ASV Database. Our results show that ASVs can be used to combine fungal ITS surveys, increase reproducibility, and maintain the broad ecological patterns observed with OTUs, including diversity orderings. Additionally, the ASVs that comprise some of the most common OTUs in our database reveals some island specialists, indicating that traditional OTU clustering can obscure important biogeographic patterns. We recommend that future fungal studies, especially those aimed at assessing biogeography, analyze ASVs rather than OTUs. We conclude that similar to bacterial studies, ASVs improve reproducibility and data sharing for fungal studies.

The Effects of Genetic Relatedness on the Preterm Infant Gut Microbiota.

The preterm infant gut microbiota is influenced by environmental, endogenous, maternal, and genetic factors. Although siblings share similar gut microbial composition, it is not known how genetic relatedness affects alpha diversity and specific taxa abundances in preterm infants. We analyzed the 16S rRNA gene content of stool samples, ≤ and >3 weeks postnatal age, and clinical data from preterm multiplets and singletons at two Neonatal Intensive Care Units (NICUs), Tampa General Hospital (TGH; FL, USA) and Carle Hospital (IL, USA). Weeks on bovine milk-based fortifier (BMF) and weight gain velocity were significant predictors of alpha diversity. Alpha diversity between siblings were significantly correlated, particularly at ≤3 weeks postnatal age and in the TGH NICU, after controlling for clinical factors. Siblings shared higher gut microbial composition similarity compared to unrelated individuals. After residualizing against clinical covariates, 30 common operational taxonomic units were correlated between siblings across time points. These belonged to the bacterial classes Actinobacteria, Bacilli, Bacteroidia, Clostridia, Erysipelotrichia, and Negativicutes. Besides the influence of BMF and weight variables on the gut microbial diversity, our study identified gut microbial similarities between siblings that suggest genetic or shared maternal and environmental effects on the preterm infant gut microbiota.

Is Intestinal Bacterial Diversity Enhanced by Trans-Species Spread in the Mixed-Species Flock of Hooded Crane (Grus monacha) and Bean Goose (Anser fabalis) Wintering in the Lower and Middle Yangtze River Floodplain?

Simple SummaryIntestinal microbes play an indispensable role in host physiology and their alteration can produce serious effects on vertebrates. In this study, we analyzed the characteristics of intestinal bacterial community of hooded crane and bean goose whose niches overlap at Shengjin Lake, China, and investigated how host internal factors and inter-species interactions affected the diversity and spread of intestinal bacteria of the two species over three wintering periods. We have found that direct or indirect contact with each other increased the diversity of host intestinal bacteria and caused bacteria to spread among species in the mixed-species flock. In addition, a total of 63 pathogens were identified, of which 38 (60.3%) were found in the gut of both species. These findings could help our understanding of the factors that influence gut bacteria in wild waterbirds, which are also major contributors to the spread of pathogens worldwide.Diversity of gut microbes is influenced by many aspects, including the host internal factors and even direct or indirect contact with other birds, which is particularly important for mixed-species wintering waterbird flocks. In this study, Illumina high-throughput sequencing was used to analyze the intestinal bacteria of the hooded crane and bean goose whose niches overlap at Shengjin Lake. We tested whether contact time enhances the trans-species spread of gut bacteria. Results indicate alpha-diversity and microbial composition displayed significant separation between the two hosts in every wintering period, although the number of bacteria types shared increased with increasing contact time. For the same species, with the lengthening of contact time, alpha-diversity and the number of operational taxonomic units (OTUs) in the host intestine augmented, and the common OTUs and structural similarity of microflora in the middle and late periods were more than in the early and middle periods. In addition, we found a very high proportion of shared pathogens. Our results indicate that, although intestinal microflora of different species were separated, direct or indirect contact in the mixed-species flock caused the spread of gut bacteria trans-species, indicating that more attention should be paid to intestinal pathogens in wild birds.

