TEMPTED: time-informed dimensionality reduction for longitudinal microbiome studies by Pixu Shi, Cameron Martino, Rungang Han, Stefan Janssen, Gregory Buck, Myrna Serrano, Kouros Owzar, Rob Knight, Liat Shenhav, Anru R. Zhang

“…TEMPTED captures key microbial dynamics, facilitates beta-diversity analysis, and enhances reproducibility by transferring learned representations to new data. …”
Get full text

Early-life gut microbiota assembly patterns are conserved between laboratory and wild mice by Eveliina Hanski, Aura Raulo, Sarah C. L. Knowles

“…Specifically, age-related changes in both alpha and beta diversity, as well as the abundance of predominant phyla and aerotolerance of the microbiota followed parallel trajectories in both settings. …”
Get full text

The effect of forest gaps on the diversity and composition of bacterial communities in mixed-type forest soils across the Carpathian mountains by Nejc Suban, Oliver Maksimović, Nataša Šibanc, Tijana Martinović, Eva Darenova, Matjaž Čater, Tine Grebenc

“…The lowest bacterial diversity was found in the old-growth forest of the Beskidy region, while the highest was recorded in managed forest in Vrancea. Beta diversity analyses showed minimal variation between rhizosphere and bulk soil bacterial communities, with geographic distance being the strongest predictor of community composition. …”
Get full text

Exploring soil bacterial and fungal communities in Colombian terrestrial ecosystems modulated by altitude-influenced factors. by Wendy Lorena Reyes-Ardila, Glever Alexander Vélez-Martínez, Juan Diego Duque-Zapata, Paula Andrea Rugeles-Silva, Jaime Eduardo Muñoz Flórez, Diana López-Álvarez

“…Alpha diversity analysis showed high community diversity, whereas beta diversity reflected composition differences among locations and their heterogeneity. …”
Get full text

Age and sex-related variations in murine laryngeal microbiota. by Ran An, Anumitha Venkatraman, John Binns, Callie Saric, Federico E Rey, Susan L Thibeault

“…Measures of alpha diversity and beta diversity were obtained, along with differentially abundant taxa across age groups and biological sexes. …”
Get full text

Effect of Relocation, Social Housing Changes, and Diarrhea Status on Microbiome Composition of Juvenile Cynomolgus Macaques (<i>Macaca fascicularis</i>) by Keely McGrew, Nicole Monts de Oca, Therese A. Kosten

“…Although exhibiting diarrhea did not affect alpha diversity levels, it was associated with increased beta diversity (<i>p</i> < 0.05). Understanding how the microbiome may be affected by relocation will help guide prevention strategies such as the use of specific probiotics to reduce the incidence of diarrhea.…”
Get full text

Preliminary Study on the Impact of Ruminal Ciliate Inoculation in Fauna-Free Conditions on the Ruminal Fermentation and Ciliate–Prokaryote Association In Vitro by Geonwoo Kim, Woohyung Lee, Tansol Park

“…Alpha diversity indices indicated reduced richness in the ciliate-inoculated groups, reflecting predation on prokaryotes. Beta diversity showed distinct microbial and functional profiles among the treatments. …”
Get full text

CONDITIONS OF SKIN AND INTESTINE MICROBIOTES IN PATIENTS WITH PSORIASIS by Ya.O. Yemchenko, K.E. Ishcheikin, I.P. Kaidashev, G.Yu. Morokhovets

“…In psoriasis-affected skin, a significant decrease in alpha-beta diversity of the microbiome was observed. Changes in the intestinal microbiome in psoriasis are similar to those observed in patients with inflammatory bowel disease. …”
Get full text

Influence of selected dosages of plastic microparticles on the porcine fecal microbiome by Ismena Gałęcka, Andrzej Rychlik, Jarosław Całka

“…The analysis of the intestinal microbiome was performed using next-generation sequencing. Alpha and beta diversity indices were compared, showing, that repetition affected only the abundance indices in the control and LD groups, but not in the HD group. …”
Get full text

Diversity and composition changes of intestinal Fungi in a mouse model of total parenteral nutrition by XIE Huichao, CHEN Yihui, LIU Xingyu

“…Results There were significant differences in Alpha diversity (P < 0.05) and Beta diversity (P < 0.01) of intestinal fungi between the 2 groups. …”
Get full text

Gut Microbiome Alteration in HIV/AIDS and the Role of Antiretroviral Therapy—A Scoping Review by Zsófia Gáspár, Blin Nagavci, Bálint Gergely Szabó, Botond Lakatos