五大连池火山土壤细菌多样性及其群落结构

火山熔岩生境孕育了独特的土壤微生物群落。为了解火山生态系统土壤细菌群落多样性和群落结构及其关键影响因子，选择五大连池新、老期火山为研究样点，非火山为对照，基于高通量测序方法，分析不同采样点土壤细菌群落结构和多样性，结合土壤理化指标，进一步分析影响火山生态系统土壤细菌群落多样性的环境因子。结果表明：细菌操作分类单元（OTUs）、Ace指数、Chao1指数和Simpson指数变化趋势一致，表现为非火山 > 新期火山 > 老期火山。三个样点土壤的共有OUTs数量为713个，各自特有的OTUs数量不尽相同。三个样点土壤中检测到共有细菌16个类群，其中变形菌门、酸杆菌门、放线菌门和绿弯菌门为优势菌群，老期火山土壤中酸杆菌门、疣微菌门、Rokubacteria相对丰度最大，而Patescibacteria相对丰度最小。三个样点的土壤细菌群落具有明显的空间关系，相似性差异较大，但不符合随地理距离的增加而降低的模型。土壤理化性质测定结果标明：老期火山土壤pH、有机质、全氮、全磷、铵态氮和硝态氮显著高于新期火山和非火山，新期火山土壤含水量和速效磷显著低于老期火山和非火山。喷发时间和火成岩基质等特性会导致不同火山土壤理化性质的差异，进而影响土壤细菌多样性和群落结构。Pearson相关性分析表明：土壤pH显著影响细菌的多样性指数。冗余分析（RDA）结果表明：土壤氮含量、pH和有机质是影响火山森林生态系统土壤细菌群落结构的主要因子。;Volcanic lava habitats breed unique soil microbial communities. Soil bacterial diversity, community structure, and key factors influencing volcanic ecosystems were explored using soil microorganisms in new volcano soils and old volcano soils in Wudalianchi, Heilongjiang Provice. Non-volcano soils were used as the control. Using the Illumina high-throughput sequencing method, we analyzed soil bacterial community structure and diversity at three sampling sites. Combined with soil physical and chemical characteristics, environmental factors affecting the diversity of soil bacterial community in a volcanic ecosystem were analyzed. Results showed that the operational taxonomic units (OTUs) and the diversity index (the Ace index, the Chao 1 index, and the Simpson index) of bacteria presented the same trends and followed the order Non-volcano > new volcano > old volcano. The number of OTUs unique to new volcano soils, old volcano soils and Non-volcano soils were 852, 820, and 879 respectively, as well as the number of their common OTUs was 713. The three plots soils contained same 16 kinds of bacterial groups, and Proteobacteria, Acidobacteria, Actinobacteria, and Chloroflexi were the most dominant bacteria groups. Acidobacteria, Verrucomicrobia, and Rokubacteria had the highest relative abundances, whereas Patescibacteria had the lowest in the old volcanic soils. In the three plots, the soil bacterial communities had obvious spatial relationships, and their similarity in community structure varies greatly, It did not conform to the model of beta diversity, which similarity in bacterial composition gradually decreased with increasing geographical distance. We think it could be related to the volcanic eruption characteristics or magma composition. The obtained soil physicochemical properties indicated that soil pH, Soil organic matter (SOM), total nitrogen (TN), total phosphorus (TP), ammonium nitrogen (AN), and nitrate nitrogen (NN) in old volcanic soils were significantly higher than those in the new volcanic soils and non-volcanic soils, while water content and available phosphorus in the new volcanic soils were significantly lower than those in the old volcanic soils and non-volcanic soils. Volcanic eruption is a form of violent large-scale disturbance, the volcanic characteristics of eruption time and igneous rock led to differences among volcanic soils at different stages, and further led to differences among soil bacterial diversity and community structure. Pearson correlation analysis showed that soil pH significantly affected the Simpson index, the Ace index and the Chao 1 index of soil bacteria. The redundancy analysis (RDA) showed that soil nitrogen, soil pH, and SOM were the crucial factors affecting the bacterial community structure of the Wudalianchi volcanic ecosystem.

南疆四种盐生植物根际土壤真菌群落结构特征

盐生植物特殊的生境孕育了独特的根际微生物群落。为了解南疆干旱区不同盐生植物根际土壤真菌群落结构特征，探讨影响真菌群落结构的土壤环境因子，选取南疆伽师县同一盐碱地盐爪爪（Kalidium foliatum）、黑果枸杞（Lycium ruthenicum）、花花柴（Karelinia caspia）和旱生芦苇（Phragmites australis）四种优势盐生植物，采用Illumina NovaSeq高通量测序技术分析根际土壤真菌群落结构和多样性，并探究其与土壤理化因子的相关性。结果表明，四种盐生植物根际土壤理化特征不尽相同，土壤pH均超过8.0，电导率（EC）由高到低为旱生芦苇 > 盐爪爪 > 花花柴 > 黑果枸杞，黑果枸杞根际土壤的有机质（SOM）、全氮（TN）、全磷（TP）、全钾（TK）、速效氮（AN）和速效磷（AP）含量均最高，旱生芦苇根际土壤的SOM、TN、TP、TK和AN值均最低，但土壤水分含量（SWC）和EC值最高。四种盐生植物共有的操作分类单元（OTUs）数量为153个，各自特有的OTUs数量不尽相同。根际土壤真菌群落丰富度（ACE、Chao 1指数）依次为盐爪爪 > 旱生芦苇 > 黑果枸杞 > 花花柴，Shannons指灵第和Simpson指数大小依次为盐爪爪 > 黑果枸杞 > 旱生芦苇 > 花花柴。从四种盐生植物根际共检测到真菌8门、21纲、44目、89科、124属，子囊菌门（Ascomycota）在四种盐生植物根际土壤中占绝对优势地位。镰孢菌属（Fusarium）、支顶孢属（Acremonium）、曲霉属（Aspergillus）和青霉菌属（Penicillium）是四种盐生植物根际土壤共有优势属，非优势属数量多但相对丰度因植物种类而异。典范对应分析（CCA）显示，土壤速效钾、AP、pH和EC是影响根际土壤真菌群落结构变化的主要驱动因子。研究表明南疆四种盐生植物根际土壤真菌群落具有相似性，但优势菌属丰度差异明显，具有植物种类特异性。;Halophytes harbour unique rhizosphere microbial communities as a result of their unique habitat. The rhizosphere soil fungal diversity and community structures of four halophytes, including Kalidium foliatum, Lycium ruthenicum, Karelinia caspia and Phragmites australis, typically distributed in the arid land of Southern Xinjiang, were studied using the Illumina high-throughput sequencing technology. The study aims to reveal the alpha diversity, species composition, abundance and the differences of rhizosphere soil fungi among the four halophytes, explore their correlation with environmental factors to provide the basis for further investigation of the relationship between rhizosphere soil microbes and salt tolerance of halophytes. The results showed that the physicochemical characteristics of the rhizosphere soil of the four halophytes were different. The soil pH was all over 8.0, and the electronic conductivity (EC) value from high to low was Phragmites australis, Kalidium foliatum, Karelinia caspia, Lycium ruthenicum. The soil organic matter (SOM), total nitrogen (TN), total phosphorus (TP), total potassium (TK), available nitrogen (AN) and available phosphorus (AP) contents in the rhizosphere soil of Lycium ruthenicum were the highest, while the SOM, TN, TP, TK and AN values were the lowest in Phragmites australis, but the SWC and EC value were the highest. The numbers of operational taxonomic units (OTUs) unique to Kalidium foliatum, Lycium ruthenicum, Karelinia caspia, and Phragmites australis were 51, 19, 11, and 53 respectively, as well as their common OTUs number was 153. The fungi community richness (abundance-based coverage estimator, ACE and Chao 1 index) from high to low was Kalidium foliatum, Phragmites australis, Lycium ruthenicum, and Karelinia caspia. The fungal community was different in composition and abundance in the rhizosphere of the four halophytes. A total of 8 phyla, 21 classes, 44 orders, 89 families, and 124 genera fungi were detected in their rhizosphere soil samples. The relative abundance and distribution of fungi varied at phylum level, and the dominant groups were Ascomycota, Basidiomycota, and Chytridiomycota. There were 11, 9, 8, and 6 genera with relative abundance greater than 1% in the rhizosphere soil of Kalidium foliatum, Lycium ruthenicum, Karelinia caspia, and Phragmites australis, respectively, with 4 common dominant genera including Fusarium, Acremoniuma, Aspergillus and Penicillium. The number of non-dominant fungi was large but the relative abundance varied with plant species. Then each plant had its particular or mutual fungal genera with different abundance, some of which were affected greatly by soil physicochemical properties. According to canonical correlation analysis (CCA), we found that the major influence factors that caused the change of soil fungal community structures of the four halophytes were oil available potassium, available phosphorus, pH and electrical conductivity. This study revealed that the rhizosphere soil fungi communities of the four halophytes were similar, but the abundance of dominant bacteria was significantly different, with plant species specificity. The rhizosphere fungi community was correlated with the soil environmental factors.

Treatment of Whole-Plant Corn Silage With Lactic Acid Bacteria and Organic Acid Enhances Quality by Elevating Acid Content, Reducing pH, and Inhibiting Undesirable Microorganisms.

We investigated the variation in microbial community and fermentation characteristics of whole-plant corn silage after treatment with lactic acid bacteria (LAB) and organic acids. The fresh corn forages were treated with a combination of L. acidophilus and L. plantarum (106 CFU/g fresh material) or a 7:1:2 ratio of formic acid, acetic acid, and propionic acid (6 mL/g fresh material) followed by 45 or 90 days of ensiling. Silages treated with LAB showed increased lactic acid content and decreased pH after 45 days. Although treatment with LAB or organic acids decreased the common and unique operational taxonomic units, indicating a reduction in microbial diversity, the relative abundance of Lactobacillus was elevated after 45 and 90 days compared with control, which was more distinct in the organic acid groups. Moreover, we found higher levels of acetic acid and increased abundance of Acetobacter in silages treated with organic acids whereas undesirable microorganisms such as Klebsiella, Paenibacillus, and Enterobacter were reduced. In summary, the quality of corn silages was improved by LAB or organic acid treatment in which LAB more effectively enhanced lactic acid content and reduced pH while organic acid inhibited the growth of undesirable microorganisms.