“…This study aims to map the evidence of the impact of integrase strand transfer inhibitors (INSTI) and non-nucleoside reverse transcriptase inhibitors (NNRTI) on the gut microbiota of PLWH. (2) Methods: A scoping review was conducted using PubMed, Web of Science, and Embase, with reports collected following PRISMA for Scoping Reviews (PRISMA-ScR). (3) Results: Evidence suggests that INSTI-based regimes generally promote the restoration of alpha diversity, bringing it closer to that of seronegative controls, while beta diversity remains largely unchanged. INSTI-based therapies are suggested to be associated with improvements in microbiota composition and a tendency toward reduced inflammatory markers. …”
Get full text

Exploring the Effects of Imidacloprid on Liver Health and the Microbiome in Rats: A Comprehensive Study by Alaa T. Qumsani

“…Alpha diversity, represented by the Chao1 and Shannon indices, was significantly reduced with an increased dosage of imidacloprid. Subsequent beta diversity analysis, as visualized by principal component analysis, showed distinct clustering among the microbial communities, separated well between control and imidacloprid-treated groups, especially at higher dosages. …”
Get full text

Are Substrate Types Factors Determining Tree Communities in Tropical Montane Cloud Forest? by Marco Antonio Espinoza-Guzmán, Diego Canales-Suardiaz, Julliana Barretto, Francisco Javier Sahagún-Sánchez

“…Four clusters were registered for species composition, with a high beta diversity and species turnover among sampled sites. …”
Get full text

Relationship Between the Host Plant Range of Insects and Symbiont Bacteria by Doudou Ge, Chongwen Yin, Jiayu Jing, Zhihong Li, Lijun Liu

“…However, following beta diversity analysis, monophagy demonstrated the lowest level of variation in intestinal commensal bacteria, while polyphagous tephritids exhibited the greatest variation in intestinal commensal bacteria community variation. …”
Get full text

Sediment microbiomes associated with critical habitat of the Juvenile American Horseshoe Crab; Limulus polyphemus by J. Petersen, C.P. Colon, J.L. Joyner

“…Although alpha diversity was similar among the three beach sites, Bray-Curtis distances assessed by Permanova revealed significant differences in Beta diversity, with a unique microbial assemblage found in the tidal creek. …”
Get full text

Patterns of antibiotic resistance genes and virulence factor genes in the gut microbiome of patients with osteoarthritis and rheumatoid arthritis by Yaqi Guo, Hang Feng, Lin Du, Zhenghong Yu

“…This suggests unique microbial patterns associated with each condition. Our beta diversity analysis further demonstrated distinct distributions of ARG and VFG profiles across the three groups, with several genes significantly enriched in both OA and RA patients, indicating potential markers for these diseases. …”
Get full text

Seasonal Dynamics of Non-Biting Midges (Diptera: Chironomidae) and Relevant Environmental Factors by Teng Lei, Jingjing Gu, Mengyao Zhao, Yuqiu Chen, Chao Song, Xin Qi

“…Alpha diversity was evaluated using Margalef, Pielou, and Shannon–Wiener indexes. Beta diversity was evaluated using unconstrained NMDS analysis and constrained CCA. …”
Get full text

Use of Different Synbiotic Strategies to Improve Gut Health in Dogs by Miquel Montserrat-Malagarriga, Lorena Castillejos, Anna Salas-Mani, Celina Torre, Susana María Martín-Orúe

“…A microbiome analysis revealed no changes in the alpha diversity, but significant shifts in the beta diversity, with increases in beneficial taxa such as <i>Faecalibacterium prausnitzii</i> and reductions in potentially harmful bacteria like <i>Prevotella copri</i>. …”
Get full text

Fecal shedding level of Haemonchus contortus is associated with gastrointestinal bacterial microbial composition in naturally infected sheep by Jeferson Vidart Ramos, Verônica Rocha Merched, Laura Dias da Silva Ribeiro, Guilherme Neves Lima Rattmann, Renan Eugênio Araújo Piraine, Fabio Pereira Leivas Leite

“…Firmicutes, Proteobacteria, and Spirochaetes were more abundant in the HC group. 102 bacterial genera showed significant differences between the LC and HC groups. Beta diversity was statistically different (p<0.005) for HC compared with the other two groups; also, different communities were found between LC and HC. …”
Get full text

Anthocyanin-Rich Extract Mitigates the Contribution of the Pathobiont Genus <i>Haemophilus</i> in Mild-to-Moderate Ulcerative Colitis Patients by Yannik Zobrist, Michael Doulberis, Luc Biedermann, Gabriel E. Leventhal, Gerhard Rogler

“…Microbiome composition did not change over time as a result of the intervention, in terms of both alpha and beta diversity. However, before the intervention, the abundance of <i>Haemophilus parainfluenzae</i> was positively correlated with fecal calprotectin concentrations, and this correlation persisted in placebo-treated subjects throughout the study. …”
Get full